AMBER Archive (2009) - Feb 2009 By ThreadMost recent messages
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Starting: Sun Feb 01 2009 - 01:10:30 CST
Ending: Sat Feb 28 2009 - 18:23:49 CST
- [AMBER] Can bonded pair of atoms be restrainted by NMR distance restraint? liu junjun (Sun Feb 01 2009 - 01:51:39 CST)
- [AMBER] the output files oguz gurbulak (Sun Feb 01 2009 - 05:13:02 CST)
- [AMBER] strip frames from crd file aneesh cna (Mon Feb 02 2009 - 03:33:16 CST)
- [AMBER] strip frames from crd file aneesh cna (Mon Feb 02 2009 - 03:35:11 CST)
- [AMBER] md simulation on parallel PMEMD oguz gurbulak (Mon Feb 02 2009 - 07:32:31 CST)
- [AMBER] precision in the trajectory files Jenny Iskrenova (Mon Feb 02 2009 - 08:43:38 CST)
- [AMBER] Radius of Gyration Beale, John (Mon Feb 02 2009 - 11:34:35 CST)
- [AMBER] Langevin dynamics Antonios Samiotakis (Mon Feb 02 2009 - 11:54:31 CST)
- [AMBER] DFT SK parameter for P atom Qizhi Cui (Mon Feb 02 2009 - 13:59:19 CST)
- [AMBER] Micelles set-up?? Alexander Schierholt (Tue Feb 03 2009 - 04:09:52 CST)
- [AMBER] creating a restart file from md.out oguz gurbulak (Tue Feb 03 2009 - 04:44:10 CST)
- [AMBER] nab compile error with -scalapack chaitanya koppisetty (Tue Feb 03 2009 - 07:23:46 CST)
- [AMBER] -MMTSB instalation flag ? Marek Malę (Tue Feb 03 2009 - 09:31:38 CST)
- [AMBER] Unit 5 Error on OPEN:mdin on clustuer with mpirun drugdesign (Tue Feb 03 2009 - 11:03:20 CST)
- [AMBER] out error . .. (Tue Feb 03 2009 - 12:58:46 CST)
- [AMBER] MKL error ? Marek Malę (Tue Feb 03 2009 - 17:00:03 CST)
- [AMBER] a question about umbrella sampling (US) xiaoqin huang (Wed Feb 04 2009 - 11:12:02 CST)
- [AMBER] PDB of a specific frame Jason A. Ford-Green (Wed Feb 04 2009 - 13:46:52 CST)
- [AMBER] compiling errors Gard Nelson (Wed Feb 04 2009 - 18:30:22 CST)
- [AMBER] Restarting an MD Simulation Hopkins, Robert (Wed Feb 04 2009 - 18:34:16 CST)
- [AMBER] pmemd installation in intelmpi Vijay Manickam Achari (Wed Feb 04 2009 - 21:16:06 CST)
- [AMBER] Compiling Carnal Amber7 in Amber9 Vijay Manickam Achari (Wed Feb 04 2009 - 21:21:14 CST)
- [AMBER] production run terminates due to (*) symbols in xxx.rst Vijay Manickam Achari (Wed Feb 04 2009 - 22:17:38 CST)
- [AMBER] how can i deal with large number atoms Wang,Ying (Wed Feb 04 2009 - 23:04:23 CST)
- [AMBER] How to build reference coordinate file for targeted MD gmail (Thu Feb 05 2009 - 00:44:22 CST)
- [AMBER] error in executing sander.MPI in amber9 Vijay Manickam Achari (Thu Feb 05 2009 - 02:37:09 CST)
- [AMBER] Solvation potential and free energies guardiani_at_fi.infn.it (Thu Feb 05 2009 - 06:27:21 CST)
- [AMBER] parameter files for D-amino acid Vsatheesh Patil (Thu Feb 05 2009 - 07:04:12 CST)
- [AMBER] pmemd on BlueGene/P? Hannes Loeffler (Thu Feb 05 2009 - 07:09:45 CST)
- Re: [AMBER] Compiling Carnal Amber7 in Amber9 Bill Ross (Thu Feb 05 2009 - 11:36:00 CST)
- [AMBER] amber9 installation problem in SMP IA64 Vijay Manickam Achari (Fri Feb 06 2009 - 01:00:16 CST)
- [AMBER] mpirun problem in HPC Vijay Manickam Achari (Fri Feb 06 2009 - 01:01:29 CST)
- [AMBER] second derivative matrix calculation Marie Brut (Fri Feb 06 2009 - 04:47:18 CST)
- [AMBER] extract frames from a .mdcrd vallespardojl_at_chem.leidenuniv.nl (Fri Feb 06 2009 - 04:48:23 CST)
- [AMBER] MSD and stress tensors oguz gurbulak (Fri Feb 06 2009 - 05:09:12 CST)
- [AMBER] script to convert GLYCAM ff in CHARMM format ABEL Stephane 175950 (Fri Feb 06 2009 - 08:39:04 CST)
- [AMBER] Resp charge . .. (Fri Feb 06 2009 - 11:34:12 CST)
- [AMBER] ptraj fails to recognize binary REMD output Kevin Wiehe (Fri Feb 06 2009 - 11:44:21 CST)
- [AMBER] distance calculation by reading in the restraint file xiaoqin huang (Fri Feb 06 2009 - 11:52:56 CST)
- [AMBER] MD analysis oguz gurbulak (Sat Feb 07 2009 - 08:56:10 CST)
- [AMBER] Stability of a long NPT md trajectory? Bill K (Mon Feb 09 2009 - 01:07:24 CST)
- [AMBER] second derivative matrix Marie Brut (Mon Feb 09 2009 - 02:53:01 CST)
- [AMBER] NAB md function prints strange output Jochen Heil (Mon Feb 09 2009 - 05:30:21 CST)
- [AMBER] APS & ff03 Mahmoud A. A. Ibrahim (Mon Feb 09 2009 - 08:49:56 CST)
- [AMBER] parmchk s. Bill (Mon Feb 09 2009 - 09:55:20 CST)
- [AMBER] hbond analysis aneesh cna (Mon Feb 09 2009 - 11:55:25 CST)
- [AMBER] Solvating inside of a channel Daniel Smith (Mon Feb 09 2009 - 15:03:16 CST)
- [AMBER] Confusion regarding box size parul sharma (Tue Feb 10 2009 - 01:20:01 CST)
- [AMBER] Irregularity in box during md parul sharma (Tue Feb 10 2009 - 04:35:18 CST)
- [AMBER] RED-vIII: Scratch directory for Gaussian [NOT FOUND] Patrick Schopf (Tue Feb 10 2009 - 08:15:42 CST)
- [AMBER] Scaling of dipole interactions Diddo Diddens (Tue Feb 10 2009 - 08:33:18 CST)
- [AMBER] formate parameters Dmitri Nilov (Tue Feb 10 2009 - 08:47:31 CST)
- [AMBER] array out of bound in Amber10 tests Shan-ho Tsai (Tue Feb 10 2009 - 10:19:42 CST)
- [AMBER] reg . run TMD balaji nagarajan (Tue Feb 10 2009 - 11:36:28 CST)
- [AMBER] Solvating the interior of a channel Daniel Smith (Tue Feb 10 2009 - 14:42:09 CST)
- [AMBER] AMBER: chiral restraint on protein amit jain (Tue Feb 10 2009 - 18:48:12 CST)
- [AMBER] how to get amber 10 Prem Prakash Pathak (Tue Feb 10 2009 - 20:42:37 CST)
- [AMBER] nmr refinement of dimer Sally Pias (Wed Feb 11 2009 - 03:05:56 CST)
- [AMBER] lmod calculation for complexe . .. (Wed Feb 11 2009 - 03:09:04 CST)
- [AMBER] Optimization problem Daniel Emery (Thu Feb 12 2009 - 04:01:49 CST)
- [AMBER] error in xleap: ligand binding using MMand QMMM tech kureeckal ramesh (Thu Feb 12 2009 - 04:27:41 CST)
- [AMBER] H-bond information Beale, John (Thu Feb 12 2009 - 09:32:30 CST)
- [AMBER] projections of trajectories onto the first 2 principal eigenvectors Carra, Claudio (JSC-SK)[USRA] (Thu Feb 12 2009 - 12:22:20 CST)
- [AMBER] atoms fly out of the box in NVT calculations iccy liu (Thu Feb 12 2009 - 15:48:24 CST)
- [AMBER] How to jude whether the trajectory is stable or not Jeffrey (Thu Feb 12 2009 - 20:33:53 CST)
- [AMBER] Beginner question Heath Watts (Fri Feb 13 2009 - 15:18:42 CST)
- [AMBER] Question about improper torsions... Antonios Samiotakis (Fri Feb 13 2009 - 16:57:03 CST)
- [AMBER] New atom type with 7 bonds Akansha Saxena (Fri Feb 13 2009 - 17:56:47 CST)
- [AMBER] install Amber 10 to Macbook Adrien Delmont (Sat Feb 14 2009 - 05:06:50 CST)
- [AMBER] Any link to a major QM code? Francesco Pietra (Sun Feb 15 2009 - 11:58:30 CST)
- [AMBER] Error running sander.MPI Vijay Manickam Achari (Mon Feb 16 2009 - 02:23:05 CST)
- [AMBER] Error installing Amber David Patińo (Mon Feb 16 2009 - 06:02:31 CST)
- [AMBER] Iron 2+ parameters Hrvoje Brkiæ (Mon Feb 16 2009 - 07:53:57 CST)
- [AMBER] density and volume in NVT ensamble oguz gurbulak (Mon Feb 16 2009 - 07:58:13 CST)
- [AMBER] contant force pulling simulation with amber 10 li hui (Mon Feb 16 2009 - 11:01:36 CST)
- [AMBER] can ptraj output the trajectory of the residue CM? Jose Borreguero (Mon Feb 16 2009 - 13:47:34 CST)
- [AMBER] using ptraj Molecular Dynamics (Mon Feb 16 2009 - 14:31:42 CST)
- [AMBER] Normal errors on job kill? ben rodriguez (Mon Feb 16 2009 - 20:35:43 CST)
- [AMBER] Amber 9 Install - AMBERBUILDFLAGS error ben rodriguez (Mon Feb 16 2009 - 21:39:14 CST)
- [AMBER] parallel run error balaji nagarajan (Tue Feb 17 2009 - 02:19:23 CST)
- [AMBER] constph tutorial help Prem Prakash Pathak (Tue Feb 17 2009 - 06:53:37 CST)
- [AMBER] (no subject) Beale, John (Tue Feb 17 2009 - 07:02:25 CST)
- [AMBER] MD simulation with a partially flexible system Jeffrey (Tue Feb 17 2009 - 08:38:10 CST)
- [AMBER] DM complexation . .. (Tue Feb 17 2009 - 09:10:49 CST)
- [AMBER] How to get the energy of a molecule in a whole system Wang,Ying (Tue Feb 17 2009 - 10:28:39 CST)
- [AMBER] restraint angle m m (Tue Feb 17 2009 - 11:17:00 CST)
- [AMBER] PMF calculation Arnaud (Tue Feb 17 2009 - 12:10:18 CST)
- [AMBER] Need suggestion on payment for Ph.D student majored in molecular simulation Xu Dong (Tue Feb 17 2009 - 12:54:58 CST)
- [AMBER] glycam and solvateoct command Heath Watts (Tue Feb 17 2009 - 13:51:13 CST)
- [AMBER] problem compiling nmode.c Shan-ho Tsai (Tue Feb 17 2009 - 14:38:00 CST)
- [AMBER] reg.Targeted molecular dynamics balaji nagarajan (Tue Feb 17 2009 - 23:26:49 CST)
- [AMBER] protein monomerizartion times and simulation with implicit solvent drugdesign (Wed Feb 18 2009 - 04:27:17 CST)
- [AMBER] Re: AMBER: GBSA EGB = NaN Markus Kaukonen (Wed Feb 18 2009 - 06:26:28 CST)
- [AMBER] IG not change at each restart of NPT simulation Jeffrey (Wed Feb 18 2009 - 06:49:47 CST)
- [AMBER] How to constrain the hydrogen bonding distances... Majeed Shaik (Wed Feb 18 2009 - 08:11:37 CST)
- [AMBER] ./configure_amber: line 1211: cd: netcdf/src: No such file or directory Andrew Olson (Wed Feb 18 2009 - 11:08:57 CST)
- [AMBER] question about ptraj hydrogen bond analysis monica bhattacharee (Wed Feb 18 2009 - 13:45:17 CST)
- [AMBER] (NTB /= 0 && NTP /= 0) but IFBOX == 0 error Majeed Shaik (Wed Feb 18 2009 - 14:09:17 CST)
- [AMBER] Re: AMBER: How do you evaluate forces on a fixed atom? Bill Kowallis (Wed Feb 18 2009 - 19:55:47 CST)
- [AMBER] test charge Dan Kaps (Wed Feb 18 2009 - 20:27:32 CST)
- [AMBER] distance matrix plot and secondary structure analysis Siddharth Rastogi (Thu Feb 19 2009 - 00:17:47 CST)
- [AMBER] Protein motions comparison Dmitry Osolodkin (Thu Feb 19 2009 - 05:58:24 CST)
- [AMBER] secstruct Beale, John (Thu Feb 19 2009 - 07:22:20 CST)
- [AMBER] dipole correlation function Jeffrey (Thu Feb 19 2009 - 08:18:20 CST)
- [AMBER] paper of interest for FF development/solvent models David Mobley (Thu Feb 19 2009 - 09:15:04 CST)
- [AMBER] (no subject) Andrew Olson (Thu Feb 19 2009 - 13:46:24 CST)
- [AMBER] Antechamber kureeckal ramesh (Thu Feb 19 2009 - 19:36:03 CST)
- [AMBER] Problem with NVT and NPT parul sharma (Fri Feb 20 2009 - 07:07:36 CST)
- [AMBER] Parmchk wrongly calculates missing parameters (fwd) Gijs Schaftenaar (Fri Feb 20 2009 - 07:16:17 CST)
- [AMBER] ACS computational chemistry awards - March 9th deadline Carlos Simmerling (Fri Feb 20 2009 - 10:27:18 CST)
- [AMBER] order of "upper" and "lower" bounds in the makeDIS_RST inputs Piotr Cieplak (Fri Feb 20 2009 - 15:40:14 CST)
- [AMBER] reg.targeted molecular dynamics balaji nagarajan (Fri Feb 20 2009 - 23:10:50 CST)
- [AMBER] A beginner's question for using AMBER to do cell membrane simulation and molecular transportation Xu Dong (Sat Feb 21 2009 - 14:27:29 CST)
- [AMBER] PME doesn't work parul sharma (Mon Feb 23 2009 - 03:43:40 CST)
- [AMBER] PMEMD vs GROMACS? Sasha Buzko (Mon Feb 23 2009 - 13:55:27 CST)
- [AMBER] problem with amber installation nicholus bhattacharjee (Tue Feb 24 2009 - 00:50:12 CST)
- [AMBER] follow-up to previous discussion: nmr refinement of dimer Sally Pias (Tue Feb 24 2009 - 01:50:41 CST)
- [AMBER] About the croase grainded FF James W (Tue Feb 24 2009 - 01:58:12 CST)
- [AMBER] (no subject) Beale, John (Tue Feb 24 2009 - 05:59:51 CST)
- [AMBER] amber tools reading netcdf files Jeremy Harris (Tue Feb 24 2009 - 09:54:09 CST)
- [AMBER] perform an analysis using ptraj oguz gurbulak (Tue Feb 24 2009 - 10:19:11 CST)
- [AMBER] Equilibration Scaling to System Size Hopkins, Robert (Tue Feb 24 2009 - 16:31:37 CST)
- [AMBER] problem about trajectory analysis Adrien Delmont (Wed Feb 25 2009 - 08:24:41 CST)
- [AMBER] (no subject) waleed zalloum (Wed Feb 25 2009 - 10:41:14 CST)
- [AMBER] ptraj analyze Beale, John (Wed Feb 25 2009 - 10:56:59 CST)
- [AMBER] Simulated annealing Ibrahim Moustafa (Wed Feb 25 2009 - 18:26:37 CST)
- [AMBER] Error in using Amber sri noraima othman (Wed Feb 25 2009 - 21:27:29 CST)
- [AMBER] tleap errors !! Sampath Koppole (Thu Feb 26 2009 - 03:47:48 CST)
- [AMBER] MD simulation at constant pH Francesco Pietra (Thu Feb 26 2009 - 04:52:47 CST)
- [AMBER] Current Amber10 bugfix.all doesn't apply cleanly Mark Dixon (Thu Feb 26 2009 - 05:54:03 CST)
- [AMBER] PLUMED release 1.0.0 available Massimiliano Bonomi (Thu Feb 26 2009 - 07:11:54 CST)
- [AMBER] extra torsion terms in tleap.top-file Astrid Maaß (Thu Feb 26 2009 - 08:32:30 CST)
- [AMBER] H-Bonds Beale, John (Thu Feb 26 2009 - 08:38:04 CST)
- [AMBER] (no subject) Lake, Thomas (Thu Feb 26 2009 - 10:19:53 CST)
- [AMBER] A problem with xleap and pdb file nancy4619 (Fri Feb 27 2009 - 06:28:01 CST)
- [AMBER] Re: Antechamber kureeckal ramesh (Fri Feb 27 2009 - 06:56:58 CST)
- [AMBER] I need a professional help about xleap and pdb file nancy4619 (Fri Feb 27 2009 - 07:56:14 CST)
- [AMBER] using Gromacs for analysis oguz gurbulak (Fri Feb 27 2009 - 11:03:54 CST)
- [AMBER] Partial entropy calculations ? Marek Malę (Fri Feb 27 2009 - 12:21:29 CST)
- [AMBER] PCL waleed zalloum (Sat Feb 28 2009 - 11:17:51 CST)
- [AMBER] a query Molecular Dynamics (Sat Feb 28 2009 - 13:45:46 CST)
- [AMBER] IMPORTANT INFO: Regarding Anonymous postings to the AMBER mailing list. Ross Walker (Sat Feb 28 2009 - 16:19:16 CST)
- [AMBER] Question about NAB module Wei Huang (Sat Feb 28 2009 - 18:23:49 CST)
Last message date: Thu Dec 31 2009 - 22:57:46 CST
Archived on: Thu Dec 31 2009 - 22:58:32 CST
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