AMBER Archive (2009) - Apr 2009 By ThreadMost recent messages
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Starting: Wed Apr 01 2009 - 02:26:46 CDT
Ending: Thu Apr 30 2009 - 19:37:17 CDT
- [AMBER] constant-pH: appearance of not titrated residues during the Monte Carlo simulation Therese Malliavin (Wed Apr 01 2009 - 04:06:19 CDT)
- [AMBER] run protein with structural Ca+ sarah genare (Wed Apr 01 2009 - 06:01:24 CDT)
- [AMBER] Failure to compile amber9 serial ifort gcc Francesco Pietra (Wed Apr 01 2009 - 06:04:18 CDT)
- [AMBER] fillratio error in mmpbsa m m (Wed Apr 01 2009 - 06:42:45 CDT)
- [AMBER] calculation of Pi-Pi interaction energy aneesh cna (Wed Apr 01 2009 - 07:01:51 CDT)
- [AMBER] calculation of Pi-Pi interaction energy Jacopo Sgrignani (Wed Apr 01 2009 - 07:24:28 CDT)
- [AMBER] yacc parser Francesco Pietra (Wed Apr 01 2009 - 09:58:01 CDT)
- [AMBER] make test.serial.QMMM michael bane (Wed Apr 01 2009 - 10:44:51 CDT)
- [AMBER] ptraj and namd charmm dcd Sandro L. Fornili (Wed Apr 01 2009 - 10:59:37 CDT)
- [AMBER] AmberTools compilation error Kijeong Kwac (Wed Apr 01 2009 - 14:04:00 CDT)
- [AMBER] Help: An error happened when I calculate mm/pbsa thirsty (Thu Apr 02 2009 - 03:12:25 CDT)
- [AMBER] Umbrella test Arnaud (Thu Apr 02 2009 - 04:51:01 CDT)
- [AMBER] please help me out bharat lakhani (Thu Apr 02 2009 - 05:13:48 CDT)
- [AMBER] Counter-ions waleed zalloum (Thu Apr 02 2009 - 05:15:12 CDT)
- [AMBER] problem in input balaji nagarajan (Thu Apr 02 2009 - 05:29:39 CDT)
- [AMBER] number of waters in first and second solvation shell Siddharth Rastogi (Thu Apr 02 2009 - 06:40:21 CDT)
- [AMBER] explicit ion with igb=1 Bala subramanian (Thu Apr 02 2009 - 08:39:10 CDT)
- [AMBER] Averaging simulations Naser Alijabbari (Thu Apr 02 2009 - 10:21:41 CDT)
- [AMBER] Error in trajin and rms Pansy Patel (Thu Apr 02 2009 - 13:58:47 CDT)
- [AMBER] parallel installation of amber on sun Per Jr. Greisen (Thu Apr 02 2009 - 14:02:47 CDT)
- [AMBER] long polymer chain and image command in ptraj iccy liu (Thu Apr 02 2009 - 14:11:26 CDT)
- [AMBER] Contour plot Beale, John (Thu Apr 02 2009 - 14:31:22 CDT)
- [AMBER] How to delete the frames at specific intervals Mannan (Thu Apr 02 2009 - 20:16:49 CDT)
- [AMBER] How to find out residence time of water molecules Mannan (Thu Apr 02 2009 - 20:52:36 CDT)
- [AMBER] (no subject) chenquan (Fri Apr 03 2009 - 05:12:14 CDT)
- [AMBER] How to create parameter file for unknown residue nicholus bhattacharjee (Fri Apr 03 2009 - 05:33:03 CDT)
- [AMBER] Could not find angle parameter chenquan (Fri Apr 03 2009 - 05:46:47 CDT)
- [AMBER] antechamber & multiple low-energy conformations Alessandro Nascimento (Fri Apr 03 2009 - 07:01:39 CDT)
- [AMBER] amber9 serial compilation issues Francesco Pietra (Fri Apr 03 2009 - 13:38:12 CDT)
- [AMBER] NALA-ALA-CALA peptide with antechamber Alan (Fri Apr 03 2009 - 11:33:17 CDT)
- [AMBER] ptraj problem Ed Pate (Fri Apr 03 2009 - 15:13:37 CDT)
- [AMBER] Generate AM1-CM2 charges using antechamber Sishi Tang (Fri Apr 03 2009 - 17:36:46 CDT)
- [AMBER] parameter for amoeba Hemant Kumar (Sat Apr 04 2009 - 06:46:01 CDT)
- [AMBER] LYN again Marius Retegan (Sat Apr 04 2009 - 08:12:09 CDT)
- [AMBER] deffision Nancy (Sat Apr 04 2009 - 09:30:50 CDT)
- [AMBER] error in MM PBSA Vikas Sharma (Sat Apr 04 2009 - 12:06:57 CDT)
- [AMBER] error in MM PBSA Vikas Sharma (Sun Apr 05 2009 - 01:09:35 CDT)
- [AMBER] error in MM PBSA Vikas Sharma (Sun Apr 05 2009 - 23:27:21 CDT)
- [AMBER] pmemd compilation/make failed - mkl_vml_service_threader_z_1i_c_1o Vijay Manickam Achari (Mon Apr 06 2009 - 02:27:24 CDT)
- [AMBER] sander.MPI parallel run problem Dechang Li (Mon Apr 06 2009 - 02:44:12 CDT)
- [AMBER] faulty .rst file with "************" signs for the coordinates of a certain molecule. Soni Mufaddal Saifee (Mon Apr 06 2009 - 04:07:51 CDT)
- [AMBER] MM-PBSA error while running heat.in Vikas Sharma (Mon Apr 06 2009 - 04:32:55 CDT)
- [AMBER] ssh and make test.parallel Francesco Pietra (Mon Apr 06 2009 - 04:58:39 CDT)
- [AMBER] problem with secstruct action command in ptraj nicholus bhattacharjee (Mon Apr 06 2009 - 06:49:44 CDT)
- [AMBER] testing RRR with antechamber Alan (Mon Apr 06 2009 - 07:10:27 CDT)
- [AMBER] zwitterionic form of ARG and antechamber Alan (Mon Apr 06 2009 - 07:33:31 CDT)
- [AMBER] Amber with AMOEBA force-field Tomasio, Susana (Mon Apr 06 2009 - 07:41:18 CDT)
- [AMBER] Sander waleed_zalloum_at_yahoo.com (Mon Apr 06 2009 - 08:17:34 CDT)
- [AMBER] MM-PBSA: decompose energy error Lucilla Angeli (Mon Apr 06 2009 - 09:35:58 CDT)
- [AMBER] Sander Stalling Steve Seibold (Mon Apr 06 2009 - 11:21:51 CDT)
- [AMBER] Do I need to modify the cap residues nicholus bhattacharjee (Mon Apr 06 2009 - 11:45:20 CDT)
- [AMBER] Negative "number of measurements" in PTRAJ Jenny Iskrenova (Mon Apr 06 2009 - 12:28:59 CDT)
- [AMBER] Amber on GPU Sasha Buzko (Mon Apr 06 2009 - 19:56:31 CDT)
- [AMBER] deffision coefficient Nancy (Mon Apr 06 2009 - 20:18:32 CDT)
- [AMBER] A question about SMD force constant Jackie. J. Shen (Mon Apr 06 2009 - 20:40:13 CDT)
- [AMBER] ambmask question Ed Pate (Mon Apr 06 2009 - 23:36:40 CDT)
- [AMBER] Problems with running two separate jobs in the same time Antonija Tomić (Tue Apr 07 2009 - 03:08:53 CDT)
- [AMBER] how to add charge in metal ion bharat lakhani (Tue Apr 07 2009 - 04:11:23 CDT)
- [AMBER] missing violations of the covalent geometry Helena P M Tossavainen (Tue Apr 07 2009 - 04:36:44 CDT)
- [AMBER] errors while testing Per Jr. Greisen (Tue Apr 07 2009 - 05:00:19 CDT)
- [AMBER] Problem with CAP residues Tomasio, Susana (Tue Apr 07 2009 - 05:17:27 CDT)
- [AMBER] TI production runs stop after a certain Step number Hannes Wallnoefer (Tue Apr 07 2009 - 06:48:45 CDT)
- [AMBER] problem in calculation of binding energy in final step (MM-PBSA) Maryam Hamzehee (Tue Apr 07 2009 - 08:59:03 CDT)
- [AMBER] test/amoeba - forrtl: severe (64): input conversion error Tomasio, Susana (Tue Apr 07 2009 - 10:16:08 CDT)
- [AMBER] Testing parallel amber10: no libmkl_lapack.so Francesco Pietra (Tue Apr 07 2009 - 13:56:25 CDT)
- [AMBER] PBSA Radii option quantum_mania_at_yahoo.com (Tue Apr 07 2009 - 14:31:18 CDT)
- [AMBER] MMPB(GB)SA on trimer quantum_mania_at_yahoo.com (Tue Apr 07 2009 - 20:01:39 CDT)
- [AMBER] compare MMPBSA result m m (Wed Apr 08 2009 - 01:28:06 CDT)
- [AMBER] problem with antechamber aneesh cna (Wed Apr 08 2009 - 01:32:32 CDT)
- [AMBER] please help me out bharat lakhani (Wed Apr 08 2009 - 04:18:41 CDT)
- [AMBER] Failures of tests Per Jr. Greisen (Wed Apr 08 2009 - 10:41:34 CDT)
- [AMBER] Thermodynamic Integration and belly Ignacio J. General (Wed Apr 08 2009 - 14:52:51 CDT)
- [AMBER] force fields Mark M Huntress (Wed Apr 08 2009 - 19:23:38 CDT)
- [AMBER] please help me out bharat lakhani (Thu Apr 09 2009 - 00:10:22 CDT)
- [AMBER] how to plot this kind of map? lnin_1431_at_sina.com (Thu Apr 09 2009 - 03:36:45 CDT)
- [AMBER] hpux sander.serial failure info Yiannis Georgiadis (Thu Apr 09 2009 - 17:28:28 CDT)
- [AMBER] RST file waleed zalloum (Thu Apr 09 2009 - 09:06:37 CDT)
- [AMBER] Release of R.E.D. Server FyD (Thu Apr 09 2009 - 03:31:30 CDT)
- [AMBER] antechamber problems Jia Xu (Thu Apr 09 2009 - 12:12:44 CDT)
- [AMBER] Sander and multiple residues Dan Kaps (Thu Apr 09 2009 - 13:48:55 CDT)
- [AMBER] igb=0 vs. igb=6 give different answers Hugh Heldenbrand (Thu Apr 09 2009 - 15:51:02 CDT)
- [AMBER] basepair balaji nagarajan (Fri Apr 10 2009 - 00:30:57 CDT)
- [AMBER] Amber 1.2 tools test suite failure? Jim Parker (Sat Apr 11 2009 - 12:41:54 CDT)
- [AMBER] install and test Amber 10 parallel on Ubuntu 8.10 Jim Parker (Sat Apr 11 2009 - 19:20:25 CDT)
- [AMBER] why amber10/dat/leap/gleap/ and amber10/dat/leap/parm Alan (Sun Apr 12 2009 - 04:30:15 CDT)
- [AMBER] problem with explicit solvent in TMD balaji nagarajan (Mon Apr 13 2009 - 06:37:21 CDT)
- [AMBER] Energy minimisation and NaN vivek.viv.sharma_at_gmail.com (Mon Apr 13 2009 - 06:55:55 CDT)
- [AMBER] atom types in pdb files Dan Kaps (Mon Apr 13 2009 - 09:23:58 CDT)
- [AMBER] Thermodynamic Integration and belly Ignacio J. General (Mon Apr 13 2009 - 10:24:15 CDT)
- [AMBER] error saving prmtop and inpcrd files of complex in MM-PBSA Vikas Sharma (Mon Apr 13 2009 - 15:11:07 CDT)
- [AMBER] restrained minimization quantum_mania_at_yahoo.com (Mon Apr 13 2009 - 19:12:35 CDT)
- [AMBER] Possibility to use ff99 + GAFF + GLYCAM_06 in one time for complex system ? Marek Mal (Mon Apr 13 2009 - 22:29:17 CDT)
- [AMBER] chosing complex in amber Vikas Sharma (Tue Apr 14 2009 - 00:18:43 CDT)
- [AMBER] Questions on targeted MD with explicit solvent Hu, Shaowen (JSC-SK)[Universities Space Research Association USRA]. (Tue Apr 14 2009 - 08:51:40 CDT)
- [AMBER] [qm/mm] qmcharge for acidic a.a. in proteins sychen (Tue Apr 14 2009 - 11:33:03 CDT)
- [AMBER] antechamber and wrong net charge with gasteiger method Alan (Tue Apr 14 2009 - 12:41:30 CDT)
- [AMBER] my FF m m (Tue Apr 14 2009 - 17:21:38 CDT)
- [AMBER] water bonding with protein Mark M Huntress (Tue Apr 14 2009 - 21:55:39 CDT)
- [AMBER] hbond_ptraj_eror balaji nagarajan (Wed Apr 15 2009 - 01:53:29 CDT)
- [AMBER] mean of character in frcmod.ff03 chenquan (Wed Apr 15 2009 - 07:26:38 CDT)
- [AMBER] help- regarding - TMD balaji nagarajan (Wed Apr 15 2009 - 11:19:59 CDT)
- [AMBER] please help me out bharat lakhani (Thu Apr 16 2009 - 01:41:08 CDT)
- [AMBER] missing amber force field parameters Neha Gandhi (Thu Apr 16 2009 - 04:19:57 CDT)
- [AMBER] pmemd in amber10 - compile failed in HPC Vijay Manickam Achari (Thu Apr 16 2009 - 05:13:49 CDT)
- [AMBER] 1-4 vdW, GB MM difference Jimmy Heimdal (Thu Apr 16 2009 - 06:57:01 CDT)
- [AMBER] ambertools failed - SMP IA64 Vijay Manickam Achari (Thu Apr 16 2009 - 08:17:34 CDT)
- [AMBER] Van der Waals atom types Antonio Morreale (Thu Apr 16 2009 - 09:39:14 CDT)
- [AMBER] Amber and CHARMM summer school David A. Case (Thu Apr 16 2009 - 10:04:18 CDT)
- [AMBER] Bad value during integer read by sander Collins Nganou (Thu Apr 16 2009 - 10:09:45 CDT)
- [AMBER] sulfonamide parameters valeria.lapietra_at_unina.it (Thu Apr 16 2009 - 10:16:49 CDT)
- [AMBER] polarizable force field for 18-crown-6 Gert von Helden (Thu Apr 16 2009 - 12:33:15 CDT)
- [AMBER] help regarding force fields Vikas Sharma (Fri Apr 17 2009 - 01:06:32 CDT)
- [AMBER] Right force fields Vikas Sharma (Fri Apr 17 2009 - 01:22:16 CDT)
- [AMBER] radius of gyration Beale, John (Fri Apr 17 2009 - 06:39:31 CDT)
- [AMBER] Density in MD simulation Ibrahim Moustafa (Fri Apr 17 2009 - 11:09:16 CDT)
- [AMBER] Possibility to use ff99 + GAFF + GLYCAM_06 in one time for complex system ? quantum_mania_at_yahoo.com (Fri Apr 17 2009 - 12:52:28 CDT)
- [AMBER] Backbone restraint Rilei Yu (Fri Apr 17 2009 - 21:30:38 CDT)
- [AMBER] help_me to know the reason balaji nagarajan (Fri Apr 17 2009 - 23:30:07 CDT)
- [AMBER] please read this mail bharat lakhani (Sat Apr 18 2009 - 02:38:12 CDT)
- [AMBER] about saltcon zgong.hust (Sat Apr 18 2009 - 21:45:53 CDT)
- [AMBER] Atom type error Vikas Sharma (Sun Apr 19 2009 - 04:48:01 CDT)
- [AMBER] Possibility to use ff99 + GAFF + GLYCAM_06 in one time for complex system ? - Last detail Marek Mal (Mon Apr 20 2009 - 06:52:36 CDT)
- [AMBER] Partial interactions Ignacio J. General (Mon Apr 20 2009 - 16:07:24 CDT)
- [AMBER] My step size Vikas Sharma (Tue Apr 21 2009 - 01:50:16 CDT)
- [AMBER] atom numbers Vikas Sharma (Tue Apr 21 2009 - 06:12:27 CDT)
- [AMBER] Number of LES copies in ptraj Thomas Exner (Tue Apr 21 2009 - 10:28:41 CDT)
- [AMBER] Set start timestep for mdcrd traj output quantum_mania_at_yahoo.com (Tue Apr 21 2009 - 11:38:53 CDT)
- [AMBER] Set start timestep for mdcrd traj output quantum_mania_at_yahoo.com (Tue Apr 21 2009 - 11:31:45 CDT)
- [AMBER] Flexible ring simulation Dong Xu (Tue Apr 21 2009 - 18:04:55 CDT)
- [AMBER] per atom energies in sander/pmemd Tamara Rogers (Tue Apr 21 2009 - 18:41:27 CDT)
- [AMBER] Disulfide bond Dong Xu (Tue Apr 21 2009 - 20:37:46 CDT)
- [AMBER] bintraj and amber 10 Naser Alijabbari (Wed Apr 22 2009 - 01:31:51 CDT)
- [AMBER] help regarding step size Vikas Sharma (Wed Apr 22 2009 - 03:57:31 CDT)
- [AMBER] uncharged c and n terminal amino acids Christopher Materese (Wed Apr 22 2009 - 13:05:38 CDT)
- [AMBER] Problem with RNA hairpin unwinding in explicit water Sasha Buzko (Wed Apr 22 2009 - 16:55:58 CDT)
- [AMBER] Amber Sulfate Ion Parameters Gary Clark (Wed Apr 22 2009 - 17:31:00 CDT)
- [AMBER] error in output file Vikas Sharma (Thu Apr 23 2009 - 06:39:42 CDT)
- [AMBER] nmod no run proprely in mmbsa mohamed mohamed (Thu Apr 23 2009 - 07:20:36 CDT)
- [AMBER] Regarding syntax for freezing different atoms Jorgen Simonsen (Thu Apr 23 2009 - 07:50:43 CDT)
- [AMBER] Amber Installation problem ¼ (Thu Apr 23 2009 - 08:10:42 CDT)
- [AMBER] NAB bug with parmbsc0 David A. Case (Thu Apr 23 2009 - 11:25:27 CDT)
- Re: [AMBER] Problem with RNA hairpin unwinding in explicit water Bill Ross (Thu Apr 23 2009 - 12:53:40 CDT)
- [AMBER] Unit name with loadMol2 command Nicholas Musolino (Thu Apr 23 2009 - 14:30:30 CDT)
- [AMBER] CY3 dye parameters jcmoore_at_student.umass.edu (Thu Apr 23 2009 - 16:42:59 CDT)
- [AMBER] Amber Installation problem ¼ (Thu Apr 23 2009 - 20:35:46 CDT)
- [AMBER] Equilibrium bond lengths and angle values Dmitri Nilov (Fri Apr 24 2009 - 08:19:56 CDT)
- [AMBER] Simulated annealing waleed zalloum (Fri Apr 24 2009 - 09:31:36 CDT)
- [AMBER] question Tatyana Fedotova (Fri Apr 24 2009 - 14:55:40 CDT)
- [AMBER] restraint constant Dong Xu (Sat Apr 25 2009 - 17:15:22 CDT)
- [AMBER] Papers on Amber package usage Andrew Voronkov (Sun Apr 26 2009 - 00:07:42 CDT)
- [AMBER] amber question Vikas Sharma (Sun Apr 26 2009 - 01:00:06 CDT)
- [AMBER] Water-molecules sikander azam (Sun Apr 26 2009 - 08:11:33 CDT)
- [AMBER] Install ¼ (Sun Apr 26 2009 - 08:45:45 CDT)
- [AMBER] Using smd with fixed atom nandy_at_physics.iisc.ernet.in (Sun Apr 26 2009 - 09:57:45 CDT)
- [AMBER] AmberTools compiling error Farly Walsh (Sun Apr 26 2009 - 19:40:38 CDT)
- [AMBER] Error with calculation of the potential energy Per Jr. Greisen (Mon Apr 27 2009 - 06:03:44 CDT)
- [AMBER] Mixing of forcefields in case of covaletly bonded systems Marek Mal (Mon Apr 27 2009 - 07:06:38 CDT)
- [AMBER] Polarizable force field problem: non constant total Energy, EPOLZ is increasing Tommaso Cupido (Mon Apr 27 2009 - 09:10:12 CDT)
- [AMBER] pmemd compilation error john smith (Mon Apr 27 2009 - 22:30:21 CDT)
- [AMBER] Best rms fit for correlation and covariance analysis Cihan Aydin (Tue Apr 28 2009 - 00:02:14 CDT)
- [AMBER] dipole autocorrelation functions aneesh cna (Tue Apr 28 2009 - 01:23:05 CDT)
- Fwd: [AMBER] MM-GBSA Free enegy decomposition Rajesh Raju (Tue Apr 28 2009 - 06:28:17 CDT)
- [AMBER] transport properties oguz gurbulak (Tue Apr 28 2009 - 09:11:05 CDT)
- [AMBER] reg-TMD balaji nagarajan (Tue Apr 28 2009 - 10:23:34 CDT)
- Re: [AMBER] Best rms fit for correlation and covariance analysis Bill Ross (Tue Apr 28 2009 - 11:57:10 CDT)
- [AMBER] Restraining counterions? Francesco Pietra (Tue Apr 28 2009 - 12:32:18 CDT)
- Re: [AMBER] Restraining counterions? Bill Ross (Tue Apr 28 2009 - 13:59:52 CDT)
- [AMBER] ANAL problems E.M. (Tue Apr 28 2009 - 15:12:04 CDT)
- Re: [AMBER] ANAL problems Bill Ross (Tue Apr 28 2009 - 15:40:59 CDT)
- [AMBER] Using AMBER force fields in NAMD Michael Zimmermann (Tue Apr 28 2009 - 16:25:56 CDT)
- [AMBER] parallel problem of QM/MM calculation for AMBER 9 liu junjun (Tue Apr 28 2009 - 16:53:06 CDT)
- [AMBER] The PDB file was not recognized by Amber, what can i do? Houyang Chen (Tue Apr 28 2009 - 17:00:05 CDT)
- [AMBER] Nonterminal, was not found in name map Sunita Patel (Tue Apr 28 2009 - 19:50:08 CDT)
- [AMBER] REd program! R. A. (Tue Apr 28 2009 - 23:37:38 CDT)
- [AMBER] (no subject) waleed zalloum (Wed Apr 29 2009 - 07:15:12 CDT)
- [AMBER] input error in TI calculation Hannes Wallnoefer (Wed Apr 29 2009 - 10:40:58 CDT)
- [AMBER] chain restrain x TI Josmar R. da Rocha (Wed Apr 29 2009 - 17:04:52 CDT)
- [AMBER] Amber FF and Glycam Dong Xu (Wed Apr 29 2009 - 20:42:55 CDT)
- [AMBER] MM-PBSA energy decomposition Dong Xu (Wed Apr 29 2009 - 21:03:34 CDT)
- [AMBER] hbond-error in amber9 balaji nagarajan (Wed Apr 29 2009 - 21:09:17 CDT)
- [AMBER] Influence about HIS-HIE-HIS-HIP Rilei Yu (Wed Apr 29 2009 - 22:25:48 CDT)
- [AMBER] how to add charge on metal ions bharat lakhani (Thu Apr 30 2009 - 01:44:46 CDT)
- [AMBER] Request an error Collins Nganou (Thu Apr 30 2009 - 12:41:48 CDT)
- [AMBER] (no subject) Collins Nganou (Thu Apr 30 2009 - 14:34:36 CDT)
- [AMBER] Make parallel test faillure Collins Nganou (Thu Apr 30 2009 - 14:36:55 CDT)
- RE: [Subject Filtered] [AMBER] hbond-error in amber9 8% Hopkins, Robert (Thu Apr 30 2009 - 19:02:34 CDT)
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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