Amber Archive Sep 2011 by author
873 messages
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Starting
Wed Aug 31 2011 - 22:00:02 PDT,
Ending
Fri Sep 30 2011 - 19:30:02 PDT
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Aaron Greenwood
[AMBER] Serial Version of libFpbsa.a
(Fri Sep 16 2011 - 11:15:02 PDT)
[AMBER] libmkl_ia32.a missing from MKL em64t
(Wed Sep 07 2011 - 09:57:33 PDT)
Abhishek Mukhopadhyay
[AMBER] Water density/potential visualization
(Thu Sep 08 2011 - 09:56:54 PDT)
Adrian Roitberg
Re: [AMBER] Large pressure fluctuations over the whole run
(Mon Sep 26 2011 - 15:25:32 PDT)
aiswarya pawar
Re: [AMBER] Residence time
(Wed Sep 07 2011 - 04:18:14 PDT)
[AMBER] Residence time
(Wed Sep 07 2011 - 00:14:18 PDT)
aiswarya.pawar.gmail.com
[AMBER] How to start with
(Fri Sep 16 2011 - 06:19:24 PDT)
[AMBER] Format conversion
(Wed Sep 07 2011 - 11:18:12 PDT)
amir abbasi
[AMBER] pulling DNA
(Wed Sep 14 2011 - 05:38:39 PDT)
Andrew Jewett
Re: [AMBER] How to use WHAM to analysis Replica Exchange Simulations
(Tue Sep 06 2011 - 15:47:21 PDT)
Andrew Petersen
[AMBER] sander/amoeba parameter format
(Thu Sep 22 2011 - 09:53:40 PDT)
Andrew Voronkov
Re: [AMBER] How to avoid Zn parametrization?
(Wed Sep 14 2011 - 03:18:08 PDT)
Anglea A.
[AMBER] non-bond interaction
(Tue Sep 27 2011 - 00:01:24 PDT)
Anselm Horn
[AMBER] MM/GBSA question - pairwise decomposition
(Mon Sep 26 2011 - 12:11:55 PDT)
Re: [AMBER] visualization of secstruc with e.g. gnuplot
(Tue Sep 13 2011 - 11:23:50 PDT)
Antje Wolf
Re: [AMBER] MMPBSA.py energy decomposition inconsistencies
(Fri Sep 16 2011 - 09:13:21 PDT)
Re: [AMBER] MMPBSA.py energy decomposition inconsistencies
(Thu Sep 15 2011 - 23:51:40 PDT)
Re: [AMBER] MMPBSA.py energy decomposition inconsistencies
(Thu Sep 15 2011 - 08:34:24 PDT)
[AMBER] MMPBSA.py energy decomposition inconsistencies
(Thu Sep 15 2011 - 05:13:17 PDT)
Aparna P
Re: [AMBER] Model building
(Thu Sep 29 2011 - 04:16:46 PDT)
Re: [AMBER] Model building
(Mon Sep 26 2011 - 22:01:58 PDT)
Re: [AMBER] Model building
(Sat Sep 24 2011 - 21:31:03 PDT)
Re: [AMBER] Model building
(Fri Sep 23 2011 - 01:05:29 PDT)
Re: [AMBER] RMSD
(Thu Sep 22 2011 - 02:14:39 PDT)
[AMBER] Model building
(Thu Sep 22 2011 - 01:00:57 PDT)
[AMBER] Grid
(Fri Sep 16 2011 - 01:27:00 PDT)
Re: [AMBER] vlimit exeeding problem
(Tue Sep 13 2011 - 04:24:07 PDT)
Re: [AMBER] vlimit exeeding problem
(Mon Sep 12 2011 - 22:46:22 PDT)
Re: [AMBER] vlimit exeeding problem
(Mon Sep 12 2011 - 22:04:17 PDT)
[AMBER] vlimit exeeding problem
(Sun Sep 11 2011 - 23:46:33 PDT)
Astrid Maaß
Re: [AMBER] how to fill in missing parameters in tleap?
(Mon Sep 12 2011 - 06:11:15 PDT)
Re: [AMBER] how to fill in missing parameters in tleap?
(Fri Sep 09 2011 - 04:24:22 PDT)
Re: [AMBER] how to fill in missing parameters in tleap?
(Thu Sep 08 2011 - 23:24:15 PDT)
Re: [AMBER] how to fill in missing parameters in tleap?
(Wed Sep 07 2011 - 00:14:07 PDT)
Re: [AMBER] how to fill in missing parameters in tleap?
(Tue Sep 06 2011 - 02:07:37 PDT)
Baker D.J.
Re: [AMBER] Running amber v11 over multiple gpus/nodes
(Fri Sep 16 2011 - 00:47:39 PDT)
Re: [AMBER] Running amber v11 over multiple gpus/nodes
(Wed Sep 14 2011 - 08:18:03 PDT)
[AMBER] Running amber v11 over multiple gpus/nodes
(Wed Sep 14 2011 - 04:14:25 PDT)
[AMBER] Amber for GPUs
(Tue Sep 06 2011 - 05:06:42 PDT)
Bala subramanian
[AMBER] giving acceptor mask in ptraj for hbond utility
(Tue Sep 27 2011 - 11:16:05 PDT)
Baldoni Hector Armando
Re: [AMBER] help ! zinc parameters
(Thu Sep 22 2011 - 07:02:00 PDT)
Ben Roberts
Re: [AMBER] Xleap Installation
(Wed Sep 21 2011 - 06:51:05 PDT)
Bill Miller III
Re: [AMBER] AmberTools1.5 parallel implementation of mmpbsa.py - Incomplete installation?
(Thu Sep 29 2011 - 06:59:20 PDT)
Re: [AMBER] MMPBSA.py discrepancies in results
(Thu Sep 29 2011 - 04:16:04 PDT)
Re: [AMBER] MMPBSA.py discrepancies in results
(Wed Sep 28 2011 - 09:03:04 PDT)
Re: [AMBER] MMPBSA.py discrepancies in results
(Wed Sep 28 2011 - 06:27:31 PDT)
Re: [AMBER] Serious error (or bug) with free energy decomposition MMPBSA.py..The binding free energy values differs in decomposition analysis..
(Sat Sep 17 2011 - 13:55:51 PDT)
Re: [AMBER] FATAL: allocation failure in vector(), please help me to fix that problem
(Fri Sep 16 2011 - 03:49:55 PDT)
Re: [AMBER] energy
(Wed Sep 14 2011 - 09:00:13 PDT)
Re: [AMBER] Error in computing entropy! problem with number of frames in NMODE
(Wed Sep 14 2011 - 04:24:46 PDT)
Re: [AMBER] Problem with mmpbsa
(Tue Sep 13 2011 - 05:50:37 PDT)
Re: [AMBER] problem with MM-PBSA
(Wed Sep 07 2011 - 10:56:31 PDT)
Re: [AMBER] problem with MM-PBSA
(Tue Sep 06 2011 - 04:39:22 PDT)
Re: [AMBER] MMPBSA Ala scan error
(Tue Sep 06 2011 - 04:31:49 PDT)
Re: [AMBER] Energy change
(Mon Sep 05 2011 - 13:59:29 PDT)
Re: [AMBER] MMPBSA Ala scan error
(Mon Sep 05 2011 - 13:53:29 PDT)
Re: [AMBER] Energy
(Mon Sep 05 2011 - 13:32:04 PDT)
Re: [AMBER] MM_PBSA triple trajectory approch
(Sat Sep 03 2011 - 06:14:27 PDT)
Re: [AMBER] MM_PBSA triple trajectory approch
(Sat Sep 03 2011 - 05:19:17 PDT)
Bill Ross
Re: [AMBER] nmode analysis - different SCEE values in SANDMIN and NMODE output files ?
(Wed Sep 21 2011 - 12:24:56 PDT)
Re: [AMBER] rst or mdcrd file to view the structures?
(Tue Sep 20 2011 - 10:24:03 PDT)
Re: [AMBER] rst or mdcrd file to view the structures?
(Mon Sep 19 2011 - 20:36:33 PDT)
Re: [AMBER] help ! zinc parameters
(Mon Sep 19 2011 - 13:30:19 PDT)
Re: [AMBER] Bond command using xleap or tleap
(Fri Sep 16 2011 - 15:10:30 PDT)
Re: [AMBER] help ! zinc parameters
(Fri Sep 16 2011 - 08:39:20 PDT)
Re: [AMBER] Bond command using xleap or tleap
(Thu Sep 15 2011 - 17:39:59 PDT)
Re: [AMBER] turning on 1-2 and 1-3 interactions
(Thu Sep 08 2011 - 10:54:42 PDT)
Re: [AMBER] Non standard residue parameterization
(Mon Sep 05 2011 - 20:50:19 PDT)
Re: [AMBER] SHAKE error help
(Fri Sep 02 2011 - 21:09:54 PDT)
bin wang
[AMBER] How to build the surface of crystalline cellulose?
(Mon Sep 19 2011 - 20:19:31 PDT)
[AMBER] How to build the surface of crystalline cellulose?
(Mon Sep 19 2011 - 15:16:44 PDT)
Brian Radak
Re: [AMBER] ambertool question !!!
(Mon Sep 26 2011 - 11:36:16 PDT)
Re: [AMBER] Instantaneous temperature in TI simulation
(Mon Sep 26 2011 - 06:05:47 PDT)
Re: [AMBER] Instantaneous temperature in TI simulation
(Fri Sep 23 2011 - 13:07:58 PDT)
Re: [AMBER] Amber parmbsc0 vs ff99
(Thu Sep 22 2011 - 08:24:56 PDT)
Re: [AMBER] Amber parmbsc0 vs ff99
(Thu Sep 22 2011 - 06:50:40 PDT)
Re: [AMBER] Restart-Files in Sander
(Thu Sep 22 2011 - 06:25:48 PDT)
Re: [AMBER] Instantaneous temperature in TI simulation
(Wed Sep 21 2011 - 13:44:41 PDT)
Re: [AMBER] Instantaneous temperature in TI simulation
(Wed Sep 21 2011 - 06:40:07 PDT)
Re: [AMBER] Instantaneous temperature in TI simulation
(Tue Sep 20 2011 - 11:23:48 PDT)
Re: [AMBER] Instantaneous temperature in TI simulation
(Tue Sep 20 2011 - 07:59:36 PDT)
[AMBER] Instantaneous temperature in TI simulation
(Tue Sep 20 2011 - 06:01:54 PDT)
Re: [AMBER] Can we extract information from out file for MBAR analysis for PMF analysis?
(Wed Sep 14 2011 - 12:33:50 PDT)
Re: [AMBER] Can we extract information from out file for MBAR analysis?
(Wed Sep 14 2011 - 11:14:41 PDT)
Re: [AMBER] How to extract time angle, time, Energy from for MBAR analysis?
(Wed Sep 14 2011 - 07:01:18 PDT)
Re: [AMBER] Fwd: false positive on too large QM region?
(Tue Sep 13 2011 - 11:59:53 PDT)
Re: [AMBER] Fwd: false positive on too large QM region?
(Thu Sep 08 2011 - 13:42:56 PDT)
Re: [AMBER] Fwd: false positive on too large QM region?
(Thu Sep 08 2011 - 11:52:43 PDT)
[AMBER] Fwd: false positive on too large QM region?
(Thu Sep 08 2011 - 07:42:56 PDT)
[AMBER] false positive on too large QM region?
(Wed Sep 07 2011 - 14:37:58 PDT)
Re: [AMBER] How to use WHAM to analysis Replica Exchange Simulations
(Tue Sep 06 2011 - 08:49:57 PDT)
Bruno Luís Pinto de Oliveira
[AMBER] help ! zinc parameters
(Thu Sep 22 2011 - 06:07:20 PDT)
Bruno Rodrigues
Re: [AMBER] Fwd: fixing rmsd values (follow-up)
(Tue Sep 27 2011 - 14:39:47 PDT)
Re: [AMBER] fixing rmsd values
(Mon Sep 26 2011 - 08:54:25 PDT)
Re: [AMBER] Problems of Hbond calculation
(Mon Sep 26 2011 - 05:39:53 PDT)
Re: [AMBER] RMSD
(Mon Sep 26 2011 - 05:35:51 PDT)
Re: [AMBER] How to recover rst or can I readin mdcrd for a MD by -c?
(Sat Sep 24 2011 - 05:37:50 PDT)
Re: [AMBER] Amber parmbsc0 force field
(Fri Sep 23 2011 - 22:22:44 PDT)
Re: [AMBER] Self-Diffusion coefficient
(Tue Sep 20 2011 - 11:13:53 PDT)
[AMBER] Self-Diffusion coefficient
(Mon Sep 19 2011 - 14:43:31 PDT)
Re: [AMBER] Residue transformation
(Mon Sep 12 2011 - 20:16:48 PDT)
Re: [AMBER] PBS script
(Thu Sep 08 2011 - 21:38:58 PDT)
Re: [AMBER] PBS script
(Thu Sep 08 2011 - 21:36:12 PDT)
Carlos Simmerling
Re: [AMBER] Fwd: fixing rmsd values (follow-up)
(Tue Sep 27 2011 - 14:14:33 PDT)
Re: [AMBER] Fwd: fixing rmsd values (follow-up)
(Tue Sep 27 2011 - 11:51:37 PDT)
Re: [AMBER] GB protocol problems for large RNAs (follow-up)
(Tue Sep 27 2011 - 09:34:23 PDT)
[AMBER] October 20 deadline for ACS COMP division awards for junior faculty and graduate students
(Tue Sep 13 2011 - 10:46:56 PDT)
Re: [AMBER] Residence time
(Wed Sep 07 2011 - 11:53:49 PDT)
Re: [AMBER] Some question regarding force field for periodic system
(Wed Sep 07 2011 - 04:09:38 PDT)
Re: [AMBER] Residence time
(Wed Sep 07 2011 - 04:08:13 PDT)
Re: [AMBER] mbondi3
(Tue Sep 06 2011 - 11:38:25 PDT)
Carlos Sosa
Re: [AMBER] AmberTools Parallel Compilation Issue
(Fri Sep 23 2011 - 08:24:39 PDT)
Re: [AMBER] AmberTools Parallel Compilation Issue
(Fri Sep 23 2011 - 06:51:42 PDT)
case
Re: [AMBER] thermodynamic integration on protein mutation
(Mon Sep 26 2011 - 19:22:06 PDT)
Re: [AMBER] Large pressure fluctuations over the whole run
(Mon Sep 26 2011 - 19:19:59 PDT)
Re: [AMBER] Antechamber
(Sun Sep 25 2011 - 14:09:14 PDT)
Re: [AMBER] Error: peek_ewald_inpcrd: SHOULD NOT BE HERE
(Sun Sep 25 2011 - 14:03:34 PDT)
Re: [AMBER] nmode calculations
(Sun Sep 25 2011 - 13:59:09 PDT)
Re: [AMBER] Amber parmbsc0 force field
(Sat Sep 24 2011 - 06:04:47 PDT)
Re: [AMBER] problem with nmodes calculation-260-residue protein
(Sat Sep 24 2011 - 05:58:05 PDT)
Re: [AMBER] Instantaneous temperature in TI simulation
(Sat Sep 24 2011 - 05:51:43 PDT)
Re: [AMBER] force field of molecular crystals
(Mon Sep 19 2011 - 19:06:23 PDT)
Re: [AMBER] Bond command using xleap or tleap
(Sat Sep 17 2011 - 06:18:04 PDT)
Re: [AMBER] antechamber am1bcc stops with no error message
(Sun Sep 11 2011 - 18:48:34 PDT)
Re: [AMBER] SHAKE error help
(Sat Sep 10 2011 - 17:17:26 PDT)
Re: [AMBER] the result of pseudorotation angle
(Sat Sep 10 2011 - 06:01:47 PDT)
Re: [AMBER] SHAKE error help
(Fri Sep 09 2011 - 14:43:43 PDT)
Re: [AMBER] libmkl_ia32.a missing from MKL em64t
(Wed Sep 07 2011 - 12:57:56 PDT)
Re: [AMBER] How to Generate Structure with Correct Valence for an Unnatural Amino Acid in Position 1
(Wed Sep 07 2011 - 12:41:32 PDT)
Re: [AMBER] Is there any module which can calculate interaction energy, as ANAL in Amber 8?
(Tue Sep 06 2011 - 05:38:45 PDT)
Re: [AMBER] Creating prmtop and inpcrd files
(Tue Sep 06 2011 - 05:37:21 PDT)
Re: [AMBER] Non standard residue parameterization
(Tue Sep 06 2011 - 05:29:55 PDT)
Re: [AMBER] Non standard residue parameterization
(Mon Sep 05 2011 - 17:18:11 PDT)
Re: [AMBER] problem while using Antechamber
(Mon Sep 05 2011 - 17:16:34 PDT)
Re: [AMBER] Amber tools
(Mon Sep 05 2011 - 17:12:47 PDT)
Re: [AMBER] replace unit in leap
(Mon Sep 05 2011 - 17:11:46 PDT)
Re: [AMBER] SHAKE error help
(Mon Sep 05 2011 - 05:51:58 PDT)
Re: [AMBER] SHAKE error help
(Sat Sep 03 2011 - 11:05:41 PDT)
Re: [AMBER] antechamber error
(Sat Sep 03 2011 - 05:59:25 PDT)
Re: [AMBER] problem in installing xleap
(Sat Sep 03 2011 - 05:57:44 PDT)
Re: [AMBER] SHAKE error help
(Sat Sep 03 2011 - 05:50:13 PDT)
Catein Catherine
Re: [AMBER] How to recover rst or can I readin mdcrd for a MD by -c?
(Sat Sep 24 2011 - 23:03:19 PDT)
[AMBER] How to recover rst or can I readin mdcrd for a MD by -c?
(Fri Sep 23 2011 - 19:18:57 PDT)
Re: [AMBER] load parmbsc0 and X-Ol for RNA
(Fri Sep 23 2011 - 19:14:09 PDT)
Re: [AMBER] Can we extract information from out file for MBAR analysis for PMF analysis?
(Wed Sep 14 2011 - 11:36:11 PDT)
[AMBER] Can we extract information from out file for MBAR analysis?
(Wed Sep 14 2011 - 10:50:20 PDT)
[AMBER] How to extract time angle, time, Energy from for MBAR analysis?
(Wed Sep 14 2011 - 06:37:53 PDT)
Re: [AMBER] Why cut=999.9 was used in Tutorial A7 for REMD calculation?
(Mon Sep 12 2011 - 10:33:58 PDT)
[AMBER] Why cut=999.9 was used in Tutorial A7 for REMD calculation?
(Sun Sep 11 2011 - 23:30:13 PDT)
[AMBER] How to use WHAM to analysis Replica Exchange Simulations
(Tue Sep 06 2011 - 07:20:41 PDT)
CHAMI F.
Re: [AMBER] writing box info to pdb file extracted from an mdcrd trajectory
(Wed Sep 07 2011 - 09:01:06 PDT)
[AMBER] writing box info to pdb file extracted from an mdcrd trajectory
(Fri Sep 02 2011 - 07:28:59 PDT)
Chen, Changjun
Re: [AMBER] velocity modification in PMEMD, CUDA version
(Fri Sep 09 2011 - 03:04:15 PDT)
Re: [AMBER] velocity modification in PMEMD, CUDA version
(Tue Sep 06 2011 - 20:15:42 PDT)
[AMBER] velocity modification in PMEMD, CUDA version
(Mon Sep 05 2011 - 19:29:29 PDT)
Chidambar Kulkarni
Re: [AMBER] dihedral parameters
(Tue Sep 27 2011 - 09:09:05 PDT)
Re: [AMBER] Mol2 file creation
(Tue Sep 27 2011 - 09:05:04 PDT)
[AMBER] Mol2 file creation
(Mon Sep 26 2011 - 20:57:36 PDT)
Re: [AMBER] dihedral parameters
(Mon Sep 26 2011 - 20:51:18 PDT)
Re: [AMBER] Dihedral parameters
(Thu Sep 15 2011 - 22:36:36 PDT)
Re: [AMBER] Dihedral parameters
(Thu Sep 15 2011 - 08:42:59 PDT)
[AMBER] Dihedral parameters
(Thu Sep 15 2011 - 07:14:55 PDT)
Re: [AMBER] Creating prmtop and inpcrd files
(Tue Sep 06 2011 - 06:45:43 PDT)
[AMBER] Creating prmtop and inpcrd files
(Mon Sep 05 2011 - 23:57:53 PDT)
Chinh Su Tran To
Re: [AMBER] sander mpi error when unfolding the protein
(Thu Sep 29 2011 - 03:00:46 PDT)
Re: [AMBER] sander mpi error when unfolding the protein
(Thu Sep 29 2011 - 01:10:59 PDT)
[AMBER] sander mpi error when unfolding the protein
(Thu Sep 29 2011 - 00:43:24 PDT)
Re: [AMBER] rst or mdcrd file to view the structures?
(Tue Sep 20 2011 - 22:30:17 PDT)
Re: [AMBER] rst or mdcrd file to view the structures?
(Tue Sep 20 2011 - 00:54:30 PDT)
Re: [AMBER] rst or mdcrd file to view the structures?
(Mon Sep 19 2011 - 22:47:38 PDT)
Re: [AMBER] rst or mdcrd file to view the structures?
(Mon Sep 19 2011 - 19:44:37 PDT)
Re: [AMBER] rst or mdcrd file to view the structures?
(Mon Sep 19 2011 - 03:00:53 PDT)
[AMBER] rst or mdcrd file to view the structures?
(Sun Sep 18 2011 - 22:34:54 PDT)
Chirag Vora
Re: [AMBER] some questions on GAFF
(Fri Sep 02 2011 - 13:13:07 PDT)
Christina Bergonzo
Re: [AMBER] PNEB on GPUs
(Thu Sep 29 2011 - 05:25:59 PDT)
Cindy Pembroke
[AMBER] GBSW AMBER
(Thu Sep 29 2011 - 00:52:16 PDT)
clwg
[AMBER] the result of pseudorotation angle
(Sat Sep 10 2011 - 01:31:08 PDT)
d944286.oz.nthu.edu.tw
Re: [AMBER] Glycam06g and ff99SB cause the difference of DIHED (notattributed to the scaling factor)
(Tue Sep 20 2011 - 08:32:38 PDT)
[AMBER] Glycam06g and ff99SB cause the difference of DIHED (not attributed to the scaling factor)
(Sun Sep 18 2011 - 22:50:38 PDT)
Daniel Roe
Re: [AMBER] giving acceptor mask in ptraj for hbond utility
(Tue Sep 27 2011 - 11:36:32 PDT)
Re: [AMBER] RMSD
(Tue Sep 27 2011 - 05:43:10 PDT)
Re: [AMBER] Model building
(Tue Sep 27 2011 - 04:47:16 PDT)
Re: [AMBER] AmberTools 1.4 Installation on Mac OSX 10.6
(Sat Sep 24 2011 - 08:48:53 PDT)
Re: [AMBER] AmberTools 1.4 Installation on Mac OSX 10.6
(Sat Sep 24 2011 - 05:44:13 PDT)
Re: [AMBER] hydrogen bonding
(Fri Sep 23 2011 - 07:56:17 PDT)
Re: [AMBER] how to generate a correlation matrix for both protein and substrate atoms
(Fri Sep 23 2011 - 04:40:38 PDT)
Re: [AMBER] Model building
(Fri Sep 23 2011 - 04:33:19 PDT)
Re: [AMBER] Amber parmbsc0
(Thu Sep 22 2011 - 04:58:12 PDT)
Re: [AMBER] Model building
(Thu Sep 22 2011 - 04:54:50 PDT)
Re: [AMBER] RMSD
(Thu Sep 22 2011 - 04:42:56 PDT)
Re: [AMBER] ptraj: problem with distance and multi-atom masks
(Tue Sep 20 2011 - 04:37:00 PDT)
Re: [AMBER] cpptraj-segmentation fault
(Tue Sep 20 2011 - 04:18:48 PDT)
Re: [AMBER] ptraj: problem with distance and multi-atom masks
(Mon Sep 19 2011 - 09:44:48 PDT)
Re: [AMBER] cpptraj-segmentation fault
(Thu Sep 15 2011 - 22:10:27 PDT)
Re: [AMBER] cpptraj-segmentation fault
(Thu Sep 15 2011 - 05:42:56 PDT)
Re: [AMBER] cpptraj-segmentation fault
(Mon Sep 12 2011 - 05:52:38 PDT)
Re: [AMBER] cpptraj-segmentation fault
(Mon Sep 05 2011 - 17:26:46 PDT)
Re: [AMBER] cpptraj-segmentation fault
(Fri Sep 02 2011 - 15:30:14 PDT)
Daniel Sindhikara
[AMBER] Solvent model charges off by factor of 18.2223 or typo?
(Sun Sep 25 2011 - 23:57:08 PDT)
Re: [AMBER] Water density/potential visualization
(Thu Sep 08 2011 - 22:16:49 PDT)
Re: [AMBER] results from independent simulations
(Wed Sep 07 2011 - 21:13:22 PDT)
Re: [AMBER] How to use WHAM to analysis Replica Exchange Simulations
(Tue Sep 06 2011 - 15:28:54 PDT)
Danny Xu
[AMBER] antechamber am1bcc stops with no error message
(Mon Sep 05 2011 - 21:37:38 PDT)
Darren Jindal
[AMBER] error using saveamberparm on pdb with nonstandard residues
(Mon Sep 12 2011 - 19:32:18 PDT)
David A Case
Re: [AMBER] Failure to compile AmberTools 1.5 on linux
(Fri Sep 30 2011 - 05:25:43 PDT)
Re: [AMBER] how NOT to label terminal residue
(Fri Sep 30 2011 - 05:18:53 PDT)
Re: [AMBER] GBSW AMBER
(Thu Sep 29 2011 - 05:37:30 PDT)
Re: [AMBER] Chirality restraints
(Thu Sep 29 2011 - 05:35:59 PDT)
Re: [AMBER] Parallel limit?
(Thu Sep 29 2011 - 05:32:26 PDT)
Re: [AMBER] bug in respgen ?
(Wed Sep 28 2011 - 07:11:30 PDT)
Re: [AMBER] solvateBox or setBox or set box
(Wed Sep 28 2011 - 05:17:24 PDT)
Re: [AMBER] GB protocol problems for large RNAs (follow-up)
(Tue Sep 27 2011 - 12:43:12 PDT)
Re: [AMBER] Mol2 file creation
(Tue Sep 27 2011 - 04:53:35 PDT)
Re: [AMBER] Regarding Force field
(Mon Sep 26 2011 - 05:03:26 PDT)
Re: [AMBER] load parmbsc0 and X-Ol for RNA
(Fri Sep 23 2011 - 13:10:33 PDT)
Re: [AMBER] Sleap and TIP4P BOX
(Fri Sep 23 2011 - 06:20:18 PDT)
Re: [AMBER] AmberTools Parallel Compilation Issue
(Fri Sep 23 2011 - 06:15:59 PDT)
Re: [AMBER] ICST
(Thu Sep 22 2011 - 06:13:56 PDT)
Re: [AMBER] Sleap and TIP4P BOX
(Thu Sep 22 2011 - 05:59:31 PDT)
Re: [AMBER] Sleap and TIP4P BOX
(Wed Sep 21 2011 - 06:39:29 PDT)
Re: [AMBER] Instantaneous temperature in TI simulation
(Wed Sep 21 2011 - 04:52:54 PDT)
Re: [AMBER] problem with TI calculations
(Wed Sep 21 2011 - 04:50:38 PDT)
Re: [AMBER] Instantaneous temperature in TI simulation
(Tue Sep 20 2011 - 07:33:55 PDT)
Re: [AMBER] new residue parameters transfer
(Tue Sep 20 2011 - 04:48:08 PDT)
Re: [AMBER] force field of molecular crystals
(Mon Sep 19 2011 - 12:00:07 PDT)
Re: [AMBER] AMOEBA potentials
(Thu Sep 15 2011 - 12:08:01 PDT)
Re: [AMBER] tleap command "set default Dielectric constant" not valid?
(Thu Sep 15 2011 - 12:04:17 PDT)
Re: [AMBER] Bond command using xleap or tleap
(Thu Sep 15 2011 - 11:51:01 PDT)
Re: [AMBER] undefined reference
(Tue Sep 13 2011 - 10:01:42 PDT)
Re: [AMBER] undefined reference
(Tue Sep 13 2011 - 06:45:10 PDT)
Re: [AMBER] error using saveamberparm on pdb with nonstandard residues
(Tue Sep 13 2011 - 04:51:18 PDT)
Re: [AMBER] Amber 11 configure error with openmpi
(Mon Sep 12 2011 - 13:34:10 PDT)
Re: [AMBER] CCA-Phe terminal using Antechamber
(Thu Sep 01 2011 - 07:33:11 PDT)
Re: [AMBER] problem in installing xleap
(Thu Sep 01 2011 - 05:07:57 PDT)
David Case
Re: [AMBER] Electrpostatic interaction vs Coulombic interaction
(Wed Sep 14 2011 - 18:34:22 PDT)
Re: [AMBER] MMGBSA binding free energy shows large change with saltcon parameter, but not for MMPBSA binding free energy value
(Tue Sep 13 2011 - 16:59:58 PDT)
David Condon
Re: [AMBER] load parmbsc0 and X-Ol for RNA
(Sun Sep 25 2011 - 14:03:06 PDT)
[AMBER] load parmbsc0 and X-Ol for RNA
(Fri Sep 23 2011 - 06:25:16 PDT)
[AMBER] Dihedral Rotation
(Sat Sep 17 2011 - 12:27:11 PDT)
Re: [AMBER] AMBER expense
(Fri Sep 16 2011 - 17:08:34 PDT)
[AMBER] AMBER expense
(Fri Sep 16 2011 - 13:24:23 PDT)
Dean Cuebas
Re: [AMBER] Dihedral parameters
(Thu Sep 15 2011 - 15:08:36 PDT)
Devlina Chakravarty
[AMBER] Problem with mmpbsa
(Tue Sep 13 2011 - 05:33:33 PDT)
dhilip kumar ramalingam
Re: [AMBER] Sufficient CPU cores/GPU ratio ?
(Tue Sep 13 2011 - 07:45:57 PDT)
Re: [AMBER] Problem with mmpbsa
(Tue Sep 13 2011 - 05:50:09 PDT)
Dmitry Nilov
Re: [AMBER] ambertool question !!!
(Mon Sep 26 2011 - 12:11:28 PDT)
Emmanuel Baribefe Naziga
Re: [AMBER] inpcrd file
(Wed Sep 14 2011 - 17:12:39 PDT)
Fabrício Bracht
[AMBER] Difficulties trying to derive charge for new acetylated serine
(Tue Sep 20 2011 - 22:36:32 PDT)
[AMBER] Bond command using xleap or tleap
(Wed Sep 14 2011 - 12:53:09 PDT)
[AMBER] Residue transformation
(Mon Sep 12 2011 - 15:10:10 PDT)
fatahiya
Re: [AMBER] RMSD
(Mon Sep 26 2011 - 19:08:39 PDT)
Re: [AMBER] RMSD
(Sun Sep 25 2011 - 22:00:59 PDT)
[AMBER] RMSD
(Wed Sep 21 2011 - 23:13:02 PDT)
[AMBER] inpcrd file
(Tue Sep 13 2011 - 23:47:04 PDT)
francesco oteri
Re: [AMBER] On Cationic Dummy Atom
(Thu Sep 29 2011 - 02:26:32 PDT)
Francesco Pietra
Re: [AMBER] Failure to compile AmberTools 1.5 on linux
(Fri Sep 30 2011 - 08:34:02 PDT)
[AMBER] Failure to compile AmberTools 1.5 on linux
(Fri Sep 30 2011 - 02:43:18 PDT)
Fredrick Devadoss
[AMBER] attachment for my previous mail
(Wed Sep 14 2011 - 07:00:38 PDT)
[AMBER] Need Help! (TMD - NSCM - IWRAP reg!)
(Wed Sep 14 2011 - 06:51:22 PDT)
FyD
Re: [AMBER] Failure to compile AmberTools 1.5 on linux
(Fri Sep 30 2011 - 04:57:53 PDT)
Re: [AMBER] bug in respgen ?
(Wed Sep 28 2011 - 09:03:53 PDT)
Re: [AMBER] GAMESS to RESP input file
(Mon Sep 26 2011 - 04:58:34 PDT)
Re: [AMBER] about Glycam_06g.dat and thiol-glycosidic linkage
(Mon Sep 26 2011 - 04:51:12 PDT)
Re: [AMBER] bug in respgen ?
(Mon Sep 26 2011 - 04:33:35 PDT)
Re: [AMBER] bug in respgen ?
(Mon Sep 26 2011 - 03:19:08 PDT)
Re: [AMBER] bug in respgen ?
(Fri Sep 23 2011 - 07:27:13 PDT)
Re: [AMBER] RESP charge fitting
(Fri Sep 23 2011 - 05:21:13 PDT)
Re: [AMBER] about Glycam_06g.dat and thiol-glycosidic linkage
(Fri Sep 23 2011 - 05:12:44 PDT)
Re: [AMBER] about Glycam_06g.dat and thiol-glycosidic linkage
(Fri Sep 23 2011 - 02:37:32 PDT)
Re: [AMBER] bug in respgen ?
(Thu Sep 22 2011 - 00:25:43 PDT)
Re: [AMBER] again GLYCAM06 + 99SB + GAFF ?
(Thu Sep 22 2011 - 00:12:38 PDT)
Re: [AMBER] about Glycam_06g.dat and thiol-glycosidic linkage
(Wed Sep 21 2011 - 23:45:31 PDT)
Re: [AMBER] Difficulties trying to derive charge for new acetylated serine
(Wed Sep 21 2011 - 08:55:17 PDT)
Re: [AMBER] help ! zinc parameters
(Wed Sep 21 2011 - 08:02:16 PDT)
Re: [AMBER] again GLYCAM06 + 99SB + GAFF ?
(Wed Sep 21 2011 - 00:08:17 PDT)
Re: [AMBER] help ! zinc parameters
(Tue Sep 20 2011 - 02:14:09 PDT)
Re: [AMBER] about Glycam_06g.dat and thiol-glycosidic linkage
(Tue Sep 20 2011 - 01:19:34 PDT)
Re: [AMBER] scaling factors in carbohydrate-protein interaction
(Tue Sep 20 2011 - 00:54:21 PDT)
Re: [AMBER] again GLYCAM06 + 99SB + GAFF ?
(Mon Sep 19 2011 - 04:23:41 PDT)
Re: [AMBER] scaling factors in carbohydrate-protein interaction
(Sat Sep 17 2011 - 23:14:46 PDT)
Re: [AMBER] again GLYCAM06 + 99SB + GAFF ?
(Fri Sep 16 2011 - 03:42:46 PDT)
Re: [AMBER] How to interpret GLYCAM prep file?
(Thu Sep 15 2011 - 00:54:20 PDT)
Re: [AMBER] help ! zinc parameters
(Thu Sep 15 2011 - 00:23:58 PDT)
Re: [AMBER] How to avoid Zn parametrization?
(Thu Sep 15 2011 - 00:10:18 PDT)
Re: [AMBER] again GLYCAM06 + 99SB + GAFF ?
(Tue Sep 13 2011 - 08:46:23 PDT)
Re: [AMBER] again GLYCAM06 + 99SB + GAFF ?
(Tue Sep 13 2011 - 08:41:21 PDT)
Re: [AMBER] again GLYCAM06 + 99SB + GAFF ?
(Wed Sep 07 2011 - 23:57:43 PDT)
Re: [AMBER] How to Generate Structure with Correct Valence for an Unnatural Amino Acid in Position 1
(Tue Sep 06 2011 - 08:01:41 PDT)
gal.fradin.live.biu.ac.il
Re: [AMBER] Parameters for Boron containing molecules
(Sat Sep 10 2011 - 21:57:43 PDT)
[AMBER] Parameters for Boron containing molecules
(Thu Sep 08 2011 - 05:08:16 PDT)
Garo Garabedyan
Re: [AMBER] Compiling Amber11 on Blue Gene/P
(Fri Sep 30 2011 - 01:18:53 PDT)
Re: [AMBER] Compiling Amber11 on Blue Gene/P
(Wed Sep 14 2011 - 11:33:23 PDT)
Re: [AMBER] Compiling Amber11 on Blue Gene/P
(Tue Sep 13 2011 - 23:12:20 PDT)
[AMBER] Compiling Amber11 on Blue Gene/P
(Tue Sep 13 2011 - 12:45:37 PDT)
George A. Khoury
[AMBER] How to Generate Structure with Correct Valence for an Unnatural Amino Acid in Position 1
(Tue Sep 06 2011 - 07:00:43 PDT)
George Tzotzos
Re: [AMBER] AmberTools1.5 parallel implementation of mmpbsa.py - Incomplete installation?
(Thu Sep 29 2011 - 07:07:51 PDT)
[AMBER] AmberTools1.5 parallel implementation of mmpbsa.py - Incomplete installation?
(Thu Sep 29 2011 - 06:54:50 PDT)
Re: [AMBER] MMPBSA.py discrepancies in results
(Thu Sep 29 2011 - 02:31:07 PDT)
Re: [AMBER] MMPBSA.py discrepancies in results
(Wed Sep 28 2011 - 14:43:57 PDT)
Re: [AMBER] MMPBSA.py discrepancies in results
(Wed Sep 28 2011 - 09:04:58 PDT)
Re: [AMBER] MMPBSA.py discrepancies in results
(Wed Sep 28 2011 - 08:44:13 PDT)
Re: [AMBER] MMPBSA.py discrepancies in results
(Wed Sep 28 2011 - 07:43:42 PDT)
Re: [AMBER] MMPBSA.py discrepancies in results
(Wed Sep 28 2011 - 06:33:16 PDT)
[AMBER] MMPBSA.py discrepancies in results
(Wed Sep 28 2011 - 06:20:28 PDT)
[AMBER] Failure building Amber 11 parallel on AmberTools1.5
(Tue Sep 27 2011 - 13:24:03 PDT)
Re: [AMBER] AmberTools 1.4 Installation on Mac OSX 10.6
(Sat Sep 24 2011 - 04:08:22 PDT)
[AMBER] AmberTools 1.4 Installation on Mac OSX 10.6
(Sat Sep 24 2011 - 02:41:03 PDT)
Re: [AMBER] ptraj clustering
(Mon Sep 12 2011 - 13:26:03 PDT)
[AMBER] ptraj clustering
(Mon Sep 12 2011 - 08:02:40 PDT)
Gould, Ian R
[AMBER] Quick initial impressions of PNY water cooled GTX 580 and some numbers for the usual GPU benchmarks
(Fri Sep 30 2011 - 08:15:36 PDT)
Re: [AMBER] Sufficient CPU cores/GPU ratio ?
(Tue Sep 13 2011 - 11:04:32 PDT)
Guenegou, Guillaume [JRDFR]
Re: [AMBER] Sleap and TIP4P BOX
(Fri Sep 23 2011 - 06:48:05 PDT)
Re: [AMBER] Sleap and TIP4P BOX
(Fri Sep 23 2011 - 00:22:42 PDT)
Re: [AMBER] Sleap and TIP4P BOX
(Wed Sep 21 2011 - 07:07:57 PDT)
[AMBER] Sleap and TIP4P BOX
(Wed Sep 21 2011 - 04:42:51 PDT)
[AMBER] Aromatic bonds disappear during sdf creation with sleap
(Mon Sep 12 2011 - 05:10:29 PDT)
[AMBER] Sleap : amoeba and gaff
(Mon Sep 05 2011 - 05:10:45 PDT)
Gustavo Seabra
[AMBER] Fwd: amber
(Tue Sep 13 2011 - 06:59:55 PDT)
Re: [AMBER] Fwd: false positive on too large QM region?
(Thu Sep 08 2011 - 13:13:22 PDT)
Re: [AMBER] Fwd: false positive on too large QM region?
(Thu Sep 08 2011 - 11:30:18 PDT)
Re: [AMBER] false positive on too large QM region?
(Wed Sep 07 2011 - 17:19:36 PDT)
Hernán Meier
Re: [AMBER] Large pressure fluctuations over the whole run
(Mon Sep 26 2011 - 15:04:51 PDT)
[AMBER] Large pressure fluctuations over the whole run
(Thu Sep 22 2011 - 16:14:54 PDT)
Himanshu Joshi
Re: [AMBER] Problem with pme cuda :launching kernel kPMEGetGridWeights
(Mon Sep 19 2011 - 03:49:05 PDT)
Re: [AMBER] Problem with pme cuda :launching kernel kPMEGetGridWeights
(Mon Sep 19 2011 - 02:29:31 PDT)
Re: [AMBER] Problem with pme cuda :launching kernel kPMEGetGridWeights
(Fri Sep 16 2011 - 23:29:40 PDT)
[AMBER] Problem with pme cuda :launching kernel kPMEGetGridWeights
(Fri Sep 16 2011 - 23:24:49 PDT)
Hirdesh Kumar
Re: [AMBER] Query regarding MMPBSA in Amber11
(Thu Sep 29 2011 - 21:28:11 PDT)
Re: [AMBER] Query regarding MMPBSA in Amber11
(Thu Sep 29 2011 - 01:54:29 PDT)
[AMBER] Query regarding MMPBSA in Amber11
(Wed Sep 28 2011 - 21:47:34 PDT)
[AMBER] Error: peek_ewald_inpcrd: SHOULD NOT BE HERE
(Tue Sep 20 2011 - 23:07:50 PDT)
hongphuc nguyen
[AMBER] problem with nmodes calculation-260-residue protein
(Fri Sep 23 2011 - 02:15:37 PDT)
[AMBER] FATAL: allocation failure in vector(), please help me to fix that problem
(Fri Sep 16 2011 - 01:26:55 PDT)
Re: [AMBER] Error in computing entropy! problem with number of frames in NMODE
(Thu Sep 15 2011 - 20:12:42 PDT)
[AMBER] Error in computing entropy! problem with number of frames in NMODE
(Wed Sep 14 2011 - 02:50:58 PDT)
Horacio Pérez-Sánchez
[AMBER] SASA calculation in Amber
(Wed Sep 21 2011 - 09:45:19 PDT)
Hu Ge
[AMBER] Parallel limit?
(Wed Sep 28 2011 - 20:31:37 PDT)
Hugh Heldenbrand
Re: [AMBER] Amber parmbsc0 vs ff99
(Thu Sep 22 2011 - 08:02:40 PDT)
Ignacio J. General
Re: [AMBER] Energy of solute molecule
(Mon Sep 05 2011 - 07:15:14 PDT)
InSuk Joung
Re: [AMBER] fixing rmsd values
(Mon Sep 26 2011 - 10:29:35 PDT)
Re: [AMBER] Proble related to correlation function
(Wed Sep 07 2011 - 11:26:16 PDT)
Re: [AMBER] Non-periodic behavior of NMR restraints upon restart in a periodic system
(Thu Sep 01 2011 - 12:16:56 PDT)
Irene Newhouse
[AMBER] problems with prmtops & MMGBSA
(Fri Sep 09 2011 - 18:05:58 PDT)
Ismail, Mohd F.
Re: [AMBER] problem in installing xleap
(Fri Sep 02 2011 - 09:20:04 PDT)
Re: [AMBER] solvateBox
(Fri Sep 02 2011 - 09:07:36 PDT)
Re: [AMBER] solvateBox
(Thu Sep 01 2011 - 21:02:52 PDT)
Re: [AMBER] solvateBox
(Thu Sep 01 2011 - 20:36:33 PDT)
[AMBER] solvateBox
(Thu Sep 01 2011 - 14:18:12 PDT)
Re: [AMBER] problem in installing xleap
(Wed Aug 31 2011 - 23:35:56 PDT)
Ivan Gladich
Re: [AMBER] From amber to gromacs
(Fri Sep 30 2011 - 05:02:04 PDT)
Jan-Philip Gehrcke
Re: [AMBER] Survey Request - 10 minutes of your time please to help future AMBER development (http://surveys.nvidia.com/index.jsp?pi=f7d3e68a3e1b44841571e6ab4ce2f021)
(Thu Sep 29 2011 - 04:00:16 PDT)
[AMBER] Automatic creation of charge and radius files for Delphi
(Tue Sep 20 2011 - 03:13:21 PDT)
Jason Swails
Re: [AMBER] MMPBSA: how to include only some residues
(Fri Sep 30 2011 - 16:40:28 PDT)
Re: [AMBER] Energetic analysis with MMPBSA.py considering just one molecule ?
(Fri Sep 30 2011 - 15:55:26 PDT)
Re: [AMBER] Energetic analysis with MMPBSA.py considering just one molecule ?
(Fri Sep 30 2011 - 14:11:52 PDT)
Re: [AMBER] Energetic analysis with MMPBSA.py considering just one molecule ?
(Fri Sep 30 2011 - 12:27:36 PDT)
Re: [AMBER] Amber 10/ambertool Installation error
(Fri Sep 30 2011 - 07:22:43 PDT)
Re: [AMBER] Compiling Amber11 on Blue Gene/P
(Fri Sep 30 2011 - 06:54:52 PDT)
Re: [AMBER] On Cationic Dummy Atom
(Thu Sep 29 2011 - 22:12:19 PDT)
Re: [AMBER] Query regarding MMPBSA in Amber11
(Thu Sep 29 2011 - 22:11:13 PDT)
Re: [AMBER] Energetic analysis with MMPBSA.py considering just one molecule ?
(Thu Sep 29 2011 - 22:10:47 PDT)
Re: [AMBER] Fwd: fixing rmsd values (follow-up)
(Thu Sep 29 2011 - 17:55:15 PDT)
Re: [AMBER] Energetic analysis with MMPBSA.py considering just one molecule ?
(Thu Sep 29 2011 - 15:12:20 PDT)
Re: [AMBER] how NOT to label terminal residue
(Thu Sep 29 2011 - 14:06:24 PDT)
Re: [AMBER] AmberTools1.5 parallel implementation of mmpbsa.py - Incomplete installation?
(Thu Sep 29 2011 - 07:18:31 PDT)
Re: [AMBER] Query regarding MMPBSA in Amber11
(Thu Sep 29 2011 - 06:53:18 PDT)
Re: [AMBER] PNEB on GPUs
(Thu Sep 29 2011 - 06:13:45 PDT)
Re: [AMBER] Query regarding MMPBSA in Amber11
(Wed Sep 28 2011 - 22:36:25 PDT)
Re: [AMBER] PCA
(Wed Sep 28 2011 - 22:31:11 PDT)
Re: [AMBER] Parameter files :problem to save
(Wed Sep 28 2011 - 21:39:38 PDT)
Re: [AMBER] PNEB on GPUs
(Wed Sep 28 2011 - 21:35:29 PDT)
Re: [AMBER] Parallel limit?
(Wed Sep 28 2011 - 21:14:09 PDT)
Re: [AMBER] PNEB on GPUs
(Wed Sep 28 2011 - 21:09:36 PDT)
Re: [AMBER] PNEB on GPUs
(Wed Sep 28 2011 - 21:02:32 PDT)
Re: [AMBER] MMPBSA.py discrepancies in results
(Wed Sep 28 2011 - 15:22:06 PDT)
Re: [AMBER] MMPBSA.py discrepancies in results
(Wed Sep 28 2011 - 11:43:01 PDT)
Re: [AMBER] MMPBSA.py discrepancies in results
(Wed Sep 28 2011 - 08:23:33 PDT)
Re: [AMBER] MMPBSA.py discrepancies in results
(Wed Sep 28 2011 - 07:16:55 PDT)
Re: [AMBER] sander outout using mdin=5 and idecomp=2
(Wed Sep 28 2011 - 05:58:29 PDT)
Re: [AMBER] Parallel compile error of Amber11
(Tue Sep 27 2011 - 20:40:06 PDT)
Re: [AMBER] Failure building Amber 11 parallel on AmberTools1.5
(Tue Sep 27 2011 - 17:26:16 PDT)
Re: [AMBER] dihedral parameters
(Tue Sep 27 2011 - 05:01:07 PDT)
Re: [AMBER] dihedral parameters
(Mon Sep 26 2011 - 18:08:39 PDT)
Re: [AMBER] Some common doubts about MMPBSA.py decomposition
(Mon Sep 26 2011 - 17:45:24 PDT)
Re: [AMBER] nmode calculations
(Sat Sep 24 2011 - 17:17:02 PDT)
Re: [AMBER] AmberTools 1.4 Installation on Mac OSX 10.6
(Sat Sep 24 2011 - 17:13:04 PDT)
Re: [AMBER] AmberTools 1.4 Installation on Mac OSX 10.6
(Sat Sep 24 2011 - 07:50:40 PDT)
Re: [AMBER] Amber parmbsc0 force field
(Sat Sep 24 2011 - 07:33:29 PDT)
Re: [AMBER] MMPBSA.py 3DRISM error
(Sat Sep 24 2011 - 07:29:38 PDT)
Re: [AMBER] Large pressure fluctuations over the whole run
(Thu Sep 22 2011 - 19:49:14 PDT)
Re: [AMBER] AmberTools Parallel Compilation Issue
(Thu Sep 22 2011 - 18:10:18 PDT)
Re: [AMBER] error when installing parallel sander / AmberTools1.5 Amber11
(Thu Sep 22 2011 - 17:43:14 PDT)
Re: [AMBER] XH/pi (X=C, O, N) interactions and stacking interactions in AMBER
(Thu Sep 22 2011 - 16:42:37 PDT)
Re: [AMBER] Amber parmbsc0 vs ff99
(Thu Sep 22 2011 - 09:15:28 PDT)
Re: [AMBER] Amber parmbsc0 vs ff99
(Thu Sep 22 2011 - 08:22:10 PDT)
Re: [AMBER] nmode analysis - different SCEE values in SANDMIN and NMODE output files ?
(Wed Sep 21 2011 - 21:58:09 PDT)
Re: [AMBER] nmode analysis - different SCEE values in SANDMIN and NMODE output files ?
(Wed Sep 21 2011 - 11:58:53 PDT)
Re: [AMBER] nmode analysis - different SCEE values in SANDMIN and NMODE output files ?
(Wed Sep 21 2011 - 11:21:05 PDT)
Re: [AMBER] SASA calculation in Amber
(Wed Sep 21 2011 - 10:33:56 PDT)
Re: [AMBER] iAPBS 1.2.0 - APBS 1.0.0 - Amber11 compilation error
(Tue Sep 20 2011 - 21:39:16 PDT)
Re: [AMBER] iAPBS 1.2.0 - APBS 1.0.0 - Amber11 compilation error
(Tue Sep 20 2011 - 15:19:31 PDT)
Re: [AMBER] iAPBS 1.2.0 - APBS 1.0.0 - Amber11 compilation error
(Tue Sep 20 2011 - 14:50:51 PDT)
Re: [AMBER] Instantaneous temperature in TI simulation
(Tue Sep 20 2011 - 13:08:49 PDT)
Re: [AMBER] iAPBS 1.2.0 - APBS 1.0.0 - Amber11 compilation error
(Mon Sep 19 2011 - 15:22:23 PDT)
Re: [AMBER] Unit of the partial charge as given in the topology file
(Mon Sep 19 2011 - 11:56:29 PDT)
Re: [AMBER] Serious error (or bug) with free energy decomposition MMPBSA.py..The binding free energy values differs in decomposition analysis..
(Sun Sep 18 2011 - 02:21:57 PDT)
Re: [AMBER] How to start with
(Fri Sep 16 2011 - 09:51:16 PDT)
Re: [AMBER] MMPBSA.py energy decomposition inconsistencies
(Fri Sep 16 2011 - 09:40:44 PDT)
Re: [AMBER] MMPBSA.py energy decomposition inconsistencies
(Fri Sep 16 2011 - 07:03:30 PDT)
Re: [AMBER] Dihedral parameters
(Thu Sep 15 2011 - 10:07:42 PDT)
Re: [AMBER] MMPBSA.py energy decomposition inconsistencies
(Thu Sep 15 2011 - 10:05:54 PDT)
Re: [AMBER] Dihedral parameters
(Thu Sep 15 2011 - 07:39:54 PDT)
Re: [AMBER] MMPBSA.py energy decomposition inconsistencies
(Thu Sep 15 2011 - 07:15:29 PDT)
Re: [AMBER] MMPBSA.py 3DRISM error
(Wed Sep 14 2011 - 19:15:25 PDT)
Re: [AMBER] MMPBSA.py 3DRISM error
(Wed Sep 14 2011 - 19:09:18 PDT)
Re: [AMBER] TI and MM-GBSA results
(Wed Sep 14 2011 - 10:49:33 PDT)
Re: [AMBER] AMBER
(Wed Sep 14 2011 - 10:19:24 PDT)
Re: [AMBER] Need Help! (TMD - NSCM - IWRAP reg!)
(Wed Sep 14 2011 - 07:14:20 PDT)
Re: [AMBER] MMGBSA binding free energy shows large change with saltcon parameter, but not for MMPBSA binding free energy value
(Tue Sep 13 2011 - 20:12:07 PDT)
Re: [AMBER] MMGBSA binding free energy shows large change with saltcon parameter, but not for MMPBSA binding free energy value
(Tue Sep 13 2011 - 17:43:17 PDT)
Re: [AMBER] Run amber on Cluster
(Tue Sep 13 2011 - 14:38:50 PDT)
Re: [AMBER] Amber 11 configure error with openmpi
(Mon Sep 12 2011 - 13:37:48 PDT)
Re: [AMBER] pbsa
(Mon Sep 12 2011 - 12:22:37 PDT)
Re: [AMBER] Amber 11 configure error with openmpi
(Mon Sep 12 2011 - 10:23:48 PDT)
Re: [AMBER] QM-MM atoms input
(Mon Sep 12 2011 - 06:00:13 PDT)
Re: [AMBER] Aromatic bonds disappear during sdf creation with sleap
(Mon Sep 12 2011 - 05:58:43 PDT)
Re: [AMBER] Why cut=999.9 was used in Tutorial A7 for REMD calculation?
(Mon Sep 12 2011 - 05:54:51 PDT)
Re: [AMBER] residue list
(Sun Sep 11 2011 - 20:48:31 PDT)
Re: [AMBER] problems with prmtops & MMGBSA
(Fri Sep 09 2011 - 20:12:44 PDT)
Re: [AMBER] intermolecular interaction
(Thu Sep 08 2011 - 21:00:41 PDT)
Re: [AMBER] turning on 1-2 and 1-3 interactions
(Thu Sep 08 2011 - 11:54:22 PDT)
Re: [AMBER] Parameters for Boron containing molecules
(Thu Sep 08 2011 - 08:39:58 PDT)
Re: [AMBER] MPI version of MMPBSA
(Thu Sep 08 2011 - 08:36:49 PDT)
Re: [AMBER] mbondi3
(Wed Sep 07 2011 - 12:48:41 PDT)
Re: [AMBER] results from independent simulations
(Wed Sep 07 2011 - 09:02:18 PDT)
Re: [AMBER] results from independent simulations
(Wed Sep 07 2011 - 02:17:31 PDT)
Re: [AMBER] mbondi3
(Tue Sep 06 2011 - 22:36:56 PDT)
Re: [AMBER] velocity modification in PMEMD, CUDA version
(Tue Sep 06 2011 - 22:34:27 PDT)
Re: [AMBER] Creating prmtop and inpcrd files
(Tue Sep 06 2011 - 08:44:43 PDT)
Re: [AMBER] Energy of solute molecule
(Mon Sep 05 2011 - 15:53:27 PDT)
Re: [AMBER] NAB Module compilation error cpp failed
(Mon Sep 05 2011 - 15:43:17 PDT)
Re: [AMBER] Amber tools
(Sat Sep 03 2011 - 23:04:11 PDT)
Re: [AMBER] antechamber error
(Sat Sep 03 2011 - 08:46:05 PDT)
Re: [AMBER] MM_PBSA triple trajectory approch
(Sat Sep 03 2011 - 08:23:55 PDT)
Re: [AMBER] Non standard residue parameterization
(Fri Sep 02 2011 - 20:29:37 PDT)
Re: [AMBER] Energy change
(Fri Sep 02 2011 - 10:53:06 PDT)
Re: [AMBER] Energy of solute molecule
(Fri Sep 02 2011 - 10:40:46 PDT)
Re: [AMBER] solvateBox
(Thu Sep 01 2011 - 22:42:52 PDT)
Re: [AMBER] solvateBox
(Thu Sep 01 2011 - 20:51:13 PDT)
Re: [AMBER] solvateBox
(Thu Sep 01 2011 - 18:54:44 PDT)
Re: [AMBER] solvateBox
(Thu Sep 01 2011 - 18:49:07 PDT)
Re: [AMBER] Non-periodic behavior of NMR restraints upon restart in a periodic system
(Thu Sep 01 2011 - 12:37:21 PDT)
Jed W Pitera
Re: [AMBER] Compiling Amber11 on Blue Gene/P
(Tue Sep 13 2011 - 14:09:51 PDT)
Jesper Soerensen
Re: [AMBER] MMPBSA.py 3DRISM error
(Fri Sep 23 2011 - 09:58:02 PDT)
[AMBER] MMPBSA.py 3DRISM error
(Wed Sep 14 2011 - 18:52:49 PDT)
Jesper Sørensen
Re: [AMBER] MMPBSA Ala scan error
(Tue Sep 06 2011 - 12:14:28 PDT)
Re: [AMBER] MMPBSA Ala scan error
(Tue Sep 06 2011 - 01:16:25 PDT)
[AMBER] MMPBSA Ala scan error
(Sun Sep 04 2011 - 23:41:04 PDT)
Jiri Sponer
Re: [AMBER] XH/pi (X=C, O, N) interactions and stacking interactions in AMBER
(Fri Sep 23 2011 - 08:32:52 PDT)
Re: [AMBER] Amber parmbsc0 vs ff99
(Thu Sep 22 2011 - 11:36:51 PDT)
Jodi Ann Hadden
Re: [AMBER] Sufficient CPU cores/GPU ratio ?
(Wed Sep 21 2011 - 10:54:08 PDT)
Re: [AMBER] Sufficient CPU cores/GPU ratio ?
(Fri Sep 16 2011 - 11:39:03 PDT)
Re: [AMBER] Sufficient CPU cores/GPU ratio ?
(Wed Sep 14 2011 - 08:50:21 PDT)
John S
[AMBER] moment of inertia
(Tue Sep 06 2011 - 11:27:40 PDT)
Jorge Iulek
Re: [AMBER] thermodynamic integration on protein mutation
(Tue Sep 27 2011 - 09:09:59 PDT)
[AMBER] thermodynamic integration on protein mutation
(Mon Sep 26 2011 - 17:34:51 PDT)
Julian Zachmann
[AMBER] Restart-Files in Sander
(Thu Sep 22 2011 - 06:11:00 PDT)
[AMBER] Global Minimum in Simulated Annealing using SANDER
(Tue Sep 13 2011 - 07:12:00 PDT)
jun kit
Re: [AMBER] force field of molecular crystals
(Mon Sep 19 2011 - 12:05:20 PDT)
[AMBER] force field of molecular crystals
(Mon Sep 19 2011 - 11:20:25 PDT)
[AMBER] Some question regarding force field for periodic system
(Tue Sep 06 2011 - 21:24:02 PDT)
K T
Re: [AMBER] error when installing parallel sander / AmberTools1.5 Amber11
(Thu Sep 22 2011 - 17:28:31 PDT)
kamlesh sahu
[AMBER] charges on ligand
(Mon Sep 19 2011 - 22:58:18 PDT)
Karl N. Kirschner
Re: [AMBER] about Glycam_06g.dat and thiol-glycosidic linkage
(Fri Sep 23 2011 - 03:10:57 PDT)
Kasprzak, Wojciech (NIH/NCI) [C]
[AMBER] GB protocol problems for large RNAs (follow-up)
(Tue Sep 27 2011 - 07:09:10 PDT)
[AMBER] GB protocol problems for large RNAs
(Thu Sep 22 2011 - 09:02:28 PDT)
Keith Yarem
Re: [AMBER] Non-periodic behavior of NMR restraints upon restart in a periodic system
(Thu Sep 01 2011 - 11:40:54 PDT)
Re: [AMBER] Non-periodic behavior of NMR restraints upon restart in a periodic system
(Thu Sep 01 2011 - 11:23:03 PDT)
Kenneth Tussey
Re: [AMBER] iAPBS 1.2.0 - APBS 1.0.0 - Amber11 compilation error
(Tue Sep 20 2011 - 15:05:00 PDT)
Re: [AMBER] iAPBS 1.2.0 - APBS 1.0.0 - Amber11 compilation error
(Tue Sep 20 2011 - 13:12:07 PDT)
[AMBER] iAPBS 1.2.0 - APBS 1.0.0 - Amber11 compilation error
(Mon Sep 19 2011 - 13:47:21 PDT)
kirtana S
[AMBER] Parameters
(Fri Sep 30 2011 - 19:14:57 PDT)
[AMBER] force field modification
(Thu Sep 29 2011 - 09:46:18 PDT)
Re: [AMBER] dihedral parameters
(Tue Sep 27 2011 - 14:59:00 PDT)
[AMBER] dihedral parameters
(Mon Sep 26 2011 - 14:09:39 PDT)
Re: [AMBER] nmode calculations
(Sun Sep 25 2011 - 09:58:52 PDT)
[AMBER] nmode calculations
(Fri Sep 23 2011 - 14:52:11 PDT)
[AMBER] Radial distribution
(Fri Sep 16 2011 - 10:09:19 PDT)
Re: [AMBER] energy
(Wed Sep 14 2011 - 09:40:21 PDT)
[AMBER] energy
(Wed Sep 14 2011 - 08:02:14 PDT)
Re: [AMBER] pbsa
(Mon Sep 12 2011 - 19:01:17 PDT)
Re: [AMBER] pbsa
(Mon Sep 12 2011 - 11:42:44 PDT)
Re: [AMBER] pbsa
(Mon Sep 12 2011 - 09:05:17 PDT)
[AMBER] pbsa
(Mon Sep 12 2011 - 08:56:44 PDT)
[AMBER] residue list
(Sun Sep 11 2011 - 19:40:52 PDT)
Re: [AMBER] Amber tools
(Sun Sep 04 2011 - 20:58:20 PDT)
Re: [AMBER] Energy change
(Sun Sep 04 2011 - 22:31:45 PDT)
Re: [AMBER] Energy
(Mon Sep 05 2011 - 13:51:15 PDT)
[AMBER] Energy
(Mon Sep 05 2011 - 11:56:34 PDT)
[AMBER] Amber tools
(Sat Sep 03 2011 - 22:05:35 PDT)
Re: [AMBER] Energy change
(Fri Sep 02 2011 - 10:43:55 PDT)
[AMBER] Energy change
(Thu Sep 01 2011 - 13:09:19 PDT)
Kk Zhu
Re: [AMBER] help ! zinc parameters
(Wed Sep 21 2011 - 00:06:52 PDT)
[AMBER] help! zinc parameters
(Mon Sep 19 2011 - 05:46:05 PDT)
[AMBER] help ! zinc parameters
(Thu Sep 15 2011 - 23:46:06 PDT)
[AMBER] help ! zinc parameters
(Wed Sep 14 2011 - 19:48:36 PDT)
Kshatresh Dutta Dubey
[AMBER] Amber 10/ambertool Installation error
(Fri Sep 30 2011 - 06:12:59 PDT)
[AMBER] Parameters from Jaguar output
(Mon Sep 12 2011 - 22:09:29 PDT)
kurisaki
Re: [AMBER] sander outout using mdin=5 and idecomp=2
(Wed Sep 28 2011 - 07:01:13 PDT)
Re: [AMBER] sander outout using mdin=5 and idecomp=2
(Wed Sep 28 2011 - 06:37:57 PDT)
[AMBER] sander outout using mdin=5 and idecomp=2
(Wed Sep 28 2011 - 02:13:18 PDT)
Re: [AMBER] PMEMD job was aborted
(Wed Sep 28 2011 - 01:53:09 PDT)
[AMBER] PMEMD job was aborted
(Wed Sep 28 2011 - 00:00:15 PDT)
Re: [AMBER] Parallel compile error of Amber11
(Tue Sep 27 2011 - 23:29:01 PDT)
[AMBER] Parallel compile error of Amber11
(Tue Sep 27 2011 - 20:30:52 PDT)
Lachele Foley (Lists)
Re: [AMBER] How to build the surface of crystalline cellulose?
(Wed Sep 21 2011 - 06:06:16 PDT)
Re: [AMBER] Glycam06g and ff99SB cause the difference of DIHED (not attributed to the scaling factor)
(Mon Sep 19 2011 - 06:56:41 PDT)
Re: [AMBER] scaling factors in carbohydrate-protein interaction
(Sun Sep 18 2011 - 15:12:36 PDT)
Re: [AMBER] scaling factors in carbohydrate-protein interaction
(Sat Sep 17 2011 - 19:22:31 PDT)
Re: [AMBER] about Glycam_06g.dat and thiol-glycosidic linkage
(Thu Sep 15 2011 - 13:37:09 PDT)
Re: [AMBER] about Glycam_06g.dat and thiol-glycosidic linkage
(Thu Sep 15 2011 - 11:39:44 PDT)
Re: [AMBER] about Glycam_06g.dat and thiol-glycosidic linkage
(Thu Sep 15 2011 - 10:41:01 PDT)
Re: [AMBER] about Glycam_06g.dat and thiol-glycosidic linkage
(Thu Sep 15 2011 - 08:32:33 PDT)
Re: [AMBER] How to interpret GLYCAM prep file?
(Thu Sep 15 2011 - 07:37:15 PDT)
Re: [AMBER] How to interpret GLYCAM prep file?
(Fri Sep 09 2011 - 07:52:18 PDT)
Lars Skjærven
Re: [AMBER] undefined reference
(Tue Sep 13 2011 - 07:03:39 PDT)
[AMBER] undefined reference
(Tue Sep 13 2011 - 05:48:56 PDT)
Lianhu Wei
Re: [AMBER] Run amber on Cluster
(Wed Sep 14 2011 - 11:10:28 PDT)
Re: [AMBER] Run amber on Cluster
(Wed Sep 14 2011 - 08:01:37 PDT)
[AMBER] Run amber on Cluster
(Tue Sep 13 2011 - 12:46:17 PDT)
Re: [AMBER] Amber 11 configure error with openmpi
(Tue Sep 13 2011 - 07:49:36 PDT)
[AMBER] Amber 11 configure error with openmpi
(Mon Sep 12 2011 - 10:14:33 PDT)
Linda catherine
[AMBER] PCA
(Wed Sep 28 2011 - 04:44:31 PDT)
[AMBER] ptraj
(Fri Sep 16 2011 - 06:03:14 PDT)
[AMBER] hello
(Wed Sep 14 2011 - 05:16:27 PDT)
Lorenzo Gontrani
Re: [AMBER] Grid and SDF - sorry for the mail spamming
(Thu Sep 22 2011 - 22:49:06 PDT)
[AMBER] Grid and SDF
(Thu Sep 22 2011 - 00:40:41 PDT)
[AMBER] GRID and SDF
(Thu Sep 22 2011 - 00:28:08 PDT)
[AMBER] Grid and SDF
(Wed Sep 21 2011 - 06:24:50 PDT)
[AMBER] Grid and SDF
(Wed Sep 21 2011 - 03:53:47 PDT)
M. L. Dodson
Re: [AMBER] Chromophore Building
(Tue Sep 27 2011 - 12:55:49 PDT)
Re: [AMBER] Difficulties trying to derive charge for new acetylated serine
(Wed Sep 21 2011 - 06:18:28 PDT)
Re: [AMBER] Residue transformation
(Mon Sep 12 2011 - 20:52:35 PDT)
madhumita das
[AMBER] From amber to gromacs
(Fri Sep 30 2011 - 01:31:44 PDT)
[AMBER] topology and coordinate files
(Tue Sep 20 2011 - 04:14:58 PDT)
Re: [AMBER] Non standard residue parameterization
(Mon Sep 05 2011 - 23:22:26 PDT)
Re: [AMBER] Non standard residue parameterization
(Mon Sep 05 2011 - 23:15:46 PDT)
Re: [AMBER] Non standard residue parameterization
(Mon Sep 05 2011 - 08:47:30 PDT)
[AMBER] Non standard residue parameterization
(Fri Sep 02 2011 - 03:20:19 PDT)
manikanthan bhavaraju
Re: [AMBER] TI and MM-GBSA results
(Wed Sep 14 2011 - 10:46:04 PDT)
[AMBER] TI and MM-GBSA results
(Tue Sep 13 2011 - 17:33:06 PDT)
Re: [AMBER] vlimit exeeding problem
(Mon Sep 12 2011 - 08:05:30 PDT)
Re: [AMBER] Amber tools
(Tue Sep 06 2011 - 07:04:49 PDT)
Re: [AMBER] Energy change
(Mon Sep 05 2011 - 13:58:41 PDT)
Re: [AMBER] Amber tools
(Sat Sep 03 2011 - 22:09:45 PDT)
Marc van der Kamp
Re: [AMBER] ptraj: problem with distance and multi-atom masks
(Tue Sep 20 2011 - 07:24:07 PDT)
Re: [AMBER] ptraj: problem with distance and multi-atom masks
(Tue Sep 20 2011 - 02:32:34 PDT)
[AMBER] ptraj: problem with distance and multi-atom masks
(Mon Sep 19 2011 - 02:32:47 PDT)
[AMBER] Problems with parsing .PSF files by ptraj
(Fri Sep 16 2011 - 03:14:02 PDT)
Re: [AMBER] X-PLOR formatted .psf in CHAMBER
(Thu Sep 15 2011 - 07:09:02 PDT)
Re: [AMBER] X-PLOR formatted .psf in CHAMBER
(Thu Sep 15 2011 - 06:26:14 PDT)
[AMBER] X-PLOR formatted .psf in CHAMBER
(Thu Sep 15 2011 - 05:19:29 PDT)
Re: [AMBER] QM-MM atoms input
(Mon Sep 12 2011 - 05:12:26 PDT)
Marek Maly
Re: [AMBER] Energetic analysis with MMPBSA.py considering just one molecule ?
(Fri Sep 30 2011 - 14:26:23 PDT)
Re: [AMBER] Energetic analysis with MMPBSA.py considering just one molecule ?
(Fri Sep 30 2011 - 13:35:23 PDT)
Re: [AMBER] Energetic analysis with MMPBSA.py considering just one molecule ?
(Fri Sep 30 2011 - 09:23:27 PDT)
Re: [AMBER] Energetic analysis with MMPBSA.py considering just one molecule ?
(Thu Sep 29 2011 - 19:34:43 PDT)
[AMBER] Energetic analysis with MMPBSA.py considering just one molecule ?
(Thu Sep 29 2011 - 14:32:09 PDT)
Re: [AMBER] Amber parmbsc0 vs ff99
(Thu Sep 22 2011 - 09:06:56 PDT)
Re: [AMBER] Amber parmbsc0 vs ff99
(Thu Sep 22 2011 - 08:43:12 PDT)
Re: [AMBER] Amber parmbsc0 vs ff99
(Thu Sep 22 2011 - 07:54:45 PDT)
Re: [AMBER] nmode analysis - different SCEE values in SANDMIN and NMODE output files ?
(Thu Sep 22 2011 - 04:58:49 PDT)
Re: [AMBER] nmode analysis - different SCEE values in SANDMIN and NMODE output files ?
(Wed Sep 21 2011 - 16:11:28 PDT)
Re: [AMBER] nmode analysis - different SCEE values in SANDMIN and NMODE output files ?
(Wed Sep 21 2011 - 16:00:48 PDT)
Re: [AMBER] nmode analysis - different SCEE values in SANDMIN and NMODE output files ?
(Wed Sep 21 2011 - 11:19:15 PDT)
Re: [AMBER] Sufficient CPU cores/GPU ratio ?
(Wed Sep 21 2011 - 11:10:06 PDT)
[AMBER] nmode analysis - different SCEE values in SANDMIN and NMODE output files ?
(Wed Sep 21 2011 - 10:56:43 PDT)
Re: [AMBER] Sufficient CPU cores/GPU ratio ?
(Sun Sep 18 2011 - 07:34:21 PDT)
Re: [AMBER] Sufficient CPU cores/GPU ratio ?
(Sat Sep 17 2011 - 16:08:48 PDT)
Re: [AMBER] Effect of SLI for Amber GPU calculations - AMD Bulldozers ?
(Thu Sep 15 2011 - 11:59:51 PDT)
Re: [AMBER] Effect of SLI for Amber GPU calculations - AMD Bulldozers ?
(Thu Sep 15 2011 - 11:15:37 PDT)
[AMBER] Effect of SLI for Amber GPU calculations - AMD Bulldozers ?
(Thu Sep 15 2011 - 09:52:13 PDT)
Re: [AMBER] Sufficient CPU cores/GPU ratio ?
(Wed Sep 14 2011 - 18:01:15 PDT)
Re: [AMBER] Sufficient CPU cores/GPU ratio ?
(Wed Sep 14 2011 - 17:15:32 PDT)
Re: [AMBER] Sufficient CPU cores/GPU ratio ?
(Tue Sep 13 2011 - 13:47:09 PDT)
Re: [AMBER] Sufficient CPU cores/GPU ratio ?
(Tue Sep 13 2011 - 11:41:28 PDT)
Re: [AMBER] Sufficient CPU cores/GPU ratio ?
(Tue Sep 13 2011 - 11:06:09 PDT)
Re: [AMBER] Sufficient CPU cores/GPU ratio ?
(Tue Sep 13 2011 - 11:00:47 PDT)
Re: [AMBER] Sufficient CPU cores/GPU ratio ?
(Tue Sep 13 2011 - 10:50:02 PDT)
Re: [AMBER] Sufficient CPU cores/GPU ratio ?
(Tue Sep 13 2011 - 10:17:12 PDT)
Re: [AMBER] Sufficient CPU cores/GPU ratio ?
(Tue Sep 13 2011 - 09:52:55 PDT)
Re: [AMBER] Sufficient CPU cores/GPU ratio ?
(Tue Sep 13 2011 - 07:34:01 PDT)
[AMBER] Sufficient CPU cores/GPU ratio ?
(Tue Sep 13 2011 - 07:19:29 PDT)
Mariano Rech
Re: [AMBER] Fwd: fixing rmsd values (follow-up)
(Wed Sep 28 2011 - 23:34:46 PDT)
Mark Williamson
Re: [AMBER] writing box info to pdb file extracted from an mdcrd trajectory
(Wed Sep 07 2011 - 06:51:42 PDT)
Maryam Hamzehee
Re: [AMBER] problem with MM-PBSA
(Wed Sep 07 2011 - 10:45:20 PDT)
[AMBER] problem with MM-PBSA
(Tue Sep 06 2011 - 01:55:41 PDT)
Massimiliano Porrini
Re: [AMBER] Fwd: fixing rmsd values (follow-up)
(Wed Sep 28 2011 - 11:10:52 PDT)
Re: [AMBER] Fwd: fixing rmsd values (follow-up)
(Wed Sep 28 2011 - 04:26:29 PDT)
[AMBER] Fwd: fixing rmsd values (follow-up)
(Tue Sep 27 2011 - 11:44:14 PDT)
Re: [AMBER] fixing rmsd values
(Mon Sep 26 2011 - 10:18:47 PDT)
Re: [AMBER] fixing rmsd values
(Mon Sep 26 2011 - 07:46:52 PDT)
[AMBER] fixing rmsd values
(Sun Sep 25 2011 - 08:22:13 PDT)
Re: [AMBER] radial distribution function
(Sun Sep 18 2011 - 10:15:21 PDT)
[AMBER] Initial plateau of the radial distribution function
(Fri Sep 16 2011 - 03:16:23 PDT)
[AMBER] radial distribution function
(Thu Sep 15 2011 - 05:27:03 PDT)
matheus froeyen
Re: [AMBER] error when installing parallel sander / AmberTools1.5 Amber11
(Fri Sep 23 2011 - 01:49:50 PDT)
[AMBER] error when installing parallel sander / AmberTools1.5 Amber11
(Thu Sep 22 2011 - 10:56:18 PDT)
Mattei, Alessandra
[AMBER] Energy of solute molecule
(Fri Sep 02 2011 - 10:31:35 PDT)
Matteo Guglielmi
Re: [AMBER] AmberTools Parallel Compilation Issue
(Sat Sep 24 2011 - 08:03:03 PDT)
Re: [AMBER] AmberTools Parallel Compilation Issue
(Fri Sep 23 2011 - 12:06:59 PDT)
Re: [AMBER] AmberTools Parallel Compilation Issue
(Fri Sep 23 2011 - 08:21:53 PDT)
Re: [AMBER] AmberTools Parallel Compilation Issue
(Fri Sep 23 2011 - 02:06:56 PDT)
[AMBER] AmberTools Parallel Compilation Issue
(Thu Sep 22 2011 - 17:59:09 PDT)
Matthew Tessier
Re: [AMBER] about Glycam_06g.dat and thiol-glycosidic linkage
(Fri Sep 23 2011 - 10:48:41 PDT)
Re: [AMBER] about Glycam_06g.dat and thiol-glycosidic linkage
(Thu Sep 22 2011 - 11:25:12 PDT)
Re: [AMBER] again GLYCAM06 + 99SB + GAFF ?
(Wed Sep 21 2011 - 19:04:38 PDT)
Re: [AMBER] about Glycam_06g.dat and thiol-glycosidic linkage
(Wed Sep 21 2011 - 06:46:14 PDT)
Re: [AMBER] about Glycam_06g.dat and thiol-glycosidic linkage
(Mon Sep 19 2011 - 07:41:30 PDT)
Re: [AMBER] about Glycam_06g.dat and thiol-glycosidic linkage
(Thu Sep 15 2011 - 11:53:30 PDT)
Mengjuei Hsieh
Re: [AMBER] AmberTools 1.4 Installation on Mac OSX 10.6
(Sat Sep 24 2011 - 08:31:23 PDT)
Re: [AMBER] Difference between serial and parallel MMPBSA
(Thu Sep 22 2011 - 12:58:45 PDT)
mish
Re: [AMBER] Glycam06g and ff99SB cause the difference of DIHED (not attributed to the scaling factor)
(Sun Sep 18 2011 - 23:15:53 PDT)
Nadine Utz
Re: [AMBER] Amber parmbsc0
(Thu Sep 22 2011 - 00:52:00 PDT)
[AMBER] visualization of secstruc with e.g. gnuplot
(Tue Sep 13 2011 - 04:07:16 PDT)
Neha Gandhi
[AMBER] solvateBox or setBox or set box
(Tue Sep 27 2011 - 23:36:29 PDT)
[AMBER] AMOEBA potentials
(Thu Sep 15 2011 - 02:43:14 PDT)
Niel Henriksen
Re: [AMBER] GB protocol problems for large RNAs (follow-up)
(Tue Sep 27 2011 - 09:42:32 PDT)
Re: [AMBER] fixing rmsd values
(Mon Sep 26 2011 - 10:29:22 PDT)
Re: [AMBER] fixing rmsd values
(Sun Sep 25 2011 - 08:47:23 PDT)
Re: [AMBER] Dihedral Rotation
(Mon Sep 19 2011 - 19:40:58 PDT)
Osman, Roman
Re: [AMBER] Difference between serial and parallel MMPBSA
(Thu Sep 22 2011 - 13:07:26 PDT)
Re: [AMBER] Difference between serial and parallel MMPBSA
(Sat Sep 17 2011 - 08:23:38 PDT)
[AMBER] Difference between serial and parallel MMPBSA
(Fri Sep 16 2011 - 15:18:41 PDT)
Oteri Francesco
Re: [AMBER] help ! zinc parameters
(Fri Sep 16 2011 - 08:37:07 PDT)
Ozen, Aysegul
Re: [AMBER] Water density/potential visualization
(Thu Sep 08 2011 - 10:57:03 PDT)
peker milas
Re: [AMBER] moment of inertia
(Tue Sep 06 2011 - 11:51:04 PDT)
Re: [AMBER] problem in installing xleap
(Fri Sep 02 2011 - 10:21:38 PDT)
[AMBER] PTRAJ strange behavior
(Thu Sep 01 2011 - 12:39:38 PDT)
Peter Varnai
Re: [AMBER] mbondi3
(Wed Sep 07 2011 - 10:28:39 PDT)
[AMBER] mbondi3
(Tue Sep 06 2011 - 10:56:31 PDT)
peter.stauffert.boehringer-ingelheim.com
Re: [AMBER] Running amber v11 over multiple gpus/nodes
(Wed Sep 14 2011 - 04:37:00 PDT)
Re: [AMBER] Sufficient CPU cores/GPU ratio ?
(Tue Sep 13 2011 - 10:57:29 PDT)
[AMBER] Run Amber on a system with multiple GPUs
(Fri Sep 02 2011 - 10:55:35 PDT)
Praapti Jayaswal
Re: [AMBER] cpptraj-segmentation fault
(Mon Sep 19 2011 - 22:57:09 PDT)
Re: [AMBER] cpptraj-segmentation fault
(Thu Sep 15 2011 - 21:19:40 PDT)
Re: [AMBER] cpptraj-segmentation fault
(Mon Sep 12 2011 - 21:37:17 PDT)
Re: [AMBER] cpptraj-segmentation fault
(Sun Sep 11 2011 - 23:58:39 PDT)
Re: [AMBER] cpptraj-segmentation fault
(Sun Sep 04 2011 - 21:01:05 PDT)
[AMBER] cpptraj-segmentation fault
(Wed Aug 31 2011 - 23:02:24 PDT)
Qian Wang
[AMBER] umbrella sampling with amber10
(Tue Sep 06 2011 - 13:42:28 PDT)
Qiantao Wang
Re: [AMBER] Instantaneous temperature in TI simulation
(Wed Sep 28 2011 - 13:12:44 PDT)
Re: [AMBER] Instantaneous temperature in TI simulation
(Sun Sep 25 2011 - 06:26:54 PDT)
Re: [AMBER] Instantaneous temperature in TI simulation
(Fri Sep 23 2011 - 12:25:06 PDT)
Re: [AMBER] Instantaneous temperature in TI simulation
(Fri Sep 23 2011 - 12:08:41 PDT)
Re: [AMBER] XH/pi (X=C, O, N) interactions and stacking interactions in AMBER
(Fri Sep 23 2011 - 07:41:08 PDT)
Re: [AMBER] Help needed for Amber SCC-DFTB code
(Wed Sep 21 2011 - 14:44:56 PDT)
Re: [AMBER] Instantaneous temperature in TI simulation
(Wed Sep 21 2011 - 14:12:01 PDT)
Re: [AMBER] Instantaneous temperature in TI simulation
(Wed Sep 21 2011 - 12:43:09 PDT)
Re: [AMBER] Instantaneous temperature in TI simulation
(Tue Sep 20 2011 - 12:33:51 PDT)
Re: [AMBER] Fwd: false positive on too large QM region?
(Thu Sep 08 2011 - 14:34:44 PDT)
qiao xue
[AMBER] Problems of Hbond calculation
(Sun Sep 25 2011 - 19:30:33 PDT)
Rajesh Raju
[AMBER] Some common doubts about MMPBSA.py decomposition
(Mon Sep 26 2011 - 18:13:08 PDT)
[AMBER] Some common doubts about MMPBSA.py decomposition
(Mon Sep 26 2011 - 12:24:36 PDT)
[AMBER] XH/pi (X=C, O, N) interactions and stacking interactions in AMBER
(Thu Sep 22 2011 - 16:24:39 PDT)
Re: [AMBER] Serious error (or bug) with free energy decomposition MMPBSA.py..The binding free energy values differs in decomposition analysis..
(Sun Sep 18 2011 - 11:34:22 PDT)
Re: [AMBER] Serious error (or bug) with free energy decomposition MMPBSA.py..The binding free energy values differs in decomposition analysis..
(Sat Sep 17 2011 - 14:16:34 PDT)
[AMBER] Serious error (or bug) with free energy decomposition MMPBSA.py..The binding free energy values differs in decomposition analysis..
(Sat Sep 17 2011 - 13:43:31 PDT)
Re: [AMBER] How to mutate nucleobases
(Sat Sep 17 2011 - 09:41:08 PDT)
[AMBER] How to mutate nucleobases
(Fri Sep 16 2011 - 13:42:13 PDT)
Re: [AMBER] MMGBSA binding free energy shows large change with saltcon parameter, but not for MMPBSA binding free energy value
(Tue Sep 13 2011 - 17:59:59 PDT)
[AMBER] MMGBSA binding free energy shows large change with saltcon parameter, but not for MMPBSA binding free energy value
(Tue Sep 13 2011 - 16:48:12 PDT)
[AMBER] NAB Module compilation error cpp failed
(Mon Sep 05 2011 - 10:36:00 PDT)
[AMBER] NAB Module compilation error cpp failed
(Mon Sep 05 2011 - 10:49:53 PDT)
Rajeswari A.
Re: [AMBER] Chirality restraints
(Thu Sep 29 2011 - 05:42:52 PDT)
[AMBER] Chirality restraints
(Thu Sep 29 2011 - 00:06:40 PDT)
RANAJIT SHINDE
[AMBER] Minimum distance
(Wed Sep 07 2011 - 00:00:24 PDT)
Ray Luo, Ph.D.
Re: [AMBER] Difference between serial and parallel MMPBSA
(Fri Sep 16 2011 - 20:33:19 PDT)
Re: [AMBER] TI and MM-GBSA results
(Wed Sep 14 2011 - 10:21:32 PDT)
Re: [AMBER] pbsa
(Tue Sep 13 2011 - 11:50:31 PDT)
[AMBER] Fwd: pbsa
(Mon Sep 12 2011 - 10:24:23 PDT)
Re: [AMBER] pbsa
(Mon Sep 12 2011 - 09:00:20 PDT)
Rilei Yu
Re: [AMBER] Electrpostatic interaction vs Coulombic interaction
(Wed Sep 14 2011 - 23:52:17 PDT)
[AMBER] Electrpostatic interaction vs Coulombic interaction
(Wed Sep 14 2011 - 17:48:08 PDT)
Robert Konecny
Re: [AMBER] iAPBS 1.2.0 - APBS 1.0.0 - Amber11 compilation error
(Tue Sep 20 2011 - 20:22:46 PDT)
Romelia Salomon
Re: [AMBER] problems with prmtops & MMGBSA
(Fri Sep 09 2011 - 18:23:54 PDT)
Ross Walker
Re: [AMBER] Survey Request - 10 minutes of your time please to help future AMBER development (http://surveys.nvidia.com/index.jsp?pi=f7d3e68a3e1b44841571e6ab4ce2f021)
(Thu Sep 29 2011 - 07:38:08 PDT)
Re: [AMBER] 1st DNA tutorial cannot save parameter
(Wed Sep 28 2011 - 21:49:17 PDT)
Re: [AMBER] Parameter files :problem to save
(Wed Sep 28 2011 - 21:48:40 PDT)
Re: [AMBER] Parameter files :problem to save
(Wed Sep 28 2011 - 21:43:28 PDT)
Re: [AMBER] Parallel limit?
(Wed Sep 28 2011 - 21:20:28 PDT)
Re: [AMBER] PNEB on GPUs
(Wed Sep 28 2011 - 21:16:06 PDT)
Re: [AMBER] PNEB on GPUs
(Wed Sep 28 2011 - 21:01:50 PDT)
Re: [AMBER] Parallel limit?
(Wed Sep 28 2011 - 20:45:38 PDT)
[AMBER] Survey Request - 10 minutes of your time please to help future AMBER development (http://surveys.nvidia.com/index.jsp?pi=f7d3e68a3e1b44841571e6ab4ce2f021)
(Wed Sep 28 2011 - 19:01:08 PDT)
[AMBER] Announcing the NVIDIA MD SimCluster Program (Free test drives available)
(Wed Sep 28 2011 - 14:29:36 PDT)
Re: [AMBER] PMEMD job was aborted
(Wed Sep 28 2011 - 00:09:52 PDT)
Re: [AMBER] GB protocol problems for large RNAs (follow-up)
(Tue Sep 27 2011 - 09:13:32 PDT)
Re: [AMBER] AmberTools Parallel Compilation Issue
(Fri Sep 23 2011 - 12:26:11 PDT)
Re: [AMBER] error when installing parallel sander / AmberTools1.5 Amber11
(Thu Sep 22 2011 - 11:05:10 PDT)
Re: [AMBER] GB protocol problems for large RNAs
(Thu Sep 22 2011 - 09:30:46 PDT)
Re: [AMBER] Different Temps Coupling
(Wed Sep 21 2011 - 12:42:53 PDT)
[AMBER] tx/LEaP numlock.
(Tue Sep 20 2011 - 09:38:01 PDT)
Re: [AMBER] Problem with pme cuda :launching kernel kPMEGetGridWeights
(Mon Sep 19 2011 - 08:05:02 PDT)
Re: [AMBER] Problem with pme cuda :launching kernel kPMEGetGridWeights
(Mon Sep 19 2011 - 08:00:27 PDT)
Re: [AMBER] scaling factors in carbohydrate-protein interaction
(Sun Sep 18 2011 - 18:13:59 PDT)
Re: [AMBER] Sufficient CPU cores/GPU ratio ?
(Sat Sep 17 2011 - 17:01:49 PDT)
Re: [AMBER] Problem with pme cuda :launching kernel kPMEGetGridWeights
(Sat Sep 17 2011 - 16:50:40 PDT)
Re: [AMBER] Serial Version of libFpbsa.a
(Fri Sep 16 2011 - 11:27:37 PDT)
Re: [AMBER] Running amber v11 over multiple gpus/nodes
(Fri Sep 16 2011 - 09:30:58 PDT)
Re: [AMBER] help ! zinc parameters
(Fri Sep 16 2011 - 09:18:15 PDT)
Re: [AMBER] Effect of SLI for Amber GPU calculations - AMD Bulldozers ?
(Thu Sep 15 2011 - 10:37:01 PDT)
Re: [AMBER] benchmarking Tesla S2050 1U system
(Wed Sep 14 2011 - 12:41:19 PDT)
Re: [AMBER] Compiling Amber11 on Blue Gene/P
(Wed Sep 14 2011 - 12:20:45 PDT)
Re: [AMBER] Running amber v11 over multiple gpus/nodes
(Wed Sep 14 2011 - 10:55:03 PDT)
Re: [AMBER] Run amber on Cluster
(Wed Sep 14 2011 - 10:14:02 PDT)
Re: [AMBER] Sufficient CPU cores/GPU ratio ?
(Tue Sep 13 2011 - 11:40:56 PDT)
Re: [AMBER] Sufficient CPU cores/GPU ratio ?
(Tue Sep 13 2011 - 11:40:56 PDT)
Re: [AMBER] Sufficient CPU cores/GPU ratio ?
(Tue Sep 13 2011 - 10:25:20 PDT)
Re: [AMBER] Sufficient CPU cores/GPU ratio ?
(Tue Sep 13 2011 - 09:53:34 PDT)
Re: [AMBER] vlimit exeeding problem
(Mon Sep 12 2011 - 22:57:43 PDT)
Re: [AMBER] vlimit exeeding problem
(Mon Sep 12 2011 - 22:16:19 PDT)
Re: [AMBER] Fwd: false positive on too large QM region?
(Thu Sep 08 2011 - 12:43:45 PDT)
Re: [AMBER] velocity modification in PMEMD, CUDA version
(Tue Sep 06 2011 - 20:10:29 PDT)
Sangita Kachhap
Re: [AMBER] Model building
(Thu Sep 29 2011 - 10:54:09 PDT)
Re: [AMBER] How to mutate nucleobases
(Sat Sep 17 2011 - 09:03:04 PDT)
Re: [AMBER] MM_PBSA triple trajectory approch
(Sun Sep 04 2011 - 00:03:16 PDT)
Re: [AMBER] MM_PBSA triple trajectory approch
(Sat Sep 03 2011 - 06:08:57 PDT)
[AMBER] MM_PBSA triple trajectory approch
(Sat Sep 03 2011 - 05:00:33 PDT)
Sara Ahmadi
[AMBER] Hydrogen Bonding
(Thu Sep 08 2011 - 04:22:34 PDT)
Sasha Buzko
Re: [AMBER] Run Amber on a system with multiple GPUs
(Fri Sep 02 2011 - 16:27:21 PDT)
Scott Le Grand
Re: [AMBER] Quick initial impressions of PNY water cooled GTX 580 and some numbers for the usual GPU benchmarks
(Fri Sep 30 2011 - 11:04:28 PDT)
Re: [AMBER] Parallel limit?
(Thu Sep 29 2011 - 10:02:54 PDT)
Re: [AMBER] Effect of SLI for Amber GPU calculations - AMD Bulldozers ?
(Thu Sep 15 2011 - 12:05:50 PDT)
Re: [AMBER] Sufficient CPU cores/GPU ratio ?
(Wed Sep 14 2011 - 17:51:33 PDT)
Re: [AMBER] Sufficient CPU cores/GPU ratio ?
(Tue Sep 13 2011 - 12:50:30 PDT)
Re: [AMBER] Sufficient CPU cores/GPU ratio ?
(Tue Sep 13 2011 - 11:15:27 PDT)
Sergey Samsonov
[AMBER] SMD: restraints on the pulled apart interacting proteins
(Fri Sep 09 2011 - 07:39:36 PDT)
Shesh Nath
[AMBER] AMBER
(Wed Sep 14 2011 - 00:00:24 PDT)
shome sankar bhunia
[AMBER] GAMESS to RESP input file
(Mon Sep 26 2011 - 03:46:25 PDT)
[AMBER] RESP charge fitting
(Fri Sep 23 2011 - 04:22:37 PDT)
Shruti Koulgi
Re: [AMBER] QM-MM atoms input
(Mon Sep 12 2011 - 04:18:03 PDT)
[AMBER] QM-MM atoms input
(Mon Sep 12 2011 - 04:00:58 PDT)
Siavoush Dastmalchi
Re: [AMBER] MPI version of MMPBSA
(Thu Sep 08 2011 - 02:05:16 PDT)
[AMBER] MPI version of MMPBSA
(Thu Sep 08 2011 - 00:35:59 PDT)
Sidney Elmer
Re: [AMBER] Bond command using xleap or tleap
(Fri Sep 16 2011 - 09:23:57 PDT)
Re: [AMBER] Bond command using xleap or tleap
(Thu Sep 15 2011 - 17:14:38 PDT)
Re: [AMBER] benchmarking Tesla S2050 1U system
(Thu Sep 15 2011 - 17:08:27 PDT)
Re: [AMBER] benchmarking Tesla S2050 1U system
(Wed Sep 14 2011 - 15:55:23 PDT)
[AMBER] benchmarking Tesla S2050 1U system
(Wed Sep 14 2011 - 11:52:38 PDT)
Simon Becker
Re: [AMBER] results from independent simulations
(Wed Sep 07 2011 - 02:58:54 PDT)
Sindrila Dutta banik
[AMBER] Unit of the partial charge as given in the topology file
(Mon Sep 19 2011 - 11:47:26 PDT)
[AMBER] Proble related to correlation function
(Wed Sep 07 2011 - 10:51:17 PDT)
[AMBER] Restrain of atoms during MD simulation
(Wed Sep 07 2011 - 00:37:16 PDT)
[AMBER] CCA-Phe terminal using Antechamber
(Thu Sep 01 2011 - 05:39:46 PDT)
sonali dhindwal
Re: [AMBER] problem while using Antechamber
(Mon Sep 05 2011 - 22:19:17 PDT)
[AMBER] problem while using Antechamber
(Mon Sep 05 2011 - 07:21:24 PDT)
Re: [AMBER] problem in installing xleap
(Sat Sep 03 2011 - 07:08:30 PDT)
Re: [AMBER] problem in installing xleap
(Sat Sep 03 2011 - 04:49:21 PDT)
Re: [AMBER] problem in installing xleap
(Fri Sep 02 2011 - 06:58:08 PDT)
Re: [AMBER] problem in installing xleap
(Wed Aug 31 2011 - 21:38:20 PDT)
Soonmin Jang
Re: [AMBER] antechamber error
(Tue Sep 06 2011 - 07:04:50 PDT)
[AMBER] antechamber error
(Sat Sep 03 2011 - 01:45:47 PDT)
souvik sur
[AMBER] Parameter files :problem to save
(Wed Sep 28 2011 - 21:20:48 PDT)
[AMBER] Regarding Force field
(Sun Sep 25 2011 - 22:28:36 PDT)
Re: [AMBER] Amber parmbsc0 force field
(Sat Sep 24 2011 - 07:09:53 PDT)
[AMBER] Amber parmbsc0 force field
(Fri Sep 23 2011 - 21:25:11 PDT)
[AMBER] Amber parmbsc0 vs ff99
(Thu Sep 22 2011 - 06:41:45 PDT)
[AMBER] Amber parmbsc0
(Thu Sep 22 2011 - 00:35:03 PDT)
steinbrt.rci.rutgers.edu
Re: [AMBER] sander mpi error when unfolding the protein
(Thu Sep 29 2011 - 02:23:53 PDT)
Re: [AMBER] sander mpi error when unfolding the protein
(Thu Sep 29 2011 - 00:55:22 PDT)
Re: [AMBER] non-bond interaction
(Tue Sep 27 2011 - 00:07:12 PDT)
Re: [AMBER] charges on ligand
(Tue Sep 20 2011 - 00:32:47 PDT)
Re: [AMBER] rst or mdcrd file to view the structures?
(Tue Sep 20 2011 - 00:25:51 PDT)
Re: [AMBER] rst or mdcrd file to view the structures?
(Mon Sep 19 2011 - 04:22:22 PDT)
Re: [AMBER] rst or mdcrd file to view the structures?
(Mon Sep 19 2011 - 00:38:41 PDT)
Re: [AMBER] AMBER expense
(Fri Sep 16 2011 - 16:16:20 PDT)
Re: [AMBER] help!!zinc parameters
(Fri Sep 16 2011 - 08:36:31 PDT)
Re: [AMBER] hello
(Wed Sep 14 2011 - 06:06:40 PDT)
Re: [AMBER] Global Minimum in Simulated Annealing using SANDER
(Tue Sep 13 2011 - 07:18:36 PDT)
Re: [AMBER] Fwd: amber
(Tue Sep 13 2011 - 07:14:29 PDT)
Re: [AMBER] visualization of secstruc with e.g. gnuplot
(Tue Sep 13 2011 - 06:20:05 PDT)
Re: [AMBER] Energy change
(Thu Sep 01 2011 - 23:43:24 PDT)
Steven Burger
[AMBER] turning on 1-2 and 1-3 interactions
(Thu Sep 08 2011 - 10:46:26 PDT)
su He
Re: [AMBER] intermolecular interaction
(Fri Sep 09 2011 - 07:58:06 PDT)
[AMBER] intermolecular interaction
(Thu Sep 08 2011 - 13:02:17 PDT)
Re: [AMBER] some questions on GAFF
(Fri Sep 02 2011 - 13:25:22 PDT)
[AMBER] some questions on GAFF
(Fri Sep 02 2011 - 12:58:06 PDT)
sunxi.comcast.net
[AMBER] how to generate a correlation matrix for both protein and substrate atoms
(Thu Sep 22 2011 - 22:08:13 PDT)
Thomas Cheatham
Re: [AMBER] Amber parmbsc0 vs ff99
(Thu Sep 22 2011 - 08:15:16 PDT)
Re: [AMBER] ptraj
(Fri Sep 16 2011 - 06:25:44 PDT)
Re: [AMBER] radial distribution function
(Fri Sep 16 2011 - 06:13:47 PDT)
Re: [AMBER] Grid
(Fri Sep 16 2011 - 01:57:32 PDT)
Re: [AMBER] X-PLOR formatted .psf in CHAMBER
(Thu Sep 15 2011 - 05:21:46 PDT)
Re: [AMBER] ptraj clustering
(Mon Sep 12 2011 - 12:13:35 PDT)
Thomas Cheatham III
Re: [AMBER] Fwd: fixing rmsd values (follow-up)
(Tue Sep 27 2011 - 13:55:40 PDT)
Re: [AMBER] Grid and SDF
(Thu Sep 22 2011 - 11:28:18 PDT)
Re: [AMBER] radial distribution function
(Mon Sep 19 2011 - 16:04:23 PDT)
Re: [AMBER] Self-Diffusion coefficient
(Mon Sep 19 2011 - 15:50:20 PDT)
Re: [AMBER] ptraj clustering
(Mon Sep 12 2011 - 13:37:55 PDT)
Thomas Gaillard
Re: [AMBER] GB protocol problems for large RNAs (follow-up)
(Tue Sep 27 2011 - 10:38:43 PDT)
thomas.fox.boehringer-ingelheim.com
Re: [AMBER] bug in respgen ?
(Mon Sep 26 2011 - 00:00:06 PDT)
Re: [AMBER] bug in respgen ?
(Fri Sep 23 2011 - 05:59:04 PDT)
[AMBER] bug in respgen ?
(Wed Sep 21 2011 - 00:06:21 PDT)
truongco nguyen
[AMBER] ICST
(Thu Sep 22 2011 - 02:10:49 PDT)
tsurma.umich.edu
Re: [AMBER] SHAKE error help
(Wed Sep 14 2011 - 08:21:23 PDT)
Re: [AMBER] SHAKE error help
(Sat Sep 10 2011 - 11:49:10 PDT)
Re: [AMBER] SHAKE error help
(Fri Sep 09 2011 - 12:35:42 PDT)
Re: [AMBER] SHAKE error help
(Tue Sep 06 2011 - 08:43:08 PDT)
Re: [AMBER] replace unit in leap
(Tue Sep 06 2011 - 08:41:00 PDT)
Re: [AMBER] SHAKE error help
(Mon Sep 05 2011 - 07:43:45 PDT)
[AMBER] replace unit in leap
(Sun Sep 04 2011 - 10:56:05 PDT)
[AMBER] replace unit in leap
(Sun Sep 04 2011 - 09:59:45 PDT)
Re: [AMBER] SHAKE error help
(Sat Sep 03 2011 - 14:35:49 PDT)
Re: [AMBER] SHAKE error help
(Sat Sep 03 2011 - 09:22:39 PDT)
[AMBER] SHAKE error help
(Fri Sep 02 2011 - 19:28:08 PDT)
Victor Ma
[AMBER] MMPBSA: how to include only some residues
(Fri Sep 30 2011 - 14:02:01 PDT)
Re: [AMBER] how NOT to label terminal residue
(Thu Sep 29 2011 - 14:24:45 PDT)
[AMBER] how NOT to label terminal residue
(Thu Sep 29 2011 - 13:54:44 PDT)
[AMBER] problem with TI calculations
(Tue Sep 20 2011 - 12:08:03 PDT)
Vijay Manickam Achari
Re: [AMBER] hydrogen bonding
(Fri Sep 23 2011 - 21:17:29 PDT)
[AMBER] hydrogen bonding
(Fri Sep 23 2011 - 05:17:06 PDT)
[AMBER] hydrogen boding and PBC
(Tue Sep 06 2011 - 03:19:02 PDT)
Wei Lin
[AMBER] Print Dipole Moment in Centriod MD
(Wed Sep 14 2011 - 20:56:20 PDT)
Wei Zhang
Re: [AMBER] Sleap : amoeba and gaff
(Mon Sep 05 2011 - 14:13:20 PDT)
William Cantara
Re: [AMBER] PNEB on GPUs
(Thu Sep 29 2011 - 06:03:45 PDT)
[AMBER] PNEB on GPUs
(Wed Sep 28 2011 - 20:20:30 PDT)
wrong string
[AMBER] Is there any module which can calculate interaction energy, as ANAL in Amber 8?
(Tue Sep 06 2011 - 01:09:06 PDT)
Wu Xu
Re: [AMBER] results from independent simulations
(Thu Sep 08 2011 - 05:18:55 PDT)
Re: [AMBER] results from independent simulations
(Wed Sep 07 2011 - 08:51:48 PDT)
[AMBER] results from independent simulations
(Tue Sep 06 2011 - 17:37:25 PDT)
Yao Yao
[AMBER] 1st DNA tutorial cannot save parameter
(Wed Sep 28 2011 - 17:28:30 PDT)
[AMBER] Chromophore Building
(Tue Sep 27 2011 - 12:34:19 PDT)
[AMBER] Different Temps Coupling
(Wed Sep 21 2011 - 10:35:56 PDT)
[AMBER] Xleap Installation
(Tue Sep 20 2011 - 15:40:07 PDT)
[AMBER] new residue parameters transfer
(Mon Sep 19 2011 - 22:37:30 PDT)
Yong Duan
Re: [AMBER] new residue parameters transfer
(Tue Sep 20 2011 - 05:46:13 PDT)
Yongmei Wang (ywang)
[AMBER] unsubscribe
(Fri Sep 16 2011 - 09:48:03 PDT)
Re: [AMBER] tleap command "set default Dielectric constant" not valid?
(Thu Sep 15 2011 - 12:13:22 PDT)
[AMBER] tleap command "set default Dielectric constant" not valid?
(Wed Sep 14 2011 - 21:33:29 PDT)
Yun Shi
Re: [AMBER] about Glycam_06g.dat and thiol-glycosidic linkage
(Fri Sep 23 2011 - 22:26:22 PDT)
Re: [AMBER] again GLYCAM06 + 99SB + GAFF ?
(Wed Sep 21 2011 - 07:41:36 PDT)
Re: [AMBER] again GLYCAM06 + 99SB + GAFF ?
(Tue Sep 20 2011 - 21:11:08 PDT)
Re: [AMBER] about Glycam_06g.dat and thiol-glycosidic linkage
(Mon Sep 19 2011 - 15:27:01 PDT)
Re: [AMBER] again GLYCAM06 + 99SB + GAFF ?
(Sun Sep 18 2011 - 21:38:55 PDT)
[AMBER] scaling factors in carbohydrate-protein interaction
(Sat Sep 17 2011 - 15:43:52 PDT)
Re: [AMBER] about Glycam_06g.dat and thiol-glycosidic linkage
(Fri Sep 16 2011 - 09:46:01 PDT)
Re: [AMBER] again GLYCAM06 + 99SB + GAFF ?
(Thu Sep 15 2011 - 21:56:35 PDT)
Re: [AMBER] about Glycam_06g.dat and thiol-glycosidic linkage
(Thu Sep 15 2011 - 15:30:28 PDT)
Re: [AMBER] about Glycam_06g.dat and thiol-glycosidic linkage
(Thu Sep 15 2011 - 11:07:33 PDT)
Re: [AMBER] about Glycam_06g.dat and thiol-glycosidic linkage
(Thu Sep 15 2011 - 10:03:47 PDT)
Re: [AMBER] how to fill in missing parameters in tleap?
(Wed Sep 14 2011 - 22:07:21 PDT)
Re: [AMBER] How to interpret GLYCAM prep file?
(Wed Sep 14 2011 - 16:49:42 PDT)
[AMBER] about Glycam_06g.dat and thiol-glycosidic linkage
(Wed Sep 14 2011 - 15:53:43 PDT)
Re: [AMBER] again GLYCAM06 + 99SB + GAFF ?
(Mon Sep 12 2011 - 23:55:50 PDT)
Re: [AMBER] again GLYCAM06 + 99SB + GAFF ?
(Mon Sep 12 2011 - 23:32:47 PDT)
Re: [AMBER] how to fill in missing parameters in tleap?
(Fri Sep 09 2011 - 16:51:48 PDT)
Re: [AMBER] how to fill in missing parameters in tleap?
(Thu Sep 08 2011 - 23:47:16 PDT)
Re: [AMBER] How to interpret GLYCAM prep file?
(Thu Sep 08 2011 - 23:38:15 PDT)
Re: [AMBER] how to fill in missing parameters in tleap?
(Thu Sep 08 2011 - 13:50:55 PDT)
Re: [AMBER] again GLYCAM06 + 99SB + GAFF ?
(Tue Sep 06 2011 - 22:28:44 PDT)
Re: [AMBER] how to fill in missing parameters in tleap?
(Tue Sep 06 2011 - 11:22:06 PDT)
Re: [AMBER] how to fill in missing parameters in tleap?
(Tue Sep 06 2011 - 08:21:18 PDT)
Re: [AMBER] how to fill in missing parameters in tleap?
(Mon Sep 05 2011 - 16:22:19 PDT)
Zachary Davis
[AMBER] Antechamber
(Fri Sep 23 2011 - 10:17:38 PDT)
zhukk
Re: [AMBER] help ! zinc parameters
(Mon Sep 19 2011 - 05:28:07 PDT)
Re: [AMBER] help ! zinc parameters
(Mon Sep 19 2011 - 05:25:39 PDT)
Re: [AMBER] help ! zinc parameters
(Mon Sep 19 2011 - 05:12:50 PDT)
Re: [AMBER] help!!zinc parameters
(Mon Sep 19 2011 - 04:55:16 PDT)
[AMBER] help!!zinc parameters
(Fri Sep 16 2011 - 08:16:17 PDT)
Алексей Раевский
[AMBER] ambertool question !!!
(Mon Sep 26 2011 - 11:23:58 PDT)
[AMBER] ambertool question !!!
(Mon Sep 26 2011 - 11:22:14 PDT)
杨立江
[AMBER] Help needed for Amber SCC-DFTB code
(Tue Sep 20 2011 - 22:45:23 PDT)
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Fri Sep 30 2011 - 19:30:02 PDT
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: Sun Nov 17 2024 - 05:54:23 PST
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