AMBER Archive (2008) - By ThreadMost recent messages
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Starting: Tue Jan 01 2008 - 19:53:35 CST
Ending: Wed Dec 31 2008 - 22:47:27 CST
- AMBER: ff03-compatible parameters/charges for phosphothreonine and phosphotyrosine John Chodera (Tue Jan 01 2008 - 19:44:34 CST)
- Re: AMBER: a question of ptraj WANG,YING (Wed Jan 02 2008 - 12:04:24 CST)
- AMBER: Help reg. input file snoze pa (Wed Jan 02 2008 - 12:34:56 CST)
- AMBER: AMBER-8 parallel installation - test run failure brmeher_at_iitg.ernet.in (Thu Jan 03 2008 - 04:10:58 CST)
- AMBER: question about antechamber Lynn (Thu Jan 03 2008 - 08:32:56 CST)
- AMBER: Thermodynamic integration with positional restraint? Cen Gao (Thu Jan 03 2008 - 10:43:32 CST)
- AMBER: Combine mdcrd files Francesco Pietra (Thu Jan 03 2008 - 17:01:47 CST)
- AMBER: MM-PBSA problem stephane acoca (Thu Jan 03 2008 - 21:45:10 CST)
- AMBER: check COM velocity Pankaj R. Daga (Fri Jan 04 2008 - 10:06:26 CST)
- AMBER: Combine mdcrd Francesco Pietra (Fri Jan 04 2008 - 10:37:07 CST)
- AMBER: FW: AMBER vs Gaussian : zero VDW parameters? Ross Walker (Fri Jan 04 2008 - 11:01:14 CST)
- Fwd: Re: AMBER: Combine mdcrd Francesco Pietra (Fri Jan 04 2008 - 11:23:45 CST)
- Fwd: Re: AMBER: Combine mdcrd Francesco Pietra (Fri Jan 04 2008 - 11:36:49 CST)
- AMBER: Combining multiple structures into single pdb Seth Lilavivat (Fri Jan 04 2008 - 14:21:58 CST)
- AMBER: mm/pbsa and saltcon effect Christopher Gaughan (Fri Jan 04 2008 - 15:40:17 CST)
- AMBER: amber :antechamber problem jani sahil (Fri Jan 04 2008 - 21:51:56 CST)
- AMBER: antechamber problems jani sahil (Fri Jan 04 2008 - 21:49:10 CST)
- AMBER: About RAMD Francesco Pietra (Sat Jan 05 2008 - 04:39:44 CST)
- AMBER: NMROPT=1 in minimisation Binbin Liu (Sat Jan 05 2008 - 17:38:51 CST)
- AMBER: temperature spikes Sally Pias (Sun Jan 06 2008 - 00:26:55 CST)
- AMBER: MD of protein-ligand comlex umbrita itl (Sun Jan 06 2008 - 14:54:47 CST)
- AMBER: Cluster analysis Francesco Pietra (Mon Jan 07 2008 - 10:00:40 CST)
- AMBER: Structure comparison-NMR and X-ray structure using AMBER9 Prem Prakash Pathak (Mon Jan 07 2008 - 10:11:22 CST)
- AMBER: offset residue numbering Brendan Duggan (Mon Jan 07 2008 - 14:14:30 CST)
- AMBER: Torsional Forcing to generate PES? Praveena Gopal (Mon Jan 07 2008 - 22:42:04 CST)
- AMBER: Nudged Elastic Band initial heating problem Mike Wykes (Tue Jan 08 2008 - 04:42:09 CST)
- AMBER: Problem about antechamber ÀÌë Óæ (Tue Jan 08 2008 - 10:09:03 CST)
- AMBER: solvateBox/solvateDontClip darkcz_at_tlen.pl (Tue Jan 08 2008 - 10:02:19 CST)
- AMBER: A problem about antechamber ÀÌë Óæ (Tue Jan 08 2008 - 10:03:49 CST)
- AMBER: connectivity problem rams rams (Wed Jan 09 2008 - 08:53:55 CST)
- AMBER: The energy minimization of SIngle RNA chain backy (Thu Jan 10 2008 - 02:33:20 CST)
- AMBER: input options for replica exchange simulations rebeca_at_mmb.pcb.ub.es (Thu Jan 10 2008 - 10:46:42 CST)
- AMBER: using hydrogen bond facility to monitor ion pair interaction Zhenwei Lu (Thu Jan 10 2008 - 11:09:09 CST)
- AMBER: antechamber problem gurpreet singh (Thu Jan 10 2008 - 11:49:15 CST)
- AMBER: ANTECHAMBER NAMING Shozeb Haider (Thu Jan 10 2008 - 15:19:18 CST)
- AMBER: graphite Boutheina Kerkeni (Fri Jan 11 2008 - 05:26:58 CST)
- AMBER: chromophore parameters for Molecular Dynamics Anthony Cruz (Fri Jan 11 2008 - 09:32:31 CST)
- AMBER: problems with restart of MD Vijay Singh (Fri Jan 11 2008 - 11:29:31 CST)
- AMBER: Visualizing Electrostatic Potential Seth Lilavivat (Fri Jan 11 2008 - 13:57:31 CST)
- AMBER: Amber DNA Model for X-ray Crystallography Hopkins, Robert (Fri Jan 11 2008 - 17:32:00 CST)
- AMBER: Unable to create the top & crd files for a protein+ligand pdb structure abiram abiram (Sat Jan 12 2008 - 01:54:01 CST)
- AMBER: connectivity lose during the minimizations rams rams (Sat Jan 12 2008 - 05:40:21 CST)
- AMBER: build RNA by nucgen Å·ÑôµÂ·½ (Sat Jan 12 2008 - 20:26:44 CST)
- AMBER: problem:capping jani sahil (Sat Jan 12 2008 - 20:53:24 CST)
- AMBER: problem in neturalization jani sahil (Sat Jan 12 2008 - 21:27:31 CST)
- AMBER: Distorsion in protein and ligand during MD Francesco Pietra (Sun Jan 13 2008 - 03:46:23 CST)
- AMBER: Fwd: Distorsion in protein and ligand during MD Francesco Pietra (Sun Jan 13 2008 - 03:57:43 CST)
- AMBER: ELAN_EXCEPTION @ --: 6 (Initialisation error) ELAN_EXCEPTION @ --: 6 (Initialisation error) Neko Maryam. (Sun Jan 13 2008 - 23:44:10 CST)
- AMBER: Amber : neutralizing without adding ions jani sahil (Mon Jan 14 2008 - 05:43:01 CST)
- AMBER: pmemd 9.0 compilation error Raphael Chaleil (Mon Jan 14 2008 - 08:38:12 CST)
- AMBER: QM/MM Heating Steven Winfield (Mon Jan 14 2008 - 09:22:27 CST)
- AMBER: Disturb you for help! ÀÌë Óæ (Mon Jan 14 2008 - 10:16:37 CST)
- AMBER: running AMBER in NAMD Trucated Octahedron Seth Lilavivat (Mon Jan 14 2008 - 16:19:05 CST)
- AMBER: Using VMD to calculate end-to-end distance? Lili Peng (Mon Jan 14 2008 - 16:41:55 CST)
- AMBER: How to build a dimer using amber Reena ..... (Tue Jan 15 2008 - 01:19:45 CST)
- AMBER: NPT to NVT Age.Skjevik_at_student.uib.no (Tue Jan 15 2008 - 07:58:22 CST)
- AMBER: Regarding neutral Arginine unit jani sahil (Tue Jan 15 2008 - 10:19:00 CST)
- AMBER: Problem with: Increase lastrst in the &cntrl namelist rdauria_at_uci.edu (Tue Jan 15 2008 - 22:46:04 CST)
- AMBER: DawsonSean (Wed Jan 16 2008 - 02:52:07 CST)
- AMBER: Help in radii snoze pa (Wed Jan 16 2008 - 11:08:59 CST)
- AMBER: diblock copolymer Z Insepov (Thu Jan 17 2008 - 09:27:47 CST)
- AMBER: Re: timestep problem Andrey Semichaevsky (Thu Jan 17 2008 - 12:24:00 CST)
- AMBER: PEO-PLA/PCE Z Insepov (Thu Jan 17 2008 - 14:19:47 CST)
- AMBER: GAFF atom types for flavin (again) Hans Martin Senn (Thu Jan 17 2008 - 14:47:54 CST)
- AMBER: problems of antechamber liu junjun (Thu Jan 17 2008 - 20:15:54 CST)
- AMBER: NMR refinement Wenyong Tong (Thu Jan 17 2008 - 20:54:04 CST)
- AMBER: Tinker 4.3 Paulo Couto (Fri Jan 18 2008 - 09:22:25 CST)
- AMBER: about AM1-BCC in antechamber Shun Zhu (Fri Jan 18 2008 - 16:06:30 CST)
- AMBER: A problem to loadup the molecular in the xleap ÀÌë Óæ (Fri Jan 18 2008 - 23:28:02 CST)
- AMBER: RMSD calculation using AMBER7 Biman Jana (Sat Jan 19 2008 - 07:16:46 CST)
- AMBER: problem with group input Ed Pate (Mon Jan 21 2008 - 00:53:28 CST)
- AMBER: Atomic restraints Marie Brut (Mon Jan 21 2008 - 07:34:42 CST)
- AMBER: BCC charges Thomas Exner (Tue Jan 22 2008 - 09:47:20 CST)
- AMBER: Has anyone seen a protein fall apart due to PBCs? David Cerutti (Tue Jan 22 2008 - 10:10:10 CST)
- AMBER: Systematic drift Francesco Pietra (Tue Jan 22 2008 - 16:06:46 CST)
- AMBER: Installing OpenMPI Hopkins, Robert (Tue Jan 22 2008 - 17:57:49 CST)
- AMBER: collision with surface Z Insepov (Tue Jan 22 2008 - 18:25:55 CST)
- AMBER: Re: Systematic drift Francesco Pietra (Wed Jan 23 2008 - 01:23:07 CST)
- AMBER: Amber 9: Question regarding Test Failures and Compilers Jan Schulze (Wed Jan 23 2008 - 04:01:04 CST)
- AMBER: distorted aromatic rings Marc Lindner (Wed Jan 23 2008 - 04:40:20 CST)
- AMBER: vlimit exceeded error priya priya (Wed Jan 23 2008 - 05:27:37 CST)
- AMBER: ptraj: new mask parser Vlad Cojocaru (Wed Jan 23 2008 - 05:59:24 CST)
- AMBER: regarding :scee jani sahil (Wed Jan 23 2008 - 09:50:45 CST)
- AMBER: tutorial_8_section_6 Urszula Uciechowska (Wed Jan 23 2008 - 11:04:38 CST)
- AMBER: antechamber run on charged system san_amber roy (Wed Jan 23 2008 - 12:09:34 CST)
- AMBER: Units of atomicfluct Lili Peng (Wed Jan 23 2008 - 18:27:16 CST)
- AMBER: Tough time with antechamber David Cerutti (Thu Jan 24 2008 - 01:29:38 CST)
- AMBER: Problems in execution of Replica Exchange calculations Amber 9.0 rebeca_at_mmb.pcb.ub.es (Thu Jan 24 2008 - 10:50:22 CST)
- AMBER: Help needed to analyze DNA Holliday Junction - Drug Binding MD simulations. Subramanian Arun Kumar (Thu Jan 24 2008 - 11:14:56 CST)
- AMBER: NMR refinement Seth Lilavivat (Thu Jan 24 2008 - 11:39:08 CST)
- AMBER: QM/MM: input conversion error Pankaj R. Daga (Thu Jan 24 2008 - 12:11:36 CST)
- AMBER: Number of Hydrogen Bonds? d90223013_at_ntu.edu.tw (Thu Jan 24 2008 - 19:07:39 CST)
- AMBER: flexible molecule parameterization Zhenwei Lu (Fri Jan 25 2008 - 09:36:46 CST)
- AMBER: AMBER installation problem Jun Liu (Fri Jan 25 2008 - 12:59:29 CST)
- AMBER: Reg cysteine protonaitons states in pH constant MD D.Usharani (Sun Jan 27 2008 - 23:15:58 CST)
- AMBER: Why LEap created a new H atom for CYM while generating TOPOLOGY file? Jack Lei (Mon Jan 28 2008 - 06:59:38 CST)
- AMBER: Reference for rmsd Francesco Pietra (Mon Jan 28 2008 - 11:51:02 CST)
- AMBER: How to determine the basic parameters of a Replica Exchange Molecular Dynamics(REMD? d90223013_at_ntu.edu.tw (Tue Jan 29 2008 - 01:35:08 CST)
- AMBER: radial distribution function in ptraj Lili Peng (Tue Jan 29 2008 - 03:36:37 CST)
- AMBER: Amber parallel version on CPU power of 2 only fatima.chami_at_durham.ac.uk (Tue Jan 29 2008 - 07:38:34 CST)
- AMBER: problem to compile PMEMD? fatima.chami_at_durham.ac.uk (Tue Jan 29 2008 - 16:45:41 CST)
- AMBER: Reg cysteine protonation states D.Usharani (Tue Jan 29 2008 - 21:58:22 CST)
- AMBER: setting periodic box Vijay Manickam Achari (Tue Jan 29 2008 - 22:22:05 CST)
- AMBER: Entropy calculation nag raj (Wed Jan 30 2008 - 03:51:26 CST)
- AMBER: SANDER BOMB in subroutine nonbond_list Pankaj R. Daga (Wed Jan 30 2008 - 09:13:45 CST)
- AMBER: Amber9 fails test.parallel Marc Cozzi (Wed Jan 30 2008 - 12:58:41 CST)
- AMBER: (no subject) Syed Tarique Moin (Wed Jan 30 2008 - 23:31:24 CST)
- AMBER: Entropy calculation nag raj (Thu Jan 31 2008 - 06:47:51 CST)
- AMBER: LEAP: solute concentration fatima.chami_at_durham.ac.uk (Thu Jan 31 2008 - 09:12:24 CST)
- AMBER: disulfide bridge with ff03ua FF Marcin Krol (Thu Jan 31 2008 - 12:30:56 CST)
- AMBER: benchmark walltime to ps/day calculation Andrew Ring (Thu Jan 31 2008 - 14:11:05 CST)
- AMBER: hbonds in first solvation shells Ignacio J. General (Fri Feb 01 2008 - 13:02:30 CST)
- AMBER: silica slab / FF Arturas Ziemys (Fri Feb 01 2008 - 15:42:13 CST)
- AMBER: Entropy calculations using NMODE saurabh agrawal (Sat Feb 02 2008 - 01:18:24 CST)
- AMBER: twin cut-off radii Sandeep Kaushik (Mon Feb 04 2008 - 03:17:57 CST)
- AMBER: principal component analysis rams rams (Mon Feb 04 2008 - 06:26:31 CST)
- AMBER: (no subject) Syed Tarique Moin (Mon Feb 04 2008 - 08:07:26 CST)
- AMBER: Re: bad atom type f(fluorine) in MM-PBSA kanazta1_at_yahoo.co.jp (Mon Feb 04 2008 - 11:32:51 CST)
- AMBER: time autocorrelation: ?? fatima.chami_at_durham.ac.uk (Mon Feb 04 2008 - 12:05:47 CST)
- AMBER: Using antechamber without AMBER program Surasak Chunsrivirot (Mon Feb 04 2008 - 14:58:59 CST)
- AMBER: Amber 9 installation Taufik Al-Sarraj (Mon Feb 04 2008 - 15:53:23 CST)
- AMBER: VLIMIT units; TGTFITMASK Hopkins, Robert (Mon Feb 04 2008 - 16:55:03 CST)
- AMBER: mm_pbsa: vertex atom mismatch Marc Lindner (Tue Feb 05 2008 - 04:47:23 CST)
- AMBER: infinite polymers in CHARMM David A. Case (Tue Feb 05 2008 - 10:39:45 CST)
- AMBER: silica slab Arturas Ziemys (Tue Feb 05 2008 - 11:28:55 CST)
- AMBER: Problem with energy decomposition in MMPBSA alfredoq_at_mail.fcq.unc.edu.ar (Tue Feb 05 2008 - 15:32:05 CST)
- AMBER: segmentation fault while generating the covariance matrix rams rams (Tue Feb 05 2008 - 23:12:29 CST)
- AMBER: re MD simulations of NMR structures: minimized average structure vs. ensemble member Vidana.Epa_at_csiro.au (Wed Feb 06 2008 - 00:08:19 CST)
- Fwd: AMBER: (no subject) Syed Tarique Moin (Wed Feb 06 2008 - 02:00:23 CST)
- AMBER: Query related to implicit solvent EXTDIEL S.Sundar Raman (Wed Feb 06 2008 - 06:03:02 CST)
- AMBER: Binary restart file !! Sampath Koppole (Wed Feb 06 2008 - 08:41:03 CST)
- AMBER: using NAB to calculate entropy Wang, Xuelin (Wed Feb 06 2008 - 11:52:06 CST)
- AMBER: Amber compilation with ifort Andrey Semichaevsky (Wed Feb 06 2008 - 15:23:26 CST)
- AMBER: Amber 8 Equivalent of the Amber 5 - Edit program Mohd Farid Ismail (Wed Feb 06 2008 - 16:07:55 CST)
- Re: AMBER: Amber 8 Equivalent of the Amber 5 - Edit program Bill Ross (Wed Feb 06 2008 - 18:18:38 CST)
- AMBER: Problem:neturalization jani sahil (Wed Feb 06 2008 - 23:03:35 CST)
- AMBER: A new program for doing RESP David Cerutti (Thu Feb 07 2008 - 00:56:04 CST)
- AMBER: Deleting solute from box Kevin Davies (Thu Feb 07 2008 - 14:45:48 CST)
- Re: AMBER: Deleting solute from box Bill Ross (Thu Feb 07 2008 - 15:37:27 CST)
- RE: AMBER: QMMM with printcharges Ross Walker (Thu Feb 07 2008 - 16:12:17 CST)
- AMBER: Error while compiling Amber Lili Peng (Thu Feb 07 2008 - 19:14:42 CST)
- AMBER: WARNING in readAmberTrajectory(): fsetpos() failed on when looking for box coordinates! rams rams (Thu Feb 07 2008 - 23:36:15 CST)
- AMBER: Which install compiler and flags? Sam Kaye (Fri Feb 08 2008 - 04:07:15 CST)
- AMBER: PB Bomb in pb_atmlist(): maxnba too short Eddie Mende (Fri Feb 08 2008 - 07:22:07 CST)
- AMBER: Antechamber/mopac query Lynn F. Ten Eyck (Fri Feb 08 2008 - 19:15:12 CST)
- AMBER: Input file for Minimization Campbell, Patrick (Sat Feb 09 2008 - 15:18:51 CST)
- AMBER: leaprc help snoze pa (Mon Feb 11 2008 - 11:50:30 CST)
- AMBER: mm_pbsa problem Badry Bursulaya (Mon Feb 11 2008 - 16:45:29 CST)
- AMBER: Non-polar Parameters For MM_PBSA Calculation Neil Bruce (Tue Feb 12 2008 - 05:54:02 CST)
- AMBER: PKa calculation Wang, Xuelin (Tue Feb 12 2008 - 10:45:16 CST)
- AMBER: RDCs in AMBER 10 Douglas Kojetin (Tue Feb 12 2008 - 17:39:37 CST)
- AMBER: (no subject) Syed Tarique Moin (Wed Feb 13 2008 - 04:55:02 CST)
- AMBER: AMBER 8 problems on RHEL4/Opteron/PGF 7.0-7 Atro Tossavainen (Wed Feb 13 2008 - 07:31:54 CST)
- AMBER: Is boiling point a good way to validate solvent paramters? Mike Wykes (Wed Feb 13 2008 - 08:08:25 CST)
- AMBER: sander error on Make test.serial Evan Kelly (Wed Feb 13 2008 - 14:26:25 CST)
- AMBER: ambmask problem Hopkins, Robert (Wed Feb 13 2008 - 18:42:53 CST)
- AMBER: AMBER parameters for Chlorophyll Sreeja Parameswaran (Wed Feb 13 2008 - 19:31:05 CST)
- AMBER: xmgr graphics display program Hopkins, Robert (Wed Feb 13 2008 - 20:02:23 CST)
- AMBER: mpd error in submitting parallel job Lili Peng (Thu Feb 14 2008 - 03:11:25 CST)
- AMBER: Distance restraints between com of two groups of residues Sudha Mani Karra (Thu Feb 14 2008 - 16:20:26 CST)
- AMBER: print distance between atoms during simulation within sander itsself Vlad Cojocaru (Fri Feb 15 2008 - 08:06:24 CST)
- AMBER: setbox for solvateoct model Wang, Xuelin (Fri Feb 15 2008 - 09:22:07 CST)
- AMBER: problem with ambmask David A. Case (Fri Feb 15 2008 - 12:07:54 CST)
- AMBER: matrix correl David Beveridge (Sat Feb 16 2008 - 03:09:29 CST)
- AMBER: setting perioding box in AMBER Vijay Manickam Achari (Sun Feb 17 2008 - 19:47:17 CST)
- AMBER: TERs Steve Seibold (Mon Feb 18 2008 - 07:19:39 CST)
- AMBER: parameters of nonbonded potentials Alexander Klenner (Tue Feb 19 2008 - 04:43:27 CST)
- AMBER: Generating RESP charges Christopher Illingworth (Tue Feb 19 2008 - 05:39:22 CST)
- AMBER: united atom force field: antechamber fatima.chami_at_durham.ac.uk (Tue Feb 19 2008 - 15:59:42 CST)
- AMBER: NAB to calcuate entropy Wang, Xuelin (Tue Feb 19 2008 - 17:58:15 CST)
- AMBER: Regarding:PME and neturalization jani sahil (Tue Feb 19 2008 - 23:12:45 CST)
- AMBER: is that possible fix box size in constant pressure MD Vijay Manickam Achari (Tue Feb 19 2008 - 23:39:46 CST)
- AMBER: Dimension of the solvated box? abiram abiram (Wed Feb 20 2008 - 07:54:08 CST)
- AMBER: Problem with "trajout pdb" Yi-Ming Cheng (Wed Feb 20 2008 - 10:53:32 CST)
- AMBER: saveAmberPrep in internal coordinates Xu, Huafeng (Wed Feb 20 2008 - 11:02:00 CST)
- AMBER: XLEaP Anamika Awasthi (Thu Feb 21 2008 - 03:36:20 CST)
- AMBER: simulated annealing Holly Freedman (Thu Feb 21 2008 - 13:31:48 CST)
- AMBER: Question: tweaking topology files to add SHAKE-constrained bonds David Cerutti (Thu Feb 21 2008 - 23:37:28 CST)
- AMBER: problem bull linux compiling Yannick Monclin (Fri Feb 22 2008 - 05:22:49 CST)
- AMBER: gaff paramters servaas michielssens (Fri Feb 22 2008 - 11:38:53 CST)
- AMBER: More on tweaking a topology file David Cerutti (Fri Feb 22 2008 - 21:15:40 CST)
- Fwd: Re: AMBER: Problem with "trajout pdb" Yi-Ming Cheng (Sat Feb 23 2008 - 04:21:29 CST)
- AMBER: dihedral energy in amber aneesh cna (Sat Feb 23 2008 - 04:32:08 CST)
- Re: AMBER: parameters for silicon atom Scott Brozell (Mon Feb 25 2008 - 20:24:03 CST)
- AMBER: compiling PMEMD with MKL10.0 Alessandro Nascimento (Tue Feb 26 2008 - 04:20:47 CST)
- AMBER: Force fields oguz gurbulak (Tue Feb 26 2008 - 10:12:48 CST)
- AMBER: bond breaking in proteins Eddie Mende (Tue Feb 26 2008 - 10:16:21 CST)
- AMBER: mol2 save snoze pa (Tue Feb 26 2008 - 11:09:18 CST)
- AMBER: autodock pdb to obtain parm with tleap Henar Martínez (Tue Feb 26 2008 - 11:23:43 CST)
- AMBER: bond breaking in proteins Eddie Mende (Tue Feb 26 2008 - 16:41:22 CST)
- AMBER: Using restart files Lili Peng (Tue Feb 26 2008 - 17:36:50 CST)
- AMBER: charge derivation for modified amino acids Denzil Bernard (Tue Feb 26 2008 - 19:14:44 CST)
- AMBER: "Assuming uniform neutralizing plasma" Evan Kelly (Tue Feb 26 2008 - 20:01:52 CST)
- AMBER: stops writing trajectory Swarup Gupta (Wed Feb 27 2008 - 03:55:10 CST)
- AMBER: initial command? Anamika Awasthi (Wed Feb 27 2008 - 06:01:51 CST)
- AMBER: Amber: shared memory vs cluster Francesco Pietra (Wed Feb 27 2008 - 12:08:19 CST)
- AMBER: Lennard-Jones parameters zhan chen (Thu Feb 28 2008 - 01:41:02 CST)
- AMBER: DFTB/SCC-DFTB Eddie Mende (Wed Feb 27 2008 - 13:21:42 CST)
- AMBER: varying restraint_wt with nmropt=1 Andrew Borgert (Wed Feb 27 2008 - 14:18:28 CST)
- AMBER: problem with antechamber aneesh cna (Wed Feb 27 2008 - 23:55:53 CST)
- AMBER: problems with Replica Exchange rebeca_at_mmb.pcb.ub.es (Thu Feb 28 2008 - 06:29:23 CST)
- AMBER: Plea for REMD tutorial tushar garud (Thu Feb 28 2008 - 07:56:42 CST)
- AMBER: Liquid/Gas Phase Rita Cassia (Thu Feb 28 2008 - 10:34:00 CST)
- AMBER: problems with 10-12 potential in amber8 sander Amie Demmel (Thu Feb 28 2008 - 14:59:27 CST)
- AMBER: problems with 10-12 potential in amber8 sander Amie Demmel (Thu Feb 28 2008 - 14:59:27 CST)
- AMBER: Re: Force field parameter file for CNT Andrey Semichaevsky (Thu Feb 28 2008 - 15:34:01 CST)
- AMBER: for NMR refinement Wenyong Tong (Thu Feb 28 2008 - 20:20:08 CST)
- AMBER: Visualizing Periodc box Vijay Manickam Achari (Fri Feb 29 2008 - 01:50:13 CST)
- AMBER: Plea for REMD tutorial tushar garud (Fri Feb 29 2008 - 08:57:41 CST)
- AMBER: Re: Amber Force field for CNT: leaprc.ff23 Andrey Semichaevsky (Fri Feb 29 2008 - 09:35:16 CST)
- AMBER: Non aqueous implicit solvation Mike Wykes (Fri Feb 29 2008 - 12:56:01 CST)
- AMBER: regarding:calculation of b factor using ptraj jani sahil (Sat Mar 01 2008 - 10:10:10 CST)
- AMBER: questions about run MD at different pH Kailee (Mon Mar 03 2008 - 08:51:40 CST)
- AMBER: Writing pressure in md.out file in NVT simulation Sudha Mani Karra (Mon Mar 03 2008 - 12:58:46 CST)
- AMBER: xleap screen output Francesco Pietra (Mon Mar 03 2008 - 15:02:54 CST)
- AMBER: ACS COMP Division awards- deadline this week Carlos Simmerling (Mon Mar 03 2008 - 18:14:03 CST)
- AMBER: Problem running implicit minimization Lili Peng (Mon Mar 03 2008 - 23:10:52 CST)
- AMBER: missing gaff parameters Samuele Giani (Tue Mar 04 2008 - 02:46:38 CST)
- Fwd: Re: AMBER: xleap screen output Francesco Pietra (Tue Mar 04 2008 - 11:33:34 CST)
- Fwd: Re: AMBER: xleap screen output SOLVED Francesco Pietra (Tue Mar 04 2008 - 14:44:15 CST)
- Re: Fwd: Re: AMBER: xleap screen output Bill Ross (Tue Mar 04 2008 - 11:59:58 CST)
- AMBER: a question about parameter b in the hyperbolic form of penalty function for RESP fit Ye Mei (Wed Mar 05 2008 - 03:30:50 CST)
- AMBER: Atom types/parameters for chromene anna.schrey_at_gmx.de (Wed Mar 05 2008 - 03:34:24 CST)
- AMBER: setBox command Vijay Manickam Achari (Wed Mar 05 2008 - 23:20:01 CST)
- AMBER: not equivalent oxygens in COO- / how to force order of atoms in IMPROPER? Edyta Malolepsza (Thu Mar 06 2008 - 06:23:06 CST)
- AMBER: Steve Seibold (Thu Mar 06 2008 - 12:04:01 CST)
- Re: AMBER: XMGRACE on Linux 64 Bit Bill Ross (Thu Mar 06 2008 - 18:12:51 CST)
- AMBER: Microcannonical MD Reference priya priya (Fri Mar 07 2008 - 07:40:34 CST)
- AMBER: NVE energy and temperature drift Lars Skjærven (Fri Mar 07 2008 - 09:36:48 CST)
- AMBER: Fwd: positive potential energy and large 1-4 EEL Mey Khalili (Fri Mar 07 2008 - 10:54:28 CST)
- AMBER: Inquiry on nmode for alculate frequencies & thermodynamics analysis James Thomas (Fri Mar 07 2008 - 11:30:58 CST)
- AMBER: AMBER install problem Kijeong Kwac (Fri Mar 07 2008 - 12:12:08 CST)
- AMBER: RE: Request Ross Walker (Fri Mar 07 2008 - 14:38:25 CST)
- AMBER: reg molecular dynamics Uma R (Fri Mar 07 2008 - 21:17:32 CST)
- AMBER: Negative ligand (Peroxide) Syed Tarique Moin (Sat Mar 08 2008 - 05:36:56 CST)
- AMBER: Compiler issues with Altix450 finke_at_oakland.edu (Sat Mar 08 2008 - 12:37:25 CST)
- AMBER: Clarification on error message Campbell, Patrick (Sat Mar 08 2008 - 14:09:23 CST)
- AMBER: mmpbsa INSTRNG error? Sergio Wong (Sun Mar 09 2008 - 00:06:44 CST)
- AMBER: Timing analysis on Ranger David LeBard (Sun Mar 09 2008 - 15:06:18 CDT)
- AMBER: Antechamber, net molecular charge gurpreet singh (Sun Mar 09 2008 - 23:51:58 CDT)
- AMBER: Benchmarks on Fujitsu PrimePower 2500? Craig Gough (Mon Mar 10 2008 - 00:36:28 CDT)
- Fwd: AMBER: Negative ligand (Peroxide) Syed Tarique Moin (Mon Mar 10 2008 - 00:59:43 CDT)
- AMBER: writing out a distance between two atoms in sander Vlad Cojocaru (Mon Mar 10 2008 - 08:33:55 CDT)
- AMBER: problem with antech amber Madjid Taghdir (Mon Mar 10 2008 - 10:07:16 CDT)
- AMBER: output effective Born radii Holly Freedman (Mon Mar 10 2008 - 17:57:06 CDT)
- AMBER: Re: Amber: parameters for Silicon Scott Brozell (Mon Mar 10 2008 - 18:57:29 CDT)
- AMBER: SMD using amber ChengZhong Zhang (Mon Mar 10 2008 - 20:54:23 CDT)
- AMBER: convert AMBER format input files into DL_POLY format input files? Kefa Lu (Tue Mar 11 2008 - 03:27:23 CDT)
- AMBER: solvate with methanol san_amber roy (Tue Mar 11 2008 - 04:23:40 CDT)
- AMBER: Adding New Parameters and Modifying Existing Parameters serhanyigen_at_mail.ege.edu.tr (Tue Mar 11 2008 - 06:51:18 CDT)
- AMBER: SPARC benchmarks (was re Fujitsu PRIMEPOWER) Atro Tossavainen (Tue Mar 11 2008 - 09:33:33 CDT)
- AMBER: Error during compilation of Amber8, /bin/sh: ./Makelist: not found, make[1]: *** [libobj] Error 127 David Rangel (Tue Mar 11 2008 - 22:30:14 CDT)
- AMBER: lastrst problem san_amber roy (Wed Mar 12 2008 - 10:07:23 CDT)
- AMBER: ptraj and non-bonded contacts Samuel Genheden (a03samge) (Wed Mar 12 2008 - 11:34:44 CDT)
- AMBER: study of protein stability in different ion using AMBER Prem Prakash Pathak (Thu Mar 13 2008 - 01:20:31 CDT)
- AMBER: distance restraint gurpreet singh (Thu Mar 13 2008 - 06:28:28 CDT)
- AMBER: [success] problem compiling Amber9 on Bull Linux Yannick Monclin (Thu Mar 13 2008 - 06:56:48 CDT)
- AMBER: Energy calculation and replica exchange in Amber9 Li Dawei (Thu Mar 13 2008 - 08:50:49 CDT)
- AMBER: can't make antechamber work for regular nucleotides Mey Khalili (Thu Mar 13 2008 - 09:03:45 CDT)
- AMBER: ptraj, hbond and non-bonded contacts Samuel Genheden (a03samge) (Thu Mar 13 2008 - 09:54:03 CDT)
- AMBER: Temperature Range For REMD tushar garud (Thu Mar 13 2008 - 10:20:02 CDT)
- AMBER: force field oguz gurbulak (Thu Mar 13 2008 - 17:00:58 CDT)
- AMBER: protonated histidine ( charges in parm file versus all_amino03.lib ) Lwin, ThuZar (Thu Mar 13 2008 - 19:13:57 CDT)
- AMBER: How to calculate deformability by PTRAJ ? sychen (Thu Mar 13 2008 - 20:44:36 CDT)
- AMBER: Torsion potential in GAFF / "statistic value of parm94" Alexander Metz (Fri Mar 14 2008 - 07:53:10 CDT)
- AMBER: protonated histidine ( charges in parm file versus all_amino03.lib ). Lwin, ThuZar (Fri Mar 14 2008 - 10:32:25 CDT)
- AMBER: Heating POL3 Box Troubles Paul Johns (Fri Mar 14 2008 - 13:44:44 CDT)
- AMBER: Negative ligand Syed Tarique Moin (Sat Mar 15 2008 - 04:12:09 CDT)
- AMBER: mm_pbsa positive ELE Qi Yan (Mon Mar 17 2008 - 13:20:21 CDT)
- AMBER: compiling AMBER9 with bintraj option on AMD64 Vlad Cojocaru (Fri Mar 14 2008 - 12:44:56 CDT)
- AMBER: What's making my system lose total energy? David Cerutti (Mon Mar 17 2008 - 19:20:30 CDT)
- AMBER: a minor bug in RESP Ye Mei (Tue Mar 18 2008 - 02:05:34 CDT)
- AMBER: problem with distance restrain aneesh cna (Tue Mar 18 2008 - 05:16:09 CDT)
- AMBER: replica exchange : problem with sander Guillaume Renvez (Tue Mar 18 2008 - 09:09:34 CDT)
- AMBER: Problems with neglected restaints anna.schrey_at_gmx.de (Tue Mar 18 2008 - 11:40:20 CDT)
- AMBER: Inquiry on analyzing the amplitude from nmdout results James Thomas (Wed Mar 19 2008 - 11:09:05 CDT)
- AMBER: Amber9 Installation Problem trudy_at_uoguelph.ca (Wed Mar 19 2008 - 11:28:35 CDT)
- AMBER: Amber9 Installation Problem trudy_at_uoguelph.ca (Wed Mar 19 2008 - 11:28:35 CDT)
- AMBER: MNDO parameters for Mg+2 E.M. (Wed Mar 19 2008 - 12:28:09 CDT)
- AMBER: standard residues Holly Freedman (Wed Mar 19 2008 - 15:03:02 CDT)
- AMBER: Water Topology Ivelin Georgiev (Wed Mar 19 2008 - 23:12:28 CDT)
- AMBER: potential of mean force: Unit of PMF energies and min path Catein Catherine (Thu Mar 20 2008 - 00:26:43 CDT)
- AMBER: Happy holi Bertrand P. S. Russell (Thu Mar 20 2008 - 04:03:22 CDT)
- AMBER: problem with distance restraints aneesh cna (Thu Mar 20 2008 - 05:13:31 CDT)
- AMBER: Charge scheme for simulating protonated adenine prateeksha s (Fri Mar 21 2008 - 01:58:19 CDT)
- AMBER: equilibration of peptide tushar garud (Fri Mar 21 2008 - 23:02:25 CDT)
- AMBER: cntrl namelist error Campbell, Patrick (Sat Mar 22 2008 - 10:40:16 CDT)
- AMBER: RE: Force Field Parameterizing Shultz, Jack (Mon Mar 24 2008 - 10:31:32 CDT)
- AMBER: hybrid remd imaging Geoff Wood (Mon Mar 24 2008 - 10:51:51 CDT)
- AMBER: Nmode segmentation fault James Thomas (Tue Mar 25 2008 - 06:53:21 CDT)
- AMBER: anion and cation simulaton gurpreet singh (Tue Mar 25 2008 - 11:22:29 CDT)
- AMBER: help regarding warning message snoze pa (Tue Mar 25 2008 - 11:17:43 CDT)
- Re: AMBER: addions and addions2 Bill Ross (Tue Mar 25 2008 - 12:34:52 CDT)
- AMBER: Convert dcd to mdcrd Seth Lilavivat (Tue Mar 25 2008 - 13:13:22 CDT)
- AMBER: umbrella sampling for proton transfer cniu_at_ualberta.ca (Tue Mar 25 2008 - 19:30:33 CDT)
- AMBER: NTR Restraints Daniel Smith (Tue Mar 25 2008 - 20:17:27 CDT)
- AMBER: OPLS force field aneesh cna (Wed Mar 26 2008 - 10:48:19 CDT)
- AMBER: mm-pbsa multiple trajectory approach? Seth Lilavivat (Wed Mar 26 2008 - 12:32:54 CDT)
- AMBER: residual dipolar couplings - alignment tensor energy Douglas Kojetin (Wed Mar 26 2008 - 14:46:48 CDT)
- AMBER: RMSD of two different molecules JunJun Liu (Wed Mar 26 2008 - 15:35:32 CDT)
- AMBER: how to link two different atoms in xLeap snoze pa (Wed Mar 26 2008 - 15:56:12 CDT)
- AMBER: Error with a binary restart file Kijeong Kwac (Wed Mar 26 2008 - 18:07:51 CDT)
- AMBER: PF6 parameters aneesh cna (Wed Mar 26 2008 - 23:43:58 CDT)
- AMBER: Error- MM_PBSA calculation vikky 99 (Thu Mar 27 2008 - 03:47:53 CDT)
- AMBER: FW: MD run time inquiry Campbell, Patrick (Thu Mar 27 2008 - 05:13:00 CDT)
- AMBER: Protein rotating out of box Lars Skjærven (Thu Mar 27 2008 - 16:34:48 CDT)
- AMBER: measuring contacts: error "glibc detected" rebeca_at_mmb.pcb.ub.es (Fri Mar 28 2008 - 07:26:42 CDT)
- AMBER: GAFF Eric Germaneau (Fri Mar 28 2008 - 07:38:41 CDT)
- AMBER: REMD simulation error Guillaume Renvez (Fri Mar 28 2008 - 09:01:20 CDT)
- AMBER: problem with nmod yuri pomè (Fri Mar 28 2008 - 11:42:54 CDT)
- AMBER: meet problem in adding ions and waterbox Qiang Li (Sun Mar 30 2008 - 00:43:54 CDT)
- AMBER: Regarding SHAKE gurpreet singh (Sun Mar 30 2008 - 05:38:48 CDT)
- AMBER: reproducing http://amber.scripps.edu/tutorials/advanced/tutorial6/index.htm with explicit water Markus Kaukonen (Mon Mar 31 2008 - 01:34:48 CDT)
- AMBER: Free energy landscape? HOWTO? Yi-Ming Cheng (Mon Mar 31 2008 - 03:12:05 CDT)
- AMBER: TI: perturbation method fatima.chami_at_durham.ac.uk (Mon Mar 31 2008 - 03:40:40 CDT)
- AMBER: energy problems in simulation with restraints Daniel Cappel (Mon Mar 31 2008 - 04:39:13 CDT)
- AMBER: Select specific residues (leap) Marta Rossini (Mon Mar 31 2008 - 04:28:31 CDT)
- AMBER: installation amber9 Geoff Wood (Mon Mar 31 2008 - 06:02:01 CDT)
- AMBER: multiple dihedral restraints using group mkseo (Mon Mar 31 2008 - 12:11:30 CDT)
- AMBER: memory limitation of Amber 9 yavuzturkm_at_prc.boun.edu.tr (Mon Mar 31 2008 - 13:49:40 CDT)
- AMBER: nmode James Thomas (Mon Mar 31 2008 - 13:48:43 CDT)
- AMBER: running minimisation on cis-azobenzene Chih-Ying Lin (Mon Mar 31 2008 - 14:45:20 CDT)
- AMBER: Amber 8 on Redhat 4 X86_64 yavuzturkm_at_prc.boun.edu.tr (Tue Apr 01 2008 - 00:30:32 CDT)
- AMBER: TIP5P water simulation with AMBER7 Biman Jana (Tue Apr 01 2008 - 02:14:54 CDT)
- AMBER: hybrid remd imaging Geoff Wood (Tue Apr 01 2008 - 02:47:18 CDT)
- AMBER: working with unformatted restart files in AMBER9 Vlad Cojocaru (Tue Apr 01 2008 - 08:35:57 CDT)
- AMBER: atomic posiltional fluctuation Furia Gargano (Tue Apr 01 2008 - 09:11:12 CDT)
- AMBER: B-factor Furia Gargano (Tue Apr 01 2008 - 14:05:36 CDT)
- AMBER: Simulating DNA Backbone in NAB Adelene Sim (Tue Apr 01 2008 - 14:23:16 CDT)
- AMBER: B-factor Furia Gargano (Tue Apr 01 2008 - 14:05:36 CDT)
- AMBER: Simulating DNA Backbone in NAB Adelene Sim (Tue Apr 01 2008 - 14:23:16 CDT)
- AMBER: B-factor Furia Gargano (Tue Apr 01 2008 - 14:05:36 CDT)
- AMBER: Simulating DNA Backbone in NAB Adelene Sim (Tue Apr 01 2008 - 14:23:16 CDT)
- AMBER: B-factor Furia Gargano (Tue Apr 01 2008 - 14:05:36 CDT)
- AMBER: Simulating DNA Backbone in NAB Adelene Sim (Tue Apr 01 2008 - 14:23:16 CDT)
- AMBER: B-factor Furia Gargano (Tue Apr 01 2008 - 14:05:36 CDT)
- AMBER: Simulating DNA Backbone in NAB Adelene Sim (Tue Apr 01 2008 - 14:23:16 CDT)
- AMBER: Simulating DNA Backbone in NAB Adelene Sim (Tue Apr 01 2008 - 14:23:16 CDT)
- AMBER: Simulating DNA Backbone in NAB Adelene Sim (Tue Apr 01 2008 - 14:23:16 CDT)
- AMBER: B-factor Furia Gargano (Tue Apr 01 2008 - 14:05:36 CDT)
- AMBER: Simulating DNA Backbone in NAB Adelene Sim (Tue Apr 01 2008 - 14:23:16 CDT)
- AMBER: Simulating DNA Backbone in NAB Adelene Sim (Tue Apr 01 2008 - 14:23:16 CDT)
- AMBER: B-factor Furia Gargano (Tue Apr 01 2008 - 14:05:36 CDT)
- AMBER: LEap error message for parmBSC0 force field Cenk Andac (Tue Apr 01 2008 - 18:31:17 CDT)
- AMBER: meet problems in adding ions and waterbox Qiang Li (Wed Apr 02 2008 - 00:12:31 CDT)
- AMBER: LJ parameters aneesh cna (Wed Apr 02 2008 - 06:46:22 CDT)
- AMBER: REMD simulation error Guillaume Renvez (Wed Apr 02 2008 - 07:47:20 CDT)
- AMBER: ANNOUNCE: Release of AmberTools, version 1.0 David A. Case (Wed Apr 02 2008 - 11:49:20 CDT)
- AMBER: ptraj / covariance / quasiharmonic approximation / entropy Seth Lilavivat (Wed Apr 02 2008 - 14:18:55 CDT)
- AMBER: NAD parameters Urszula Uciechowska (Thu Apr 03 2008 - 09:30:05 CDT)
- AMBER: dockmolecules in examples directory of AmberTools-1.0 M. L. Dodson (Thu Apr 03 2008 - 10:54:50 CDT)
- AMBER: MPI run problem Qi Yan (Thu Apr 03 2008 - 11:33:19 CDT)
- AMBER: problem with Mg2+ during MD Zhenwei Lu (Thu Apr 03 2008 - 11:48:13 CDT)
- AMBER: mm_pbsa error rams rams (Thu Apr 03 2008 - 11:28:56 CDT)
- AMBER: Using mdcrd files to look at minor charge changes Cooper, Matthew (Thu Apr 03 2008 - 13:45:12 CDT)
- AMBER: imem keyword using mmpbsa Sergio Wong (Thu Apr 03 2008 - 15:43:01 CDT)
- AMBER: ligand slips out of pocket Hannes Wallnoefer (Fri Apr 04 2008 - 02:58:29 CDT)
- AMBER: solvateOct produces strange residues compared to solvateCap Markus Kaukonen (Fri Apr 04 2008 - 03:08:53 CDT)
- AMBER: GAFF Eric Germaneau (Fri Apr 04 2008 - 03:18:03 CDT)
- AMBER: sander.MPI setup with SGE Sasha Buzko (Fri Apr 04 2008 - 11:59:34 CDT)
- AMBER: artifacts in ptraj avg output stephane acoca (Sat Apr 05 2008 - 03:46:55 CDT)
- AMBER: RE: amber help Ross Walker (Sat Apr 05 2008 - 22:25:19 CDT)
- AMBER: NAB examples Hu, Shaowen (JSC-SK)[USRA] (Mon Apr 07 2008 - 09:32:07 CDT)
- AMBER: restraint box dimension aneesh cna (Tue Apr 08 2008 - 05:45:20 CDT)
- AMBER: Should the two phenyl rings of the trans-azobenzene on the same plane after minimisation? Chih-Ying Lin (Tue Apr 08 2008 - 20:09:24 CDT)
- AMBER: converting from CNS file format Sally Pias (Wed Apr 09 2008 - 00:32:11 CDT)
- AMBER: Estimating dielectric constant Marcelo Puiatti (Wed Apr 09 2008 - 09:42:40 CDT)
- AMBER: Collect dihedral angles Chih-Ying Lin (Wed Apr 09 2008 - 16:35:09 CDT)
- AMBER: Force field Parameters Chih-Ying Lin (Wed Apr 09 2008 - 21:17:51 CDT)
- AMBER: tempi in Replica Exchange rebeca_at_mmb.pcb.ub.es (Thu Apr 10 2008 - 04:23:00 CDT)
- AMBER: WHAM: how frequently do I need data on the system coordinates? David Cerutti (Thu Apr 10 2008 - 11:14:23 CDT)
- AMBER: protein-ligand complex problem Lynn (Thu Apr 10 2008 - 17:51:32 CDT)
- AMBER: trans-azobenzene under minimisation Chih-Ying Lin (Thu Apr 10 2008 - 19:29:37 CDT)
- AMBER: query about Generalized Born simulation gurvisha_at_leadinvent.com (Fri Apr 11 2008 - 08:42:23 CDT)
- AMBER: Amber installation jacopo.sgrignani_at_unifi.it (Fri Apr 11 2008 - 08:23:24 CDT)
- AMBER: Imaging before HBond analysis? Evan Kelly (Fri Apr 11 2008 - 15:34:41 CDT)
- AMBER: installing pmemd with fftw YangMingjun (Sun Apr 13 2008 - 08:07:44 CDT)
- AMBER: topology file Giuseppe De Marco (Mon Apr 14 2008 - 04:38:37 CDT)
- AMBER: Error: Bond: Maximum coordination exceeded -- setting atoms pert=true overrides default limits Ted Fischer (Mon Apr 14 2008 - 07:53:42 CDT)
- AMBER: error in compilation elsize.cc snoze pa (Mon Apr 14 2008 - 11:38:07 CDT)
- AMBER: ANNOUNCEMENT: release of Amber 10 David A. Case (Mon Apr 14 2008 - 12:18:40 CDT)
- AMBER: loadPdb returns extra atoms Seth Lilavivat (Mon Apr 14 2008 - 13:50:32 CDT)
- AMBER: Problems compiling Amber with MKL Sasha Buzko (Mon Apr 14 2008 - 14:13:23 CDT)
- AMBER: JavaGenes Shultz, Jack (Mon Apr 14 2008 - 14:26:25 CDT)
- AMBER: energy decomposition vs ala scan Sergio Wong (Mon Apr 14 2008 - 21:05:41 CDT)
- AMBER: imaging problem Marcin Krol (Tue Apr 15 2008 - 06:54:30 CDT)
- AMBER: mmpbsa with gromacs trajectory jacopo.sgrignani_at_unifi.it (Tue Apr 15 2008 - 09:10:21 CDT)
- AMBER: loading pdb in leap to create parameter files Cristina Sisu (Tue Apr 15 2008 - 08:43:57 CDT)
- AMBER: Is it possible to run PIMD simulation with QM/MM potential in Amber10? cgji (Tue Apr 15 2008 - 10:27:08 CDT)
- AMBER: xleap segmentation fault on SaveAmberParm Brendan Duggan (Tue Apr 15 2008 - 14:15:46 CDT)
- AMBER: Extracting the electric field (and its gradient) on particular solute atoms John Chodera (Tue Apr 15 2008 - 19:36:01 CDT)
- AMBER: PMF calculation for binding constant or rate constant? Catein Catherine (Tue Apr 15 2008 - 21:26:46 CDT)
- AMBER: leap - using default radius 1.500000 for HO3 Nina Fischer (Wed Apr 16 2008 - 04:08:59 CDT)
- AMBER: Protonation states in Constant pH Simulations Neil Bruce (Wed Apr 16 2008 - 07:54:44 CDT)
- AMBER: Distance in z dimension Age.Skjevik_at_student.uib.no (Wed Apr 16 2008 - 09:50:55 CDT)
- AMBER: Amber9 with MPICH2 failure at runtime Sasha Buzko (Wed Apr 16 2008 - 16:43:07 CDT)
- AMBER: xLeap unit editor "seg fault" inonshar_at_post.tau.ac.il (Thu Apr 17 2008 - 00:49:01 CDT)
- AMBER: Scale LJ parameters fatima.chami_at_durham.ac.uk (Thu Apr 17 2008 - 06:20:40 CDT)
- AMBER: uccabke_at_ucl.ac.uk (Thu Apr 17 2008 - 10:02:06 CDT)
- AMBER: Performance issues on Ethernet clusters Sasha Buzko (Thu Apr 17 2008 - 13:20:52 CDT)
- AMBER: Conformation search... Anthony Cruz (Thu Apr 17 2008 - 14:32:52 CDT)
- AMBER: Short trajectory segments / frequent restarts causes explosion David Cerutti (Thu Apr 17 2008 - 16:04:14 CDT)
- AMBER: compile Amber9 on 64bit AMD Opteron Jeffrey (Fri Apr 18 2008 - 02:02:24 CDT)
- AMBER: nmode problem Hannes Wallnoefer (Fri Apr 18 2008 - 04:01:27 CDT)
- AMBER: AmberTools on OS X Leopard with Intel compilers Yu Chen (Fri Apr 18 2008 - 14:17:37 CDT)
- AMBER: hydrogens are flying in replica exchange simulations Ashish Sangwai (Fri Apr 18 2008 - 18:43:01 CDT)
- AMBER: How to add radius of an atom saurabh agrawal (Mon Apr 21 2008 - 00:45:43 CDT)
- AMBER: Average structure James Thomas (Mon Apr 21 2008 - 05:21:26 CDT)
- AMBER: nmode jacopo.sgrignani_at_unifi.it (Mon Apr 21 2008 - 12:38:44 CDT)
- AMBER: aromatic residues lost planarity during MD simulation cniu_at_ualberta.ca (Mon Apr 21 2008 - 15:18:26 CDT)
- AMBER: Can sander provide ESP with PBC? Khatcharin Siriwong (Mon Apr 21 2008 - 20:36:17 CDT)
- AMBER: How to change default radius assigned to an atom saurabh agrawal (Mon Apr 21 2008 - 23:47:14 CDT)
- AMBER: pressure varies in constant pressure membrane simulation Vijay Manickam Achari (Tue Apr 22 2008 - 00:58:29 CDT)
- AMBER: matrxi dist command priya priya (Tue Apr 22 2008 - 06:37:50 CDT)
- AMBER: minimization san_amber roy (Tue Apr 22 2008 - 09:01:52 CDT)
- AMBER: refine cyana structures! Hongyan Li (Tue Apr 22 2008 - 20:33:08 CDT)
- AMBER: RE: amber tutorial A3 Ross Walker (Tue Apr 22 2008 - 23:45:29 CDT)
- AMBER: Topology file format for Amber9 Xioling Chuang (Wed Apr 23 2008 - 00:41:32 CDT)
- AMBER: cross time correlation function fatima.chami_at_durham.ac.uk (Wed Apr 23 2008 - 07:55:28 CDT)
- AMBER: ESP on atoms (2) Khatcharin Siriwong (Wed Apr 23 2008 - 09:29:04 CDT)
- AMBER: 2D-RMSD Tom McGrory (Wed Apr 23 2008 - 10:00:57 CDT)
- AMBER: Amber10 on Leopard with Intel compilers, "Undefined symbols" error Yu Chen (Wed Apr 23 2008 - 13:03:13 CDT)
- AMBER: saveamberparm taufik.alsarraj_at_utoronto.ca (Wed Apr 23 2008 - 19:34:02 CDT)
- AMBER: saveamberparm taufik.alsarraj_at_utoronto.ca (Wed Apr 23 2008 - 19:38:16 CDT)
- AMBER: sander & imin=5 Xioling Chuang (Thu Apr 24 2008 - 02:03:09 CDT)
- AMBER: water in the binding site MMPBSA jacopo.sgrignani_at_unifi.it (Thu Apr 24 2008 - 08:51:43 CDT)
- AMBER: pmemd: "undefined reference to `mpi_(name-varies)'" Lachele Foley (Lists) (Thu Apr 24 2008 - 09:22:42 CDT)
- AMBER: double strand DNA break up (imaging) Seth Lilavivat (Thu Apr 24 2008 - 13:53:44 CDT)
- AMBER: nmode output jacopo.sgrignani_at_unifi.it (Fri Apr 25 2008 - 03:36:35 CDT)
- AMBER: query regarding loadpadb Anamika Awasthi (Fri Apr 25 2008 - 03:33:19 CDT)
- AMBER: parallel error : undefined reference to `MAIN_' Arturas Ziemys (Fri Apr 25 2008 - 16:14:59 CDT)
- AMBER: AMD Opteron: compiler recommendations? Sasha Buzko (Fri Apr 25 2008 - 16:54:57 CDT)
- AMBER: .... RESTARTED DUE TO LINMIN FAILURE ... saurabh agrawal (Sat Apr 26 2008 - 06:36:13 CDT)
- AMBER: memory usage Ye Mei (Sat Apr 26 2008 - 08:57:44 CDT)
- AMBER: NMR restraints Ilyas Yildirim (Mon Apr 28 2008 - 01:53:51 CDT)
- AMBER: Read trajectories generated by CHARMM Jeffrey (Mon Apr 28 2008 - 08:06:17 CDT)
- AMBER: query regarding energy minimization Anamika Awasthi (Mon Apr 28 2008 - 08:22:24 CDT)
- AMBER: Charge derivation: RESP vs. antechamber Catein Catherine (Tue Apr 29 2008 - 05:21:54 CDT)
- AMBER: Charge derivation: RESP vs. antechamber Catein Catherine (Tue Apr 29 2008 - 05:21:55 CDT)
- AMBER: segmentation fault in SANDER Anamika Awasthi (Tue Apr 29 2008 - 06:44:29 CDT)
- AMBER: prmtop spec trivia Lachele Foley (Lists) (Tue Apr 29 2008 - 10:07:29 CDT)
- AMBER: regarding segfault during energy minimization Anamika Awasthi (Wed Apr 30 2008 - 00:13:21 CDT)
- AMBER: distance matrix command priya priya (Wed Apr 30 2008 - 04:01:24 CDT)
- AMBER: Constat area simulation gurpreet singh (Wed Apr 30 2008 - 06:23:35 CDT)
- AMBER: Dose AMBER 10 pmemd support openmpi? Hu, Shaowen (JSC-SK)[USRA] (Wed Apr 30 2008 - 08:04:28 CDT)
- AMBER: amber 9 compilation problem on IBM SP5 Andrew Emerson (Wed Apr 30 2008 - 07:44:38 CDT)
- AMBER: about glycam06 WANG,YING (Wed Apr 30 2008 - 11:00:12 CDT)
- AMBER: calibration of constant pH simulations Lillian Chong (Wed Apr 30 2008 - 12:17:47 CDT)
- AMBER: Cysteine sulphonic acid parameters Rima Chaudhuri (Wed Apr 30 2008 - 17:48:42 CDT)
- AMBER: Discontinuous Constant pH Restarts Neil Bruce (Thu May 01 2008 - 08:41:21 CDT)
- AMBER: Water residue tracking Steve Seibold (Thu May 01 2008 - 11:19:42 CDT)
- AMBER: Installation problem of AMBER on cluster sudipta sinha (Thu May 01 2008 - 13:16:44 CDT)
- AMBER: Amber10 installation error juyong Lee (Thu May 01 2008 - 21:28:07 CDT)
- AMBER: test.parallel.QMMM problem Carra, Claudio (JSC-SK)[USRA] (Fri May 02 2008 - 08:37:28 CDT)
- AMBER: silhouette width/coefficient after clustering by PTRAJ9.9 sychen (Fri May 02 2008 - 09:22:50 CDT)
- AMBER: Water tracking Steve Seibold (Fri May 02 2008 - 10:09:35 CDT)
- AMBER: Help with NMODE Seth Lilavivat (Fri May 02 2008 - 10:24:25 CDT)
- AMBER: cfortran.h error with xlf90 compiler juyong Lee (Fri May 02 2008 - 11:35:32 CDT)
- AMBER: Compiling amber10 with xlf90 fortran compiler juyong Lee (Fri May 02 2008 - 13:27:10 CDT)
- AMBER: Mn2+ parameters in AMBER jitrayut jitonnom (Fri May 02 2008 - 13:46:25 CDT)
- AMBER: Inquiry on B-factor of NMR James Thomas (Fri May 02 2008 - 14:31:09 CDT)
- AMBER: printing dipoles in Amber10 (and earlier) Piotr Cieplak (Fri May 02 2008 - 15:29:49 CDT)
- AMBER: Example .prepi file for nonstandard amino acids finke_at_oakland.edu (Fri May 02 2008 - 17:00:45 CDT)
- AMBER: about glycam06 WANG,YING (Sat May 03 2008 - 18:22:18 CDT)
- AMBER: Amber10 Installation error - incorrect file suffix juyong Lee (Sun May 04 2008 - 07:46:10 CDT)
- AMBER: Deriving Force Field Parameters Shultz, Jack (Sun May 04 2008 - 16:32:03 CDT)
- AMBER: Jarzinsky relationship E.M. (Sun May 04 2008 - 21:39:51 CDT)
- AMBER: Torsion angle restrains and Jarzinsky E.M. (Mon May 05 2008 - 02:06:56 CDT)
- AMBER: Installation error on IBM cluster juyong Lee (Mon May 05 2008 - 03:40:59 CDT)
- AMBER: unable to compile AmberTools 1.0 Rabin (Mon May 05 2008 - 12:07:00 CDT)
- AMBER: About reading in heme and CO molecule together with myoglobin Yang, Lee-Wei (Mon May 05 2008 - 13:08:53 CDT)
- AMBER: AMBER Parallel test error jitrayut jitonnom (Mon May 05 2008 - 13:37:39 CDT)
- AMBER: DCCM correlation analysis Ibrahim Moustafa (Mon May 05 2008 - 15:21:37 CDT)
- AMBER: Units, units units E.M. (Mon May 05 2008 - 17:18:37 CDT)
- AMBER: Minimization in Octahedric Box guardiani_at_fi.infn.it (Tue May 06 2008 - 06:31:50 CDT)
- AMBER: rmsd per residue Furia Gargano (Tue May 06 2008 - 09:28:59 CDT)
- AMBER: steered MD initial state M. L. Dodson (Tue May 06 2008 - 11:04:09 CDT)
- AMBER: mm_pbsa.pl not reading parameters for nmode Seth Lilavivat (Tue May 06 2008 - 12:50:18 CDT)
- Re: AMBER: Improper dihedral parameters Bill Ross (Tue May 06 2008 - 14:23:55 CDT)
- AMBER: DFTB parameters for O-P Carra, Claudio (JSC-SK)[USRA] (Tue May 06 2008 - 15:01:55 CDT)
- AMBER: Ewald error estimate 欧阳德方 (Wed May 07 2008 - 03:25:22 CDT)
- AMBER: molsurf jacopo.sgrignani_at_unifi.it (Wed May 07 2008 - 06:11:34 CDT)
- AMBER: uninstall of AMBER sudipta sinha (Wed May 07 2008 - 10:50:37 CDT)
- AMBER: nmode: number of atoms limitation Qi Yan (Wed May 07 2008 - 13:25:58 CDT)
- AMBER: GBSA SA calculation Titus, Jamie \(bairdje\) (Wed May 07 2008 - 13:32:43 CDT)
- AMBER: Hydroxyprolines!!! Titus, Jamie \(bairdje\) (Wed May 07 2008 - 13:54:03 CDT)
- AMBER: Harmonic Force Constant Shultz, Jack (Wed May 07 2008 - 14:32:18 CDT)
- AMBER: How to transfer unformatted coordinates into formatted ones Qi Yan (Wed May 07 2008 - 14:44:10 CDT)
- AMBER: nmode: number of atoms limitation Qi Yan (Wed May 07 2008 - 13:10:48 CDT)
- AMBER: Compilation of PMEMD sudipta sinha (Thu May 08 2008 - 06:07:28 CDT)
- AMBER: mm_pbsa problem: bad atom type: IP mori_at_cerm.unifi.it (Thu May 08 2008 - 06:59:12 CDT)
- AMBER: nmode "Atom out of bounds" for min of multiple ligands Seth Lilavivat (Thu May 08 2008 - 09:30:24 CDT)
- AMBER: can amber read .xyz files? WANG,YING (Thu May 08 2008 - 10:29:57 CDT)
- AMBER: velocity autocorrelation function for SPC felxible water model Rahaman, Asif (Thu May 08 2008 - 12:07:41 CDT)
- AMBER: AmberTools on OS X fails tests Hans Martin Senn (Thu May 08 2008 - 13:59:12 CDT)
- AMBER: QM/MM Syed Tarique Moin (Fri May 09 2008 - 03:28:06 CDT)
- AMBER: distance Urszula Uciechowska (Fri May 09 2008 - 09:36:18 CDT)
- AMBER: help to install AMBER9 Jeffrey (Fri May 09 2008 - 09:47:16 CDT)
- AMBER: neutral C-terminus and N-terminus parameters for amber Lisa Perez (Fri May 09 2008 - 12:32:13 CDT)
- AMBER: cannot read big .pdb files WANG,YING (Fri May 09 2008 - 21:00:29 CDT)
- AMBER: parmbsc0 parameters for RNA.DNA systems Cenk \(Jenk\) Andac (Sat May 10 2008 - 08:47:50 CDT)
- AMBER: Calculate number of ions Dong Xu (Sat May 10 2008 - 13:32:01 CDT)
- AMBER: Solvent mixture box Francesco Pietra (Sun May 11 2008 - 12:04:52 CDT)
- AMBER: Ewald PARAMETER RANGE WRONG WANG,YING (Sun May 11 2008 - 13:01:09 CDT)
- AMBER: rms Urszula Uciechowska (Mon May 12 2008 - 06:19:41 CDT)
- AMBER: About Hydrophobic Interactions. cgji (Mon May 12 2008 - 11:14:00 CDT)
- AMBER: Problems installing Amber Tools for Amber 10 Sam Danziger (Mon May 12 2008 - 13:20:23 CDT)
- AMBER: Ligand energy minimization Dong Xu (Mon May 12 2008 - 17:07:31 CDT)
- AMBER: nab Rabin (Mon May 12 2008 - 19:40:54 CDT)
- AMBER: from Gromax to AMBER Cristina Sisu (Tue May 13 2008 - 05:00:24 CDT)
- AMBER: An enquiry about dynamic simulations of oxygen binding to myoglobin (Ann N Y Acad Sci. 1986;482:222- Catein Catherine (Tue May 13 2008 - 05:17:29 CDT)
- AMBER: CAVITY_SURFTEN & CAVITY_OFFSET default params Marcin Krol (Tue May 13 2008 - 08:44:48 CDT)
- AMBER: periodic boundary condition WANG,YING (Tue May 13 2008 - 08:55:00 CDT)
- AMBER: Free Energy Calculations - parameters for MM Seth Lilavivat (Tue May 13 2008 - 11:29:23 CDT)
- AMBER: divcon E.M. (Tue May 13 2008 - 11:58:49 CDT)
- AMBER: Amber10 testing problem Cenk \(Jenk\) Andac (Tue May 13 2008 - 14:46:02 CDT)
- AMBER: simulating the pull out of Carbon Nanotube from polymer with AMBER yuan li (Tue May 13 2008 - 21:53:10 CDT)
- AMBER: MM_PBSA problem in binding_energy mori_at_cerm.unifi.it (Wed May 14 2008 - 09:17:40 CDT)
- AMBER: about addles:¡°forrtl: severe (71): integer divide by zero¡±. ³ÉÈ« (Wed May 14 2008 - 09:57:25 CDT)
- AMBER: subscribe amber wangluohuaxue (Wed May 14 2008 - 09:40:04 CDT)
- AMBER: simulate dipole moment Qiuting Hong (Wed May 14 2008 - 15:52:33 CDT)
- AMBER: AMBER entropy calculation Thomas Leonard (Wed May 14 2008 - 18:00:45 CDT)
- AMBER: Amber10:Compiling with gcc 2.4.1 yongleli (Thu May 15 2008 - 10:36:29 CDT)
- AMBER: Points on a Sphere Justine Condo (Thu May 15 2008 - 11:27:06 CDT)
- AMBER: MKL libraries/Amber10 Francesco Pietra (Thu May 15 2008 - 13:01:34 CDT)
- AMBER: RESP and Jaguar Seth Lilavivat (Thu May 15 2008 - 15:52:35 CDT)
- AMBER: solvatebox error WANG,YING (Thu May 15 2008 - 16:47:06 CDT)
- AMBER: reading PDB trajectory Mark Abraham (Thu May 15 2008 - 22:49:55 CDT)
- AMBER: PGI amber9 problems Lorenzo Gontrani (Fri May 16 2008 - 04:52:21 CDT)
- AMBER: RESP charges of an unusual substrate Jiayun Pang (Fri May 16 2008 - 05:45:54 CDT)
- AMBER: STEERED MD fatima.chami_at_durham.ac.uk (Fri May 16 2008 - 11:25:55 CDT)
- AMBER: build proline Qiuting Hong (Fri May 16 2008 - 16:32:47 CDT)
- AMBER: Amber 10 ambpdb bug? Sam Danziger (Sat May 17 2008 - 21:17:44 CDT)
- AMBER: ambertools: static linking of user binaries is not supported on Mac OS X Alan (Mon May 19 2008 - 04:39:32 CDT)
- AMBER: parameters in ff03 and ff99 Peter Kiss (Mon May 19 2008 - 06:21:21 CDT)
- AMBER: Hybrid REMD amber10 Geoff Wood (Mon May 19 2008 - 07:41:54 CDT)
- AMBER: anal Marina Grabar (Mon May 19 2008 - 08:30:13 CDT)
- AMBER: nfft1-3 too large WANG,YING (Mon May 19 2008 - 09:46:51 CDT)
- AMBER: gasteiger is not working with ambertools 1.0 Alan (Mon May 19 2008 - 09:51:05 CDT)
- AMBER: nfft1-3 too large WANG,YING (Mon May 19 2008 - 09:46:51 CDT)
- AMBER: atom type in glycam06 tinni sona (Mon May 19 2008 - 12:06:57 CDT)
- AMBER: bye frustrated modeller (Mon May 19 2008 - 13:29:40 CDT)
- AMBER: analysis REMD rebeca (Mon May 19 2008 - 13:41:15 CDT)
- AMBER: 3rd Annual CMM Workshop on QM/MM Simulations Ross Walker (Mon May 19 2008 - 18:33:55 CDT)
- AMBER: MM-PBSA for carbohydrates Neha Gandhi (Mon May 19 2008 - 21:07:24 CDT)
- AMBER: massively parallel computation Mingfeng Yang (Tue May 20 2008 - 02:03:51 CDT)
- AMBER: xLeap compilation issues Sasha Buzko (Tue May 20 2008 - 18:41:49 CDT)
- AMBER: How to set a ZN atom radius for PB calculations Sam Danziger (Tue May 20 2008 - 19:23:30 CDT)
- AMBER: Regarding binding free energy calculation using MM_PBSA method nag raj (Wed May 21 2008 - 02:01:14 CDT)
- AMBER: $AMBERHOME/dat/slko Francesco Pietra (Wed May 21 2008 - 07:47:59 CDT)
- AMBER: ptraj analyze matrix Seth Lilavivat (Wed May 21 2008 - 09:53:28 CDT)
- AMBER: amber tools installation vijayaraj_at_clri.info (Wed May 21 2008 - 10:22:37 CDT)
- AMBER: pressure regulation methods Vlad Cojocaru (Wed May 21 2008 - 11:25:08 CDT)
- AMBER: ff99 and ff03 forcefield parameters Peter Kiss (Wed May 21 2008 - 16:01:47 CDT)
- AMBER: Parallel Self-guided Langevin simulation Dirar Homouz (Wed May 21 2008 - 17:23:27 CDT)
- AMBER: about hydrogen bond in amber force field WANG,YING (Wed May 21 2008 - 21:24:47 CDT)
- AMBER: COM RESTRAINT fatima.chami_at_durham.ac.uk (Thu May 22 2008 - 07:17:09 CDT)
- AMBER: potassium ion Lars Skjærven (Thu May 22 2008 - 08:09:59 CDT)
- AMBER: amber10 installation vijayaraj_at_clri.info (Thu May 22 2008 - 09:22:47 CDT)
- AMBER: AMBER file preparation for protein-carbohydrate complex Neha Gandhi (Thu May 22 2008 - 09:31:50 CDT)
- AMBER: Bond-angle-dihedral-improper-vdw energy terms for part of a system Pavan G (Thu May 22 2008 - 10:37:56 CDT)
- Re: AMBER: potassium ion Bill Ross (Thu May 22 2008 - 13:27:21 CDT)
- AMBER: Calculate the RESP charge Fe3+ of heme (p450) chen bents (Thu May 22 2008 - 21:16:12 CDT)
- AMBER: self-diffusion coefficient and Berendsen Jennifer.Thomas_at_cbt.uhp-nancy.fr (Fri May 23 2008 - 03:03:49 CDT)
- AMBER: help MD running error Qiuting Hong (Fri May 23 2008 - 03:40:12 CDT)
- AMBER: PBC in 2D fatima.chami_at_durham.ac.uk (Fri May 23 2008 - 08:13:39 CDT)
- AMBER: how generate the final output file using mmpbsa luzhenw1_at_msu.edu (Fri May 23 2008 - 15:49:33 CDT)
- AMBER: how to extract energy WANG,YING (Fri May 23 2008 - 20:08:13 CDT)
- AMBER: periodic bondary condition WANG,YING (Fri May 23 2008 - 20:16:34 CDT)
- AMBER: ptraj mask not working with psf file Dong Xu (Fri May 23 2008 - 21:53:27 CDT)
- AMBER: Amber9 vs Amber10+MKL benchmark Francesco Pietra (Sat May 24 2008 - 08:48:12 CDT)
- AMBER: Fw: Amber9 vs Amber10+MKL benchmark Francesco Pietra (Sat May 24 2008 - 08:51:53 CDT)
- AMBER: calculating the energy from the restart file priya priya (Sat May 24 2008 - 09:03:46 CDT)
- AMBER: Fw: Amber9 vs Amber10+MKL benchmark Francesco Pietra (Sat May 24 2008 - 09:50:45 CDT)
- AMBER: caculating nonpolar solvation energies ke dong (Sat May 24 2008 - 09:53:17 CDT)
- AMBER: trajectories into trajectory Hakkim Boy (Sun May 25 2008 - 06:30:22 CDT)
- AMBER: mass weighted rms fit Dong Xu (Sun May 25 2008 - 11:11:43 CDT)
- AMBER: using amber ports in gromacs Cristina Sisu (Sun May 25 2008 - 13:22:58 CDT)
- AMBER: is in vacuo simulation neccessary? Anamika Awasthi (Mon May 26 2008 - 00:18:58 CDT)
- AMBER: Umbrella Sampling for proteins German Erlenkamp (Mon May 26 2008 - 04:23:56 CDT)
- AMBER: peptide at the box center during NVT-MD Darek Czapiewski (Mon May 26 2008 - 05:01:45 CDT)
- AMBER: B-factor calculation from data with different write frequencies Sally Pias (Mon May 26 2008 - 23:19:42 CDT)
- AMBER: Which is best temperature controlling method sudipta sinha (Tue May 27 2008 - 05:25:02 CDT)
- Re: AMBER: B-factor calculation from data with different write frequencies Bill Ross (Tue May 27 2008 - 11:44:23 CDT)
- AMBER: error when read inpcrd WANG,YING (Tue May 27 2008 - 15:32:02 CDT)
- AMBER: bugfix (imin=5) in amber9 Xioling Chuang (Tue May 27 2008 - 23:23:09 CDT)
- AMBER: compilation problem with AMBER10 bhargav patel (Wed May 28 2008 - 00:56:15 CDT)
- AMBER: Hydration free energies of charged ions using PME Markus Kaukonen (Wed May 28 2008 - 01:51:26 CDT)
- AMBER: install amber tools Alejandro Valbuena (Wed May 28 2008 - 05:14:35 CDT)
- AMBER: Segmentation faults trying to run sander mpi Idan Gabdank (Wed May 28 2008 - 05:59:09 CDT)
- AMBER: restarting molecular dynamics Germain Vallverdu (Wed May 28 2008 - 08:18:16 CDT)
- AMBER: mbondi radii for gaff atom types Sara J (Wed May 28 2008 - 10:03:52 CDT)
- AMBER: note on the molsurf and "Assertion `sarg1 >= 0.0' failed" error Kateryna Miroshnychenko (Wed May 28 2008 - 10:08:19 CDT)
- AMBER: protonate in Amber10 Benjamin Juhl (Wed May 28 2008 - 09:55:06 CDT)
- AMBER: rmsd vs frame Francesco Pietra (Wed May 28 2008 - 17:56:24 CDT)
- AMBER: Fw: rmsd vs frame Francesco Pietra (Wed May 28 2008 - 18:19:11 CDT)
- AMBER: VMD Movie Campbell, Patrick (Wed May 28 2008 - 18:33:39 CDT)
- AMBER: silhouette width/coefficient after clustering by PTRAJ9.9 Dong Xu (Thu May 29 2008 - 00:56:48 CDT)
- AMBER: ligand unit charge is not zero amor san juan (Thu May 29 2008 - 03:44:58 CDT)
- AMBER: solvatebox fatima.chami_at_durham.ac.uk (Thu May 29 2008 - 06:46:42 CDT)
- AMBER: Installing PMEMD with Amber10 Justin A. Lemkul (Thu May 29 2008 - 08:23:05 CDT)
- AMBER: VMD Movie 2 Campbell, Patrick (Thu May 29 2008 - 12:39:20 CDT)
- AMBER: ptraj rmsd calculation Pavan G (Thu May 29 2008 - 13:08:36 CDT)
- AMBER: VMD Movie 3 Campbell, Patrick (Thu May 29 2008 - 13:12:20 CDT)
- AMBER: VMD Movie 4 Campbell, Patrick (Thu May 29 2008 - 14:37:43 CDT)
- AMBER: ptraj has trouble with x-plor psf file from VMD Dong Xu (Thu May 29 2008 - 15:23:56 CDT)
- AMBER: Ptraj | Multiple trajout commands? Ian (Fri May 30 2008 - 03:39:23 CDT)
- AMBER: Iron-Sulfur Cluster Joachim Reichelt (Fri May 30 2008 - 04:46:30 CDT)
- AMBER: nab Joachim Reichelt (Fri May 30 2008 - 04:48:56 CDT)
- AMBER: Jarzynski fatima.chami_at_durham.ac.uk (Fri May 30 2008 - 06:44:41 CDT)
- AMBER: Sander instead of PMEMD Cristina Sisu (Fri May 30 2008 - 08:47:13 CDT)
- AMBER: VMD Movie 3 Campbell, Patrick (Fri May 30 2008 - 09:56:41 CDT)
- AMBER: tleap error message Wang,Ying (Fri May 30 2008 - 11:08:14 CDT)
- AMBER: igb and ibelly Holly Freedman (Fri May 30 2008 - 14:23:21 CDT)
- AMBER: SANDER and PMEMD with openmpi Ross Walker (Fri May 30 2008 - 17:18:04 CDT)
- AMBER: MMPBSA error Cristina Sisu (Sat May 31 2008 - 09:00:08 CDT)
- AMBER: ptraj analyze modes from nmode Miguel Ortiz-Lombardía (Sat May 31 2008 - 10:40:50 CDT)
- Re: AMBER: SANDER and PMEMD with openmpi. Failure 'make test.pmemd' Francesco Pietra (Sat May 31 2008 - 13:31:04 CDT)
- AMBER: amber9 , ptraj vector commad issue Vijay Singh (Sat May 31 2008 - 18:34:23 CDT)
- AMBER: PCA - analysis Ibrahim Moustafa (Sun Jun 01 2008 - 13:00:35 CDT)
- Fw: RE: AMBER: SANDER and PMEMD with openmpi. NO MORE failure 'make test.pmemd' Francesco Pietra (Mon Jun 02 2008 - 05:22:38 CDT)
- AMBER: Building ppc64 AMBER10 with xlf fortran 11.1 Jarrod Smith (Mon Jun 02 2008 - 11:43:24 CDT)
- AMBER: VMD file generation 4 - mdcrd ptraj analysis Campbell, Patrick (Mon Jun 02 2008 - 13:26:15 CDT)
- AMBER: VMD file generation 4 - mdcrd analysis Campbell, Patrick (Mon Jun 02 2008 - 15:21:00 CDT)
- AMBER: PCA analysis Ibrahim Moustafa (Mon Jun 02 2008 - 16:09:17 CDT)
- AMBER: Missing gaff angle parameters for dimethyl esters Lin, Pohan (Mon Jun 02 2008 - 16:20:24 CDT)
- AMBER: corrupted restart file yavuzturkm_at_prc.boun.edu.tr (Tue Jun 03 2008 - 04:18:25 CDT)
- AMBER: Temperature controlling method in AMBER tinni sona (Tue Jun 03 2008 - 04:43:11 CDT)
- AMBER: solvate box : buffer list fatima.chami_at_durham.ac.uk (Tue Jun 03 2008 - 12:51:55 CDT)
- AMBER: How to calculate RMSIP after PCA analysis by PTRAJ? sychen (Wed Jun 04 2008 - 07:27:45 CDT)
- AMBER: problems with sleap Alan (Wed Jun 04 2008 - 10:40:04 CDT)
- AMBER: NMODE units and hrmax value for Langevine modes Yang, Lee-Wei (Wed Jun 04 2008 - 11:27:00 CDT)
- AMBER: amber installation on cluster Pankaj R. Daga (Wed Jun 04 2008 - 12:27:57 CDT)
- AMBER: NAB documentation for programmers ramu_at_vt.edu (Wed Jun 04 2008 - 13:59:27 CDT)
- AMBER: ptraj imaging issue Vlad Cojocaru (Wed Jun 04 2008 - 14:07:44 CDT)
- AMBER: MM-PBSA in AMBER 10 Daniel Oehme (Thu Jun 05 2008 - 00:27:39 CDT)
- AMBER: problem of install amber9 Xioling Chuang (Thu Jun 05 2008 - 03:37:27 CDT)
- AMBER: Free energy of dissociation fatima.chami_at_durham.ac.uk (Thu Jun 05 2008 - 07:02:43 CDT)
- AMBER: NAN errors in Etot, EPtot, EKtot and EELEC Praveena Gopal (Thu Jun 05 2008 - 07:04:00 CDT)
- AMBER: netcdf configure returned 1 Jens Lattig (Thu Jun 05 2008 - 08:46:45 CDT)
- AMBER: netcdf configure returned 1 - PROBLEM SOLVED Jens Lattig (Thu Jun 05 2008 - 09:42:03 CDT)
- AMBER: A problem of installing Amber10 Yicun Ni (Thu Jun 05 2008 - 10:55:53 CDT)
- AMBER: Nmode - entropy calculation of receptor - should I apply restraint? Seth Lilavivat (Thu Jun 05 2008 - 12:03:08 CDT)
- AMBER: RE: solvating RNA in 8M urea box Ross Walker (Thu Jun 05 2008 - 19:12:42 CDT)
- AMBER: Query on MM-PBSA Neha Gandhi (Fri Jun 06 2008 - 00:46:32 CDT)
- AMBER: PROBLEM: AmberTools Installation using Ubuntu Jens Lattig (Fri Jun 06 2008 - 03:13:06 CDT)
- AMBER: Ptraj / ambmask | Using distance-based masks to strip a trajectory Ian (Fri Jun 06 2008 - 04:19:58 CDT)
- AMBER: Problem While Installing Amber Ranga Swamy (Fri Jun 06 2008 - 04:34:17 CDT)
- AMBER: VMD Movie .mdcrd file ptraj Campbell, Patrick (Fri Jun 06 2008 - 08:22:50 CDT)
- AMBER: NAB documentation David Case (Fri Jun 06 2008 - 11:24:44 CDT)
- Re:AMBER:VMD Movie.mdcrd Campbell, Patrick (Fri Jun 06 2008 - 13:56:52 CDT)
- AMBER: 100 short MD runs within a single Sander script? Sebastian Stolzenberg (Fri Jun 06 2008 - 23:55:37 CDT)
- AMBER: Combine mdcrd while stripping WAT problem Francesco Pietra (Sun Jun 08 2008 - 10:40:07 CDT)
- AMBER: problem in starting sander Qiuting Hong (Sun Jun 08 2008 - 13:25:43 CDT)
- AMBER: MM-PBSA and delphi Neha Gandhi (Mon Jun 09 2008 - 00:49:54 CDT)
- AMBER: Calcium and Magnesium LJ parameters Daniel Smith (Mon Jun 09 2008 - 18:02:28 CDT)
- AMBER: Help--Great distortion of N terminal nitrogen at the very beginning of heating xiaonan zhang (Tue Jun 10 2008 - 07:24:02 CDT)
- AMBER: SMD pulling velocity fatima.chami_at_durham.ac.uk (Tue Jun 10 2008 - 09:06:38 CDT)
- AMBER: how to calculate the interaction energy Wang,Ying (Tue Jun 10 2008 - 09:52:10 CDT)
- AMBER: Simulating complexes with magnesium atoms Sasha Buzko (Tue Jun 10 2008 - 16:32:13 CDT)
- AMBER: box shape changed at NVT fatima.chami_at_durham.ac.uk (Wed Jun 11 2008 - 09:25:09 CDT)
- AMBER: sander.MPI / openmpi on PBS Arturas Ziemys (Wed Jun 11 2008 - 13:59:52 CDT)
- AMBER: 2D RMS plot Steve Spronk (Wed Jun 11 2008 - 14:18:32 CDT)
- AMBER: Coordinated Zinc Khaled Barakat (Wed Jun 11 2008 - 14:29:18 CDT)
- AMBER: Antechamber and topology file TAEJIN KIM (Wed Jun 11 2008 - 18:05:14 CDT)
- AMBER: updating documentation Alan (Thu Jun 12 2008 - 04:52:40 CDT)
- AMBER: using Velocity-Verlet algorithm oguz gurbulak (Thu Jun 12 2008 - 07:07:20 CDT)
- AMBER: anisotropic pressure scaling ntp=2 fatima.chami_at_durham.ac.uk (Thu Jun 12 2008 - 08:18:13 CDT)
- AMBER: SMD RESTRAINTS fatima.chami_at_durham.ac.uk (Thu Jun 12 2008 - 11:23:00 CDT)
- AMBER: Compile amber10 parallel with suppied LAM James W. Caldwell (Thu Jun 12 2008 - 11:31:03 CDT)
- AMBER: Sander crashes >99999 atoms plmallip_at_mail.uh.edu (Thu Jun 12 2008 - 18:26:57 CDT)
- AMBER: PCAL and polar contribution in the output file Neha Gandhi (Fri Jun 13 2008 - 00:42:54 CDT)
- AMBER: amber10 make fails for static/parallel James W. Caldwell (Fri Jun 13 2008 - 17:50:19 CDT)
- AMBER: Ewald error estimate Pavan G (Sun Jun 15 2008 - 09:22:48 CDT)
- AMBER: Problem with running refinement of NMR structures with RDCs Qi Zhang (Sun Jun 15 2008 - 15:20:21 CDT)
- AMBER: Eigenmode dynamics in Ptraj fatima.chami_at_durham.ac.uk (Mon Jun 16 2008 - 07:59:42 CDT)
- AMBER: the SPCFW water model Vlad Cojocaru (Mon Jun 16 2008 - 11:19:34 CDT)
- AMBER: sander.MPI / parallel Arturas Ziemys (Mon Jun 16 2008 - 12:00:34 CDT)
- AMBER: [Fwd: segmentation fault in nmode] Guillaume Renvez (Mon Jun 16 2008 - 09:31:12 CDT)
- AMBER: about resp charges WanJ Ding (Mon Jun 16 2008 - 14:44:55 CDT)
- AMBER: IRED to time correlation fatima.chami_at_durham.ac.uk (Mon Jun 16 2008 - 15:25:22 CDT)
- AMBER: program to calculate rmsd rams rams (Mon Jun 16 2008 - 21:28:24 CDT)
- AMBER: How to solve - Missing BELE for MM in 1 in amber. Thomas Leonard (Mon Jun 16 2008 - 22:05:59 CDT)
- AMBER: How to solve - Missing BELE for MM in 1 in amber. Thomas Leonard (Mon Jun 16 2008 - 22:06:01 CDT)
- AMBER: improving GAFF sulfonamide parameters Floris Buelens (Tue Jun 17 2008 - 04:57:46 CDT)
- AMBER: ligand complexed simulation Siddharth Rastogi (Tue Jun 17 2008 - 05:56:15 CDT)
- AMBER: suggestion for next amberTools 1.1 Alan (Tue Jun 17 2008 - 06:01:06 CDT)
- AMBER: "Dumping RAW 2D RMS data is not yet implemented"? Steve Spronk (Tue Jun 17 2008 - 09:00:08 CDT)
- AMBER: to understand GAFF: about A and B coefficients Alan (Tue Jun 17 2008 - 11:42:34 CDT)
- AMBER: multiple dihedral restraints using group (in Amber 10) mkseo (Tue Jun 17 2008 - 16:00:50 CDT)
- AMBER: MM-PBSA Neha Gandhi (Wed Jun 18 2008 - 02:37:33 CDT)
- AMBER: Eigenmode dynamics - imaging traj fatima.chami_at_durham.ac.uk (Wed Jun 18 2008 - 05:09:26 CDT)
- AMBER: about gaff.dat in ambeTools 1.0 Alan (Wed Jun 18 2008 - 09:44:02 CDT)
- AMBER: ptraj fatima.chami_at_durham.ac.uk (Wed Jun 18 2008 - 10:21:50 CDT)
- AMBER: cross correlation function using iRED matrix fatima.chami_at_durham.ac.uk (Wed Jun 18 2008 - 12:07:25 CDT)
- AMBER: tip3p water and shake Wang,Ying (Wed Jun 18 2008 - 15:07:13 CDT)
- AMBER: sp carbon notation? Laura Benton (Wed Jun 18 2008 - 18:16:35 CDT)
- AMBER: questions about gaff yzhao (Wed Jun 18 2008 - 21:01:45 CDT)
- AMBER: [Fwd: failure to load box parameters] Daniel Smith (Wed Jun 18 2008 - 22:58:10 CDT)
- AMBER: How to create average structure? Shen, Lingling (Wed Jun 18 2008 - 23:44:03 CDT)
- AMBER: how to extract x,y,z of a set of atoms from an MD trajectories fatima.chami_at_durham.ac.uk (Thu Jun 19 2008 - 04:16:52 CDT)
- AMBER: Correlation functions from iRED analysis Samuel Genheden (a03samge) (Thu Jun 19 2008 - 05:22:53 CDT)
- AMBER: Installation Problem of AMBER10 bhargav patel (Thu Jun 19 2008 - 05:57:26 CDT)
- AMBER: How to extract solvent box information from .rst or .mdcrd files? Panwang Zhou (Thu Jun 19 2008 - 09:13:18 CDT)
- AMBER: simple sander James W. Caldwell (Thu Jun 19 2008 - 18:30:39 CDT)
- AMBER: ligand complexed simulation Siddharth Rastogi (Fri Jun 20 2008 - 02:14:18 CDT)
- AMBER: GAFF for organic crystals Rabone, Jeremy (Fri Jun 20 2008 - 03:05:18 CDT)
- AMBER: rdparm help Alan (Fri Jun 20 2008 - 06:12:17 CDT)
- AMBER: AmberTools 1.0 installation error: x86_64 Matthew Danielson (Fri Jun 20 2008 - 10:44:21 CDT)
- AMBER: Amber 10 timing Ed Pate (Fri Jun 20 2008 - 12:08:37 CDT)
- AMBER: SIZE.h problems Å·ÑôµÂ·½ (Sat Jun 21 2008 - 07:33:49 CDT)
- AMBER: (no subject) Daniel B. Kaplan (Sun Jun 22 2008 - 18:46:17 CDT)
- AMBER: MM-PBSA in AMBER 10 Daniel Oehme (Mon Jun 23 2008 - 00:07:34 CDT)
- AMBER: How to adjust the problem of "Vlimit exceeded" Biman Jana (Mon Jun 23 2008 - 02:28:27 CDT)
- AMBER: How to confirm atom types of small molecule perceived by antechamber xiaonan zhang (Mon Jun 23 2008 - 03:39:30 CDT)
- AMBER: source of AMBER9 Germain Vallverdu (Mon Jun 23 2008 - 09:09:29 CDT)
- AMBER: amber10/dat/leap/cmd/README need update Alan (Mon Jun 23 2008 - 09:59:21 CDT)
- AMBER: Antechamber Question Daniel B. Kaplan (Mon Jun 23 2008 - 11:51:28 CDT)
- AMBER: problems form the pdb to the mol2 Rilei Yu (Mon Jun 23 2008 - 20:01:33 CDT)
- AMBER: problems form the pdb to the mol2 Rilei Yu (Mon Jun 23 2008 - 20:01:33 CDT)
- AMBER: problems form the pdb to the mol2 Rilei Yu (Mon Jun 23 2008 - 20:01:33 CDT)
- AMBER: problems form the pdb to the mol2 Rilei Yu (Mon Jun 23 2008 - 20:01:33 CDT)
- AMBER: problems form the pdb to the mol2 Rilei Yu (Mon Jun 23 2008 - 20:01:33 CDT)
- AMBER: problems form the pdb to the mol2 Rilei Yu (Mon Jun 23 2008 - 20:01:33 CDT)
- AMBER: dihedral energy calculation inconsistent with gaussian's result Q733 (Mon Jun 23 2008 - 21:43:36 CDT)
- AMBER: unsubscribe amber sanket.deshmukh_at_ucd.ie (Tue Jun 24 2008 - 06:07:42 CDT)
- AMBER: A-prime RNA input file Å·ÑôµÂ·½ (Tue Jun 24 2008 - 06:16:27 CDT)
- AMBER: qmmm_DFTB problem Dr. Xiaofeng (Frank) Duan (Tue Jun 24 2008 - 08:58:46 CDT)
- AMBER: Compilation of amber8 patched with ramd Francesco Pietra (Tue Jun 24 2008 - 09:32:54 CDT)
- AMBER: dihedral potential with odd periodicity Germain Vallverdu (Tue Jun 24 2008 - 09:43:26 CDT)
- AMBER: Using AMBER forces Steven Winfield (Tue Jun 24 2008 - 10:44:41 CDT)
- AMBER: rdparm Segmentation fault on Ubuntu Alan (Tue Jun 24 2008 - 10:50:12 CDT)
- AMBER: how to derive torsional angle parameters in gaff Junmei Wang (Tue Jun 24 2008 - 20:45:42 CDT)
- AMBER: Debugf AMBER9 John Palmeri (Wed Jun 25 2008 - 02:38:53 CDT)
- AMBER: TI calculations in Amber10 Samuel Genheden (a03samge) (Wed Jun 25 2008 - 06:58:28 CDT)
- AMBER: A problem of dihedral angle Harry (Yicun) Ni (Wed Jun 25 2008 - 10:31:24 CDT)
- AMBER: amber10 compile gfortran question James W. Caldwell (Wed Jun 25 2008 - 13:10:58 CDT)
- AMBER: sleap - TER-card In Hee Park (Wed Jun 25 2008 - 14:14:39 CDT)
- AMBER: rdparm Segmentation fault Alan (Wed Jun 25 2008 - 16:24:34 CDT)
- AMBER: Antechamber/mopac am1-bcc charge Dong Xu (Wed Jun 25 2008 - 17:09:39 CDT)
- AMBER: (no subject) Daniel B. Kaplan (Wed Jun 25 2008 - 21:23:43 CDT)
- AMBER: Amber:unsubscribe amber sanket.deshmukh_at_ucd.ie (Thu Jun 26 2008 - 06:53:22 CDT)
- AMBER: concerning force fields Adrien Delmont (Thu Jun 26 2008 - 10:14:15 CDT)
- AMBER: Peseckis, Steven M. (Thu Jun 26 2008 - 10:54:05 CDT)
- AMBER: ligand partial charge and conformation question Dong Xu (Thu Jun 26 2008 - 13:01:31 CDT)
- AMBER: output file AMBER9_MPI Vijay Manickam Achari (Thu Jun 26 2008 - 14:06:19 CDT)
- AMBER: Dihedral Angle Parameters Ilyas Yildirim (Thu Jun 26 2008 - 16:07:16 CDT)
- AMBER: REMD Amber10 : error in reading namelist cntrl rebeca (Fri Jun 27 2008 - 04:01:26 CDT)
- AMBER: Group specification problem fatima.chami_at_durham.ac.uk (Fri Jun 27 2008 - 07:59:09 CDT)
- AMBER: pmemd 10 output Vlad Cojocaru (Fri Jun 27 2008 - 10:48:35 CDT)
- AMBER: Test scripts James W. Caldwell (Fri Jun 27 2008 - 11:35:26 CDT)
- AMBER: ptraj - read in part of trajectory Seth Lilavivat (Fri Jun 27 2008 - 11:41:51 CDT)
- AMBER: question about the charge Harry (Yicun) Ni (Fri Jun 27 2008 - 15:37:55 CDT)
- AMBER: Seed for random number generator Francesco Pietra (Sun Jun 29 2008 - 03:22:12 CDT)
- AMBER: Constrained group fatima.chami_at_durham.ac.uk (Mon Jun 30 2008 - 04:54:02 CDT)
- AMBER: NMR refinement teresa.ierano_at_unina.it (Mon Jun 30 2008 - 05:37:48 CDT)
- AMBER: nmode analysis Joachim Reichelt (Mon Jun 30 2008 - 06:53:21 CDT)
- AMBER: hold atoms fixed Boutheina Kerkeni (Mon Jun 30 2008 - 07:51:17 CDT)
- AMBER: wrapping a restart file fatima.chami_at_durham.ac.uk (Mon Jun 30 2008 - 09:40:58 CDT)
- AMBER: (no subject) fatima.chami_at_durham.ac.uk (Mon Jun 30 2008 - 11:26:23 CDT)
- AMBER: watershell cero? rebeca (Mon Jun 30 2008 - 11:22:11 CDT)
- AMBER: MM-PBSA calculation problem Wei Huang (Mon Jun 30 2008 - 11:41:16 CDT)
- AMBER: error in reading namelist cntrl Maria Frushicheva (Mon Jun 30 2008 - 15:02:50 CDT)
- AMBER: Regarding force field ff02 and ion library Abhishek Singh (Mon Jun 30 2008 - 15:54:52 CDT)
- AMBER: missing torsion parameters John Bennett (Mon Jun 30 2008 - 16:06:07 CDT)
- AMBER: concerning force fields ( to Karl Kirschner ) Adrien Delmont (Tue Jul 01 2008 - 03:04:45 CDT)
- AMBER: Anna Reymer (Tue Jul 01 2008 - 03:36:12 CDT)
- AMBER: AMBER10: ambpdb problems Anna Reymer (Tue Jul 01 2008 - 03:37:38 CDT)
- AMBER: RDF in ptraj fatima.chami_at_durham.ac.uk (Tue Jul 01 2008 - 08:34:35 CDT)
- AMBER: "radius = 0.000" Arturas Ziemys (Tue Jul 01 2008 - 11:08:45 CDT)
- AMBER: Protonated Phosphate Problem Kliman, Michal (Tue Jul 01 2008 - 12:20:14 CDT)
- AMBER: compile amber10 on Mac Junmei Wang (Tue Jul 01 2008 - 16:45:31 CDT)
- AMBER: parameters for Fe coordinated to four CYS ? Jose Borreguero (Tue Jul 01 2008 - 19:12:37 CDT)
- AMBER: NMR refinement teresa.ierano_at_unina.it (Wed Jul 02 2008 - 03:38:57 CDT)
- AMBER: NONBONDED_PARM_INDEX Max (Wed Jul 02 2008 - 03:54:35 CDT)
- AMBER: ptraj problem with imaging fatima.chami_at_durham.ac.uk (Wed Jul 02 2008 - 11:52:32 CDT)
- AMBER: For help: Thermodynamic Integration of solvation free energy using soft-core potential yongleli (Wed Jul 02 2008 - 13:19:03 CDT)
- AMBER: RED III execution problem ben rodriguez (Wed Jul 02 2008 - 20:24:19 CDT)
- AMBER: How to obtain the oriented trajectories? Panwang Zhou (Thu Jul 03 2008 - 09:06:58 CDT)
- AMBER: PMEMD and polarized force field ff 02 Abhishek Singh (Thu Jul 03 2008 - 09:50:00 CDT)
- AMBER: PMEMD and polarized force field ff 02 Abhishek Singh (Thu Jul 03 2008 - 09:53:36 CDT)
- AMBER: bellymask for DNA backbone doesn't seem to work Seth Lilavivat (Thu Jul 03 2008 - 15:13:40 CDT)
- AMBER: about QMMM output linfu (Thu Jul 03 2008 - 21:40:33 CDT)
- AMBER: RESP calculation on Copper containing molecule Vidana.Epa_at_csiro.au (Fri Jul 04 2008 - 02:16:24 CDT)
- AMBER: Boutheina Kerkeni (Fri Jul 04 2008 - 05:34:55 CDT)
- AMBER: trouble interpreting <P2> time correlation function data Sally Pias (Sun Jul 06 2008 - 01:59:57 CDT)
- AMBER: For help: how to perform double decoupling thermodynamic integration calculation in AMBER10 yongleli (Mon Jul 07 2008 - 17:04:53 CDT)
- AMBER: Constant pH with new parameters (amber10) Markus Kaukonen (Tue Jul 08 2008 - 02:39:57 CDT)
- AMBER: [amber/glycam] dealing with fucose... Waqas Nasir (Tue Jul 08 2008 - 09:56:31 CDT)
- AMBER: Force fields for REMD with GB solvent guardiani_at_fi.infn.it (Tue Jul 08 2008 - 11:24:27 CDT)
- AMBER: analysing normal modes Vahdati N. (Tue Jul 08 2008 - 13:03:39 CDT)
- AMBER: Distance diagnolization matrix plot Siddharth Rastogi (Wed Jul 09 2008 - 02:04:08 CDT)
- AMBER: REMD temperature profile guardiani_at_fi.infn.it (Wed Jul 09 2008 - 08:47:13 CDT)
- AMBER: XLeap Problems Schwehm, Jeffrey M. (Wed Jul 09 2008 - 11:26:14 CDT)
- AMBER: amber9 / difference of igb=0 and igb=6 Arturas Ziemys (Wed Jul 09 2008 - 14:45:32 CDT)
- AMBER: Question about loading frcmod.ionsjc_tip3p in xleap Jeff Schwinefus (Wed Jul 09 2008 - 16:27:46 CDT)
- AMBER: ptraj selection Ilyas Yildirim (Wed Jul 09 2008 - 20:07:39 CDT)
- AMBER: mm_pbsa incorrect complex prmtop file xiaonan zhang (Thu Jul 10 2008 - 02:44:58 CDT)
- AMBER: replicas trapped in a few low temperatures Ye Mei (Thu Jul 10 2008 - 04:13:25 CDT)
- AMBER: antechamber and charmm Alan (Thu Jul 10 2008 - 04:43:58 CDT)
- AMBER: bond command Boutheina Kerkeni (Thu Jul 10 2008 - 12:30:46 CDT)
- AMBER: problem with restraints Barbault Florent (Thu Jul 10 2008 - 13:59:15 CDT)
- AMBER: difference between sander and NAB Hu, Shaowen (JSC-SK)[USRA] (Thu Jul 10 2008 - 14:44:41 CDT)
- AMBER: problem with rdparm Harry (Yicun) Ni (Thu Jul 10 2008 - 17:05:41 CDT)
- AMBER: timing info output from pmemd Vlad Cojocaru (Fri Jul 11 2008 - 03:49:28 CDT)
- AMBER: configure_amber (10) for pg compilers Vlad Cojocaru (Fri Jul 11 2008 - 06:51:47 CDT)
- AMBER: size of pdb Boutheina Kerkeni (Fri Jul 11 2008 - 10:13:57 CDT)
- AMBER: question about the improper torsion Harry (Yicun) Ni (Fri Jul 11 2008 - 11:34:17 CDT)
- AMBER: NMA Steve Seibold (Fri Jul 11 2008 - 11:34:00 CDT)
- AMBER: Installation on Mac OSX G5 dual processor George Tzotzos (Fri Jul 11 2008 - 15:30:21 CDT)
- AMBER: Installation of Amber 10 on Dual-Core Intel Mac George Tzotzos (Fri Jul 11 2008 - 15:33:55 CDT)
- AMBER: empty output Boutheina Kerkeni (Sat Jul 12 2008 - 10:29:47 CDT)
- AMBER: Atom type with 10-12 and 6-12 interactions in Amber9 Brad Lambeth (Sat Jul 12 2008 - 19:20:09 CDT)
- AMBER: Nmode entropy calcs Sergio Wong (Sat Jul 12 2008 - 20:09:51 CDT)
- AMBER: Model of deoxyadenosine in Cornell 95 paper Ilyas Yildirim (Sun Jul 13 2008 - 18:14:48 CDT)
- AMBER: AmberTools1.1 (and 1.0) antechamber endless loop Grange Hermitage (Sun Jul 13 2008 - 20:06:33 CDT)
- AMBER: POL3 with gaff and ff02EP Grange Hermitage (Sun Jul 13 2008 - 20:15:43 CDT)
- AMBER: Alanine scanning Khaled Barakat (Sun Jul 13 2008 - 20:50:47 CDT)
- AMBER: querry dipti lele (Mon Jul 14 2008 - 03:05:15 CDT)
- AMBER: Tutorial 6 Beale, John (Mon Jul 14 2008 - 11:48:21 CDT)
- AMBER: bad nonbon in nmode (amber9) Enghui Yap (Mon Jul 14 2008 - 11:25:29 CDT)
- AMBER: Error when performing Alanine scanning Khaled Barakat (Mon Jul 14 2008 - 20:41:26 CDT)
- AMBER: files in Amber directory ( to Junmei Wang ) John Bennett (Tue Jul 15 2008 - 06:10:40 CDT)
- AMBER: ptraj: projection command missing in dispatch.c (AMBER 10) Vlad Cojocaru (Tue Jul 15 2008 - 08:45:11 CDT)
- AMBER: sleap test failures Vlad Cojocaru (Tue Jul 15 2008 - 09:14:23 CDT)
- AMBER: test of parallel sander 10 fail Vlad Cojocaru (Tue Jul 15 2008 - 12:05:51 CDT)
- AMBER: RMSD per residue luzhenw1_at_msu.edu (Tue Jul 15 2008 - 15:28:08 CDT)
- AMBER: Ligand force field generation, and its consistency with the force field of the protein. SeungPyo Hong (Wed Jul 16 2008 - 07:15:48 CDT)
- AMBER: about RMSD per residue luzhenw1_at_msu.edu (Wed Jul 16 2008 - 08:48:05 CDT)
- AMBER: free energy Boutheina Kerkeni (Wed Jul 16 2008 - 10:54:39 CDT)
- AMBER: amber 10 and mpich2 (got eof on console error message from mpich2) Vlad Cojocaru (Thu Jul 17 2008 - 08:30:24 CDT)
- AMBER: SCC-DFTB for Zinc atom Jifeng Wang (Thu Jul 17 2008 - 10:33:15 CDT)
- AMBER: paricular atom coordinates? Vijay Singh (Thu Jul 17 2008 - 11:13:30 CDT)
- AMBER: The list-directed or NAMELIST READ statement cannot be completed rebeca (Thu Jul 17 2008 - 11:42:25 CDT)
- AMBER: AmberTools-1.1 port for FreeBSD M. L. Dodson (Thu Jul 17 2008 - 12:59:05 CDT)
- AMBER: the plot of the groove width versus time for RNA Å·ÑôµÂ·½ (Thu Jul 17 2008 - 18:35:31 CDT)
- AMBER: how to generate psf file using the AMBER topology file tinni sona (Fri Jul 18 2008 - 05:41:11 CDT)
- AMBER: Restarting Problem in MD Simulation khuram sb (Fri Jul 18 2008 - 05:37:07 CDT)
- AMBER: Problems with Frozen atoms julliane Yoneda (Fri Jul 18 2008 - 15:06:54 CDT)
- AMBER: a link for Amber ff ported to Charmm Alan (Sat Jul 19 2008 - 04:07:27 CDT)
- AMBER: parmbsc0 Dr. Suzie Byun (Sat Jul 19 2008 - 10:40:05 CDT)
- AMBER: antechamber generated input for gaussian error Grange Hermitage (Sat Jul 19 2008 - 19:53:49 CDT)
- AMBER: Trans proline dipti lele (Sun Jul 20 2008 - 00:53:00 CDT)
- AMBER: Release of version 1.2 of AmberTools David A. Case (Mon Jul 21 2008 - 12:01:29 CDT)
- AMBER: Where is ICO read from the ix array? Brad Lambeth (Mon Jul 21 2008 - 14:49:44 CDT)
- AMBER: Amber tools 1.2 test failure (installation) Myunggi Yi (Mon Jul 21 2008 - 17:17:05 CDT)
- AMBER: Problem with box dimension in AmberTools ptraj Steve Spronk (Tue Jul 22 2008 - 01:35:47 CDT)
- AMBER: amber ff and how it deals with out-plane chiral C Alan (Tue Jul 22 2008 - 02:59:05 CDT)
- AMBER: targeted MD
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