Amber Archive Jan 2015 by thread
- [AMBER] diffusion time step newamber list (Wed Dec 31 2014 - 18:14:59 PST)
- [AMBER] chamber : psf to amber parmtop Himanshu Joshi (Thu Jan 01 2015 - 04:33:47 PST)
- [AMBER] ZN metal parametrization using MCPB -reg sailu (Thu Jan 01 2015 - 05:43:40 PST)
- Re: [AMBER] Solvation free energy using soft core potential hannes.loeffler.stfc.ac.uk (Thu Jan 01 2015 - 07:26:13 PST)
- [AMBER] aMD plot 汪盛 (Thu Jan 01 2015 - 14:46:49 PST)
- [AMBER] Matrix correlation Sylvester Tumusiime (Thu Jan 01 2015 - 16:19:25 PST)
- [AMBER] Matrix correl Sylvester Tumusiime (Thu Jan 01 2015 - 19:18:34 PST)
- [AMBER] contacts with water Chinthaka Ratnaweera (Thu Jan 01 2015 - 20:51:31 PST)
- Re: [AMBER] Need help in Targeted MD Pallavi Mohanty (Thu Jan 01 2015 - 22:14:03 PST)
- Re: [AMBER] FW: clustering problem in ambertool14 Mahendra B Thapa (Fri Jan 02 2015 - 08:08:40 PST)
- Re: [AMBER] FW: FW: clustering problem in ambertool14 Mahendra B Thapa (Fri Jan 02 2015 - 12:48:39 PST)
- [AMBER] About amber parameters for free dioxygen in water solution Francesco Pietra (Sat Jan 03 2015 - 01:27:15 PST)
- [AMBER] Checking bonds commanded with leap Francesco Pietra (Sat Jan 03 2015 - 10:25:29 PST)
- [AMBER] RMSD calculation of a homodimer Ibrahim Said (Sun Jan 04 2015 - 08:21:23 PST)
- Re: [AMBER] pseudo F-statistic (pSF) Jonathan Gough (Sun Jan 04 2015 - 10:05:00 PST)
- [AMBER] ESP Charge for Fe Fatemeh Sadat Alavi (Mon Jan 05 2015 - 00:47:20 PST)
- [AMBER] nocut MD SHAKE error Anupam Goel (Mon Jan 05 2015 - 13:14:20 PST)
- [AMBER] confusion about effect of number of solvent molecules on density Vipin Ruhela (Tue Jan 06 2015 - 05:08:14 PST)
- [AMBER] Missing psi dihedral at cationic N-terminus of protein/peptide? nealec (Tue Jan 06 2015 - 16:54:01 PST)
- [AMBER] Equilibration problem large system in explicit solvent Waldner, Birgit (Wed Jan 07 2015 - 05:12:20 PST)
- [AMBER] CpptrajFile: error Ibrahim Said (Wed Jan 07 2015 - 09:04:08 PST)
- Re: [AMBER] aMD plot (Daniel Roe) 汪盛 (Wed Jan 07 2015 - 16:14:47 PST)
- [AMBER] The protein unfolded through the simulation Hadeer ELHabashy (Wed Jan 07 2015 - 17:06:36 PST)
- [AMBER] ABOUT NPT and PMEMD.CUDA Yeng-Tseng Wang (Wed Jan 07 2015 - 22:49:34 PST)
- [AMBER] extract torsion angle data Anupam Goel (Wed Jan 07 2015 - 23:34:17 PST)
- [AMBER] Using restraints to get a complex mmaestre.gate.sinica.edu.tw (Thu Jan 08 2015 - 00:32:14 PST)
- Re: [AMBER] Error during Adding Fragment（about MCPB ） Pengfei Li (Thu Jan 08 2015 - 08:45:28 PST)
- Re: [AMBER] 回复： Errors during Adding hydrogen atoms to the PDB file（MCPB program） Pengfei Li (Thu Jan 08 2015 - 08:55:12 PST)
- [AMBER] Vector command CPPTRAJ Sourav Purohit (Fri Jan 09 2015 - 00:44:35 PST)
- [AMBER] Free Energy Workshop, Münster, March 9-11, 2015 Vlad Cojocaru (Fri Jan 09 2015 - 01:20:48 PST)
- [AMBER] Constant values in prmtop Mohd Farid Ismail (Fri Jan 09 2015 - 01:45:59 PST)
- [AMBER] How to defined a steered direction in SMD? Chris (Fri Jan 09 2015 - 05:59:37 PST)
- [AMBER] cpptraj.MPI Jonathan Gough (Fri Jan 09 2015 - 10:30:54 PST)
- [AMBER] problem with rdparm in amb2gmx.pl Rebeca García Fandiño (Sat Jan 10 2015 - 02:47:35 PST)
- [AMBER] Significantly different results between MMPBSA and MMGBSA asdda asa (Sat Jan 10 2015 - 19:55:04 PST)
- [AMBER] accelerated MD on 2 GPU cards Asmita Gupta (Sun Jan 11 2015 - 04:43:26 PST)
- [AMBER] Calculating density during Radial distribution analysis Sylvester Tumusiime (Sun Jan 11 2015 - 12:45:22 PST)
- [AMBER] Error in Simulation of MN2+ containing complex 杨川 (Mon Jan 12 2015 - 00:19:32 PST)
- [AMBER] Problem in creating prepin file Jasmine (Mon Jan 12 2015 - 00:42:04 PST)
- [AMBER] Help in AMBER Robin Jain (Mon Jan 12 2015 - 00:45:11 PST)
- [AMBER] pbsa question zahra khatti (Mon Jan 12 2015 - 01:23:41 PST)
- [AMBER] diffusion coeficient zahra khatti (Mon Jan 12 2015 - 01:32:45 PST)
- [AMBER] could not find vdW (Na+) type IP Francesco Pietra (Mon Jan 12 2015 - 01:57:26 PST)
- [AMBER] Free energy decomposing calculation time with MMPBSA.py Houcemeddine Othman (Mon Jan 12 2015 - 02:12:17 PST)
- Re: [AMBER] Amber 14 Performance and Other Questions Novosielski, Ryan (Mon Jan 12 2015 - 11:11:38 PST)
- [AMBER] AmberTools14 MMPBSA CalcError with complex.prmtop and SA Bomb in use_sander=1 Kenneth Huang (Mon Jan 12 2015 - 11:45:52 PST)
- [AMBER] Intel Compilers, SSE_TYPES, and auto CPU dispatch Novosielski, Ryan (Mon Jan 12 2015 - 14:47:06 PST)
- Re: [AMBER] Intel Compilers, SSE_TYPES, and auto CPU dispatch Daniel Roe (Mon Jan 12 2015 - 17:44:32 PST)
- Re: [AMBER] Intel Compilers, SSE_TYPES, and auto CPU dispatch Novosielski, Ryan (Tue Jan 13 2015 - 09:20:39 PST)
- Re: [AMBER] Intel Compilers, SSE_TYPES, and auto CPU dispatch Jason Swails (Tue Jan 13 2015 - 09:38:38 PST)
- Re: [AMBER] Intel Compilers, SSE_TYPES, and auto CPU dispatch Novosielski, Ryan (Tue Jan 13 2015 - 09:46:29 PST)
- Re: [AMBER] Intel Compilers, SSE_TYPES, and auto CPU dispatch Jason Swails (Tue Jan 13 2015 - 10:18:57 PST)
- Re: [AMBER] Intel Compilers, SSE_TYPES, and auto CPU dispatch Novosielski, Ryan (Tue Jan 13 2015 - 10:53:55 PST)
- Re: [AMBER] Intel Compilers, SSE_TYPES, and auto CPU dispatch Brent Krueger (Tue Jan 13 2015 - 11:10:22 PST)
- Re: [AMBER] Intel Compilers, SSE_TYPES, and auto CPU dispatch Novosielski, Ryan (Tue Jan 13 2015 - 11:23:40 PST)
- Re: [AMBER] Intel Compilers, SSE_TYPES, and auto CPU dispatch Jan-Philip Gehrcke (Wed Jan 14 2015 - 04:26:33 PST)
- Re: [AMBER] Intel Compilers, SSE_TYPES, and auto CPU dispatch Hannes Loeffler (Wed Jan 14 2015 - 05:26:50 PST)
- Re: [AMBER] Intel Compilers, SSE_TYPES, and auto CPU dispatch Novosielski, Ryan (Wed Jan 14 2015 - 07:33:39 PST)
- Re: [AMBER] Intel Compilers, SSE_TYPES, and auto CPU dispatch Brent Krueger (Wed Jan 14 2015 - 07:57:19 PST)
- Re: [AMBER] Intel Compilers, SSE_TYPES, and auto CPU dispatch Novosielski, Ryan (Wed Jan 14 2015 - 08:05:29 PST)
- Re: [AMBER] Intel Compilers, SSE_TYPES, and auto CPU dispatch Scott Brozell (Wed Jan 14 2015 - 09:52:58 PST)
- [AMBER] Using DFTB parameters (Halorg) in Amber12 柳成文 (Mon Jan 12 2015 - 18:15:57 PST)
- [AMBER] Fe(III)-OH2 vs Fe(II)-OH2 force constant Francesco Pietra (Tue Jan 13 2015 - 00:09:52 PST)
- [AMBER] Torsion restrain Lara rajam (Tue Jan 13 2015 - 14:31:16 PST)
- [AMBER] Amber11: CUDA-enabled version does not work Khuong Truong Gia (Tue Jan 13 2015 - 22:02:50 PST)
- [AMBER] FEP Federica Chiappori (Wed Jan 14 2015 - 03:24:37 PST)
- [AMBER] [MGMS-DS]: Molecular Modelling Workshop March 9-11, 2015 in Erlangen, Germany Harald Lanig (Wed Jan 14 2015 - 03:39:07 PST)
- [AMBER] cpptraj: structures not aligned anymore after 'run' keyword Guillaume Roellinger (Wed Jan 14 2015 - 05:06:23 PST)
- [AMBER] help in force field Robin Jain (Wed Jan 14 2015 - 06:43:47 PST)
- [AMBER] Fwd: MMPBSA problem when using idecomp Lucia Alvarez (Wed Jan 14 2015 - 09:18:44 PST)
- [AMBER] Errors during Building Sidechain Model（MCPB program） wjli (Wed Jan 14 2015 - 20:18:51 PST)
- [AMBER] Reading chemical bonds from par7 files Francesco Pietra (Thu Jan 15 2015 - 00:18:22 PST)
- [AMBER] unusual structure after heating. why? Atila Petrosian (Thu Jan 15 2015 - 00:49:33 PST)
- [AMBER] Error while running tleap in AMBER Shreeramesh (Thu Jan 15 2015 - 05:08:05 PST)
- [AMBER] Problem with idecomp in MMPBSA lalvarez.qi.fcen.uba.ar (Thu Jan 15 2015 - 07:01:03 PST)
- [AMBER] How to fix 1-4 ELE error Kshatresh Dutta Dubey (Thu Jan 15 2015 - 07:17:18 PST)
- [AMBER] Which papers should be cited for ff14SB Jonathan Gough (Thu Jan 15 2015 - 09:56:13 PST)
- [AMBER] unusual structure after heating. why? Atila Petrosian (Thu Jan 15 2015 - 10:31:04 PST)
- [AMBER] hydrogen bond charmm vs amber newamber list (Thu Jan 15 2015 - 11:20:20 PST)
- [AMBER] unusual structure after heating. why? Atila Petrosian (Thu Jan 15 2015 - 11:38:36 PST)
- [AMBER] Extracting multiple frames by cpptraj Mahendra B Thapa (Thu Jan 15 2015 - 11:45:06 PST)
- [AMBER] unusual structure after heating. why? Atila Petrosian (Thu Jan 15 2015 - 12:08:13 PST)
- [AMBER] Purchase second GPU for AMBER? orion shih (Thu Jan 15 2015 - 21:34:05 PST)
- [AMBER] Principal Axis Karl Kirschner (Fri Jan 16 2015 - 02:01:15 PST)
- Re: [AMBER] energies too high David A Case (Fri Jan 16 2015 - 04:45:31 PST)
- [AMBER] cuda version 5 using gnu V 4.9.1 issues CHAMI F. (Fri Jan 16 2015 - 07:25:00 PST)
- [AMBER] Why there is a conflict between ibelly and igb in REMD? Jinfeng Huang (Sat Jan 17 2015 - 05:59:52 PST)
- [AMBER] AMBER 14 installation in cray machine : Problem related to parallel building Himanshu Joshi (Sat Jan 17 2015 - 09:53:47 PST)
- Re: [AMBER] FW: FW: FW: clustering problem in ambertool14 Mahendra B Thapa (Sun Jan 18 2015 - 08:01:46 PST)
- [AMBER] installation of AmberTools14 Atila Petrosian (Sun Jan 18 2015 - 10:22:16 PST)
- [AMBER] Periodic image of iwrapped structure Hadeer ELHabashy (Sun Jan 18 2015 - 15:05:13 PST)
- [AMBER] About: AMBER Advanced Tutorial 22 Hadeer ELHabashy (Sun Jan 18 2015 - 15:34:50 PST)
- [AMBER] HBond ANALYSIS Sylvester Tumusiime (Sun Jan 18 2015 - 21:44:01 PST)
- [AMBER] bad atom type: OA Houcemeddine Othman (Tue Jan 20 2015 - 02:59:01 PST)
- [AMBER] Proper output form of DCCM Analysis using ptraj Suchetana Gupta bt13d072 (Tue Jan 20 2015 - 05:40:09 PST)
- [AMBER] Trajectory processing using ptraj James Starlight (Tue Jan 20 2015 - 09:53:41 PST)
- [AMBER] Question of AM1-BCC asdda asa (Tue Jan 20 2015 - 19:46:36 PST)
- [AMBER] Querry about puckering Aparna P (Tue Jan 20 2015 - 22:36:29 PST)
- [AMBER] About statistical report of 'RMS deviation from ideal bonds/angles' Yi Zhang (Wed Jan 21 2015 - 00:13:09 PST)
- [AMBER] help in analysis Robin Jain (Wed Jan 21 2015 - 02:38:41 PST)
- [AMBER] Group defining heavy atoms Thomas Exner (Wed Jan 21 2015 - 09:20:15 PST)
- [AMBER] GPU error GTX card. BERGY (Wed Jan 21 2015 - 09:27:58 PST)
- [AMBER] R: Group defining heavy atoms Alessandro Contini (Wed Jan 21 2015 - 09:43:16 PST)
- [AMBER] Question in Amber atom types asdda asa (Wed Jan 21 2015 - 16:26:13 PST)
- [AMBER] PMEMD Error Sourav Purohit (Wed Jan 21 2015 - 23:20:07 PST)
- [AMBER] help in diffusion coefficient Robin Jain (Thu Jan 22 2015 - 01:22:03 PST)
- [AMBER] Protein Drug explicit MD simulation pradeep pant (Thu Jan 22 2015 - 05:03:30 PST)
- Re: [AMBER] NVE GPU question Ross Walker (Thu Jan 22 2015 - 10:48:28 PST)
- [AMBER] Fwd: NVE GPU question Joseph Baker (Thu Jan 22 2015 - 11:20:58 PST)
- [AMBER] How to write the Amber code(s) to calculate pi-pi stacking interactions, polar contacts Jiapu Zhang (Thu Jan 22 2015 - 22:36:32 PST)
- [AMBER] help in diffusion coefficient analysis Robin Jain (Fri Jan 23 2015 - 00:02:40 PST)
- [AMBER] How to save structure at every minimisation/optimization cycle Kshatresh Dutta Dubey (Fri Jan 23 2015 - 02:09:26 PST)
- Re: [AMBER] FW: FW: FW: FW: clustering problem in ambertool14 Mahendra B Thapa (Fri Jan 23 2015 - 06:24:53 PST)
- [AMBER] Force ramp pulling agarai.physics.iisc.ernet.in (Fri Jan 23 2015 - 09:14:07 PST)
- [AMBER] bcl script side chain optimization using Gaussian-Reg sailu (Sat Jan 24 2015 - 03:14:51 PST)
- Re: [AMBER] AMBER Digest, Vol 1109, Issue 1 sailu (Sat Jan 24 2015 - 21:09:33 PST)
- [AMBER] MMGBSA of several MD trajectories James Starlight (Sun Jan 25 2015 - 06:31:31 PST)
- [AMBER] PCA variance using Freq = 108.587 * sqrt( 0.6 / Eigenvalue ) Muthukumaran R (Sun Jan 25 2015 - 07:42:40 PST)
- [AMBER] Atom type parameterization and prmtop file asdda asa (Sun Jan 25 2015 - 16:57:41 PST)
- [AMBER] how to choose the final binding mode 徐晓庶 (Mon Jan 26 2015 - 03:23:41 PST)
- [AMBER] Lipid 14 format problem Romero, Raquel (Mon Jan 26 2015 - 04:44:48 PST)
- [AMBER] AMBER 14 DPFP single energy calculations inconsistent R.G. Mantell (Mon Jan 26 2015 - 06:42:55 PST)
- Re: [AMBER] FW: FW: FW: FW: FW: clustering problem in ambertool14 Mahendra B Thapa (Mon Jan 26 2015 - 07:42:41 PST)
- [AMBER] cbrange in gnuplot Sylvester Tumusiime (Mon Jan 26 2015 - 12:26:42 PST)
- [AMBER] xleap does not known when compiling with mpi Saeed Nasiri (Mon Jan 26 2015 - 23:50:59 PST)
- [AMBER] max GPU cards per run Harmeet Kaur (Tue Jan 27 2015 - 01:03:49 PST)
- [AMBER] ambertools14 fresh installation fails Fabian Glaser (Tue Jan 27 2015 - 05:52:45 PST)
- [AMBER] help in minimization Robin Jain (Tue Jan 27 2015 - 07:29:34 PST)
- [AMBER] GBSA speeds for big molecules Asmit Bhowmick (Tue Jan 27 2015 - 13:18:16 PST)
- [AMBER] AMBER Workshop Announcement - Haifa Israel, Sun Apr 26th to 30th. Ross Walker (Tue Jan 27 2015 - 16:55:10 PST)
- [AMBER] Targeted MD error Pallavi Mohanty (Tue Jan 27 2015 - 22:11:21 PST)
- [AMBER] problem with antechamber Maryam Hamzehee (Tue Jan 27 2015 - 22:27:46 PST)
- [AMBER] Help in AMBER+PLUMED interface Giovanni Bussi (Tue Jan 27 2015 - 23:37:44 PST)
- [AMBER] shell scripting within cpptraj input files James Starlight (Wed Jan 28 2015 - 01:21:28 PST)
- [AMBER] [cpptraj] Problem with nativecontacts Juan Eiros Zamora (Wed Jan 28 2015 - 05:02:10 PST)
- [AMBER] How to run an antechamber for ligands containing silver [Ag] atom? Shreeramesh (Wed Jan 28 2015 - 05:44:00 PST)
- [AMBER] POPC membrane separation. William Hester (Wed Jan 28 2015 - 08:13:10 PST)
- [AMBER] harmonic restraint file abdennour braka (Wed Jan 28 2015 - 08:21:56 PST)
- [AMBER] FATAL: Atom .R<RU5 13>.A<P 29> does not have a type. Mahad Gatti Iou (Wed Jan 28 2015 - 09:01:52 PST)
- [AMBER] wrap warning Fabian Glaser (Thu Jan 29 2015 - 00:33:17 PST)
- [AMBER] Regarding MCPB Pragya Priyadarshini (Thu Jan 29 2015 - 03:53:29 PST)
- [AMBER] big cavity in the trajectory Tong Zhu (Fri Jan 30 2015 - 00:29:01 PST)
- [AMBER] Regarding MCPB Pragya Priyadarshini (Fri Jan 30 2015 - 01:01:26 PST)
- [AMBER] clustering in PC subspace Asmita Gupta (Fri Jan 30 2015 - 03:09:31 PST)
- [AMBER] Clustering molecule between copies (not between frames) 浅井 賢 (Fri Jan 30 2015 - 04:06:20 PST)
- [AMBER] parameterization using antechember Debasish Mandal (Fri Jan 30 2015 - 04:07:39 PST)
- Re: [AMBER] Printer Bill Ross (Fri Jan 30 2015 - 14:06:59 PST)
- Re: [AMBER] Printing out matrix labels Hai Nguyen (Fri Jan 30 2015 - 19:20:42 PST)
- [AMBER] Help regarding potential surface scan using external interface Kshatresh Dutta Dubey (Sat Jan 31 2015 - 12:02:57 PST)
- Re: [AMBER] Problem with Ambertools14 David A Case (Sat Jan 31 2015 - 13:03:30 PST)
- [AMBER] AmberTools 14 Dhiraj Srivastava (Sat Jan 31 2015 - 19:31:38 PST)
- Last message date: Sat Jan 31 2015 - 20:00:02 PST
- Archived on: Wed Dec 25 2024 - 05:55:07 PST
