Amber Archive Feb 2015: by author

a.mohseni
- [AMBER] Fwd: MMPBSA (Wed Feb 11 2015 - 00:59:55 PST)
abdennour braka
- Re: [AMBER] harmonic restraint file (Tue Feb 03 2015 - 05:26:29 PST)
- Re: [AMBER] harmonic restraint file (Tue Feb 03 2015 - 02:47:58 PST)
Aditya Sarkar
- Re: [AMBER] pressure fluctuation problem (Mon Feb 16 2015 - 04:25:16 PST)
- [AMBER] pressure fluctuation problem (Sun Feb 15 2015 - 00:05:10 PST)
Adrian Roitberg
- Re: [AMBER] Steered MD using the jar=1 option (Fri Feb 27 2015 - 08:13:04 PST)
- Re: [AMBER] Steered MD using the jar=1 option (Mon Feb 23 2015 - 14:35:56 PST)
- Re: [AMBER] Steered MD using the jar=1 option (Mon Feb 23 2015 - 14:13:31 PST)
Ahmed Ayoub
- [AMBER] Forces from Potential (Wed Feb 18 2015 - 08:39:13 PST)
Ahmet yıldırım
- Re: [AMBER] xleap syntax error (Thu Feb 05 2015 - 12:59:18 PST)
- Re: [AMBER] xleap syntax error (Thu Feb 05 2015 - 11:47:19 PST)
- [AMBER] xleap syntax error (Thu Feb 05 2015 - 09:26:53 PST)
Alessandra Lacetera
- Re: [AMBER] Closest residues to an atom in ptraj (Wed Feb 25 2015 - 04:36:32 PST)
- [AMBER] Closest residues to an atom in ptraj (Tue Feb 24 2015 - 11:42:06 PST)
Andreas Goetz
- [AMBER] Test (Mon Feb 09 2015 - 07:41:57 PST)
anu chandra
- Re: [AMBER] Help in choosing right MD tool (Tue Feb 24 2015 - 04:22:24 PST)
- [AMBER] Help in choosing right MD tool (Mon Feb 23 2015 - 04:09:04 PST)
Anupam Goel
- Re: [AMBER] protein falls apart on explicit solvation md (Fri Feb 06 2015 - 12:28:56 PST)
- [AMBER] protein falls apart on explicit solvation md (Fri Feb 06 2015 - 12:04:36 PST)
Anya Leach
- [AMBER] MD cis-azobenzene error (Wed Feb 04 2015 - 13:38:43 PST)
Ashutosh Shandilya
- Re: [AMBER] no parameter for nicotine (Wed Feb 04 2015 - 02:11:27 PST)
Asmita Gupta
- [AMBER] reweighing aMD trajectory (Mon Feb 16 2015 - 07:46:43 PST)
Ayesha Fatima
- [AMBER] cpptraj hbond lifetime problem (Sun Feb 22 2015 - 01:59:56 PST)
- Re: [AMBER] hbond analysis (Sat Feb 21 2015 - 08:39:13 PST)
- [AMBER] hbond analysis (Fri Feb 20 2015 - 05:37:40 PST)
- [AMBER] cpptraj hbond analysis (Thu Feb 19 2015 - 01:59:46 PST)
- [AMBER] cpptraj hbond analysis (Wed Feb 18 2015 - 07:42:28 PST)
- Re: [AMBER] combining trajectories (Mon Feb 16 2015 - 22:19:31 PST)
- Re: [AMBER] combining trajectories (Mon Feb 16 2015 - 09:58:33 PST)
- [AMBER] combining trajectories (Mon Feb 16 2015 - 06:29:05 PST)
- Re: [AMBER] hbond analysis (Sat Feb 14 2015 - 04:28:05 PST)
- Re: [AMBER] hbond analysis (Fri Feb 13 2015 - 06:40:21 PST)
- [AMBER] hbond analysis (Thu Feb 12 2015 - 23:48:42 PST)
Bajarang Kumbhar
- [AMBER] AMBER: MPI run issue (Mon Feb 16 2015 - 05:38:31 PST)
belen nieto
- [AMBER] RV: segmentation fault when running parmchk (Mon Feb 23 2015 - 02:45:43 PST)
BERGY
- Re: [AMBER] pmemd.cuda error cudaMemcpy GpuBuffer:: (Tue Feb 17 2015 - 10:56:44 PST)
- Re: [AMBER] pmemd.cuda error cudaMemcpy GpuBuffer:: (Sat Feb 14 2015 - 09:43:50 PST)
- [AMBER] pmemd.cuda error cudaMemcpy GpuBuffer:: (Fri Feb 13 2015 - 22:38:35 PST)
Bill Ross
- Re: [AMBER] Solvent Box Wrapping Issue (Fri Feb 20 2015 - 14:02:00 PST)
Carlo Guardiani
- [AMBER] H-REMD failure on GPU (Wed Feb 25 2015 - 08:57:43 PST)
Carlos Simmerling
- Re: [AMBER] Average Internal Coordinates in cpptraj (Mon Feb 09 2015 - 08:49:17 PST)
- Re: [AMBER] cis peptide bond (Fri Feb 06 2015 - 10:07:14 PST)
- Re: [AMBER] cis peptide bond (Fri Feb 06 2015 - 09:32:53 PST)
- [AMBER] ACS COMP Division awards for Fall 2015 National Meeting in Boston (Thu Feb 05 2015 - 08:55:09 PST)
carmendigiovanni75.alice.it
- [AMBER] GTX980 PERFORMANCE (Fri Feb 27 2015 - 05:31:01 PST)
chemjxn.126.com
- [AMBER] MCPB (Fri Feb 06 2015 - 00:21:14 PST)
- [AMBER] parameterization (Sun Feb 01 2015 - 23:22:40 PST)
- [AMBER] (无主题) (Sun Feb 01 2015 - 22:58:20 PST)
Chris Chris
- [AMBER] Can't get shell script to work with Lipid tutorial (Thu Feb 26 2015 - 09:52:14 PST)
- Re: [AMBER] vmd_box_dims.sh (Sat Feb 07 2015 - 09:57:27 PST)
- Re: [AMBER] vmd_box_dims.sh (Sat Feb 07 2015 - 08:27:03 PST)
- [AMBER] vmd_box_dims.sh (Fri Feb 06 2015 - 20:18:22 PST)
- Re: [AMBER] Query regarding Dynamics Studies (Fri Feb 06 2015 - 07:22:06 PST)
- [AMBER] charmmlipid2amber.x (Thu Feb 05 2015 - 19:28:15 PST)
Chris Gaughan
- [AMBER] An Amber Lipid Force Field Tutorial: problem with shell script (Wed Feb 25 2015 - 20:02:58 PST)
Christina Bergonzo
- Re: [AMBER] single strand DNA in hairpin conformation (Fri Feb 20 2015 - 06:47:08 PST)
Daniel Roe
- Re: [AMBER] problem with running tutorial C1 (Sat Feb 28 2015 - 06:38:25 PST)
- [AMBER] Calculation of the number of internal waters during md simulation (Wed Feb 25 2015 - 07:12:33 PST)
- Re: [AMBER] Closest residues to an atom in ptraj (Wed Feb 25 2015 - 06:54:59 PST)
- Re: [AMBER] Unexpected behavior of trajout after invoking filter: Bug? (Tue Feb 24 2015 - 17:02:11 PST)
- Re: [AMBER] Can I use the presence of a particular hydrogen bond as a condition to filter out frames? (Tue Feb 24 2015 - 13:57:00 PST)
- Re: [AMBER] Closest residues to an atom in ptraj (Tue Feb 24 2015 - 11:59:35 PST)
- Re: [AMBER] Can I use the presence of a particular hydrogen bond as a condition to filter out frames? (Tue Feb 24 2015 - 11:20:39 PST)
- Re: [AMBER] Can I use the presence of a particular hydrogen bond as a condition to filter out frames? (Tue Feb 24 2015 - 10:51:40 PST)
- Re: [AMBER] cpptraj: H-bond clarification sought (Mon Feb 23 2015 - 10:30:33 PST)
- Re: [AMBER] Error: Expected DCD block size of 48, got -1029941464 (Mon Feb 23 2015 - 07:38:53 PST)
- Re: [AMBER] atomicfluct issue (Mon Feb 23 2015 - 07:31:38 PST)
- Re: [AMBER] cpptraj hbond lifetime problem (Sun Feb 22 2015 - 07:58:12 PST)
- Re: [AMBER] Error: Expected DCD block size of 48, got -1029941464 (Sat Feb 21 2015 - 13:50:10 PST)
- Re: [AMBER] rms: Warning: [rms] Not all arguments handled: [ rmsd.agr ] (Sat Feb 21 2015 - 13:39:48 PST)
- Re: [AMBER] Solvent Box Wrapping Issue (Fri Feb 20 2015 - 13:11:57 PST)
- Re: [AMBER] hbond analysis (Fri Feb 20 2015 - 12:59:29 PST)
- Re: [AMBER] Help calculating RMSD between two proteins (Thu Feb 19 2015 - 13:43:34 PST)
- Re: [AMBER] Help calculating RMSD between two proteins (Thu Feb 19 2015 - 12:00:43 PST)
- Re: [AMBER] problem with RMSD for small molecule (Thu Feb 19 2015 - 08:12:50 PST)
- Re: [AMBER] rmsavgcorr (Thu Feb 19 2015 - 08:11:34 PST)
- Re: [AMBER] cpptraj hbond analysis (Wed Feb 18 2015 - 08:24:35 PST)
- Re: [AMBER] Distance/Angle distribution along the trajectory using cpptraj (Wed Feb 18 2015 - 05:31:18 PST)
- Re: [AMBER] Can cpptraj-hbond report the lifetimes of H-bonds between protein and water? (Tue Feb 17 2015 - 09:45:27 PST)
- Re: [AMBER] solute-solvent hbond fraction value is more than 1.0 (Tue Feb 17 2015 - 09:20:35 PST)
- Re: [AMBER] combining trajectories (Tue Feb 17 2015 - 00:35:02 PST)
- Re: [AMBER] combining trajectories (Mon Feb 16 2015 - 10:53:20 PST)
- Re: [AMBER] combining trajectories (Mon Feb 16 2015 - 09:00:14 PST)
- Re: [AMBER] combining trajectories (Mon Feb 16 2015 - 08:25:02 PST)
- Re: [AMBER] rotational diffusion (Sun Feb 15 2015 - 08:51:51 PST)
- Re: [AMBER] Question about hbond analysis (Sun Feb 15 2015 - 08:36:16 PST)
- Re: [AMBER] Error: Restart File Corrupted (Fri Feb 13 2015 - 12:32:35 PST)
- Re: [AMBER] Calculation of the number of internal waters during md simulation (Thu Feb 12 2015 - 07:59:45 PST)
- Re: [AMBER] calculating HB lifetime (Thu Feb 12 2015 - 07:40:24 PST)
- Re: [AMBER] calculating HB lifetime (Thu Feb 12 2015 - 07:22:42 PST)
- Re: [AMBER] calculating HB lifetime (Thu Feb 12 2015 - 07:06:44 PST)
- Re: [AMBER] calculating HB lifetime (Thu Feb 12 2015 - 06:51:52 PST)
- Re: [AMBER] calculating HB lifetime (Wed Feb 11 2015 - 21:46:16 PST)
- Re: [AMBER] calculating HB lifetime (Wed Feb 11 2015 - 10:21:56 PST)
- Re: [AMBER] calculating HB lifetime (Wed Feb 11 2015 - 08:44:05 PST)
- Re: [AMBER] Calculation of the number of internal waters during md simulation (Tue Feb 10 2015 - 06:43:25 PST)
- Re: [AMBER] Assignment of charges for Guanidine (Sun Feb 08 2015 - 15:42:54 PST)
- Re: [AMBER] Strange md and RMSD behavior (Sun Feb 08 2015 - 15:39:10 PST)
- Re: [AMBER] protein falls apart on explicit solvation md (Fri Feb 06 2015 - 12:10:02 PST)
- Re: [AMBER] Calculation of the number of internal waters during md simulation (Fri Feb 06 2015 - 09:52:11 PST)
- Re: [AMBER] Assignment of charges for Guanidine (Fri Feb 06 2015 - 08:23:57 PST)
- Re: [AMBER] xleap syntax error (Thu Feb 05 2015 - 10:25:55 PST)
- Re: [AMBER] Calculation of the number of internal waters during md simulation (Thu Feb 05 2015 - 08:06:29 PST)
- Re: [AMBER] Calculation of the number of internal waters during md simulation (Thu Feb 05 2015 - 08:02:55 PST)
- Re: [AMBER] Calculation of the number of internal waters during md simulation (Tue Feb 03 2015 - 08:12:39 PST)
- Re: [AMBER] error in equil.rst steps of AMBER (Mon Feb 02 2015 - 06:52:04 PST)
- Re: [AMBER] Error: Unable to run flex; this is required for NAB and antechamber Please check your PATH, or install the program (Sun Feb 01 2015 - 15:27:36 PST)
- Re: [AMBER] AMD stuck with v-limit exceeded error (Sun Feb 01 2015 - 11:38:20 PST)
David A Case
- Re: [AMBER] An Amber Lipid Force Field Tutorial: problem with shell script (Thu Feb 26 2015 - 05:02:13 PST)
- Re: [AMBER] Bond Energy Term for a TIP3P Water (Wed Feb 25 2015 - 05:30:42 PST)
- Re: [AMBER] Create a unit of mixture (Tue Feb 24 2015 - 14:42:38 PST)
- Re: [AMBER] On the collective dynamics in terms of NMA and PCA (Tue Feb 24 2015 - 14:39:54 PST)
- Re: [AMBER] Help in choosing right MD tool (Tue Feb 24 2015 - 14:37:55 PST)
- Re: [AMBER] REGARDING WARNINGS RETURNED DURING FORCE FIELD GENERATION (Tue Feb 24 2015 - 14:33:27 PST)
- Re: [AMBER] how to find out if a prmtop file was created with ff12 or ff14 (Mon Feb 23 2015 - 10:01:36 PST)
- Re: [AMBER] Regarding ff02 force field and RESP method documentation (Mon Feb 23 2015 - 08:31:18 PST)
- Re: [AMBER] Help in choosing right MD tool (Mon Feb 23 2015 - 07:29:35 PST)
- Re: [AMBER] Fwd: Amber tleap error (Mon Feb 23 2015 - 05:47:30 PST)
- Re: [AMBER] vlimit exceeded for step (Mon Feb 23 2015 - 05:41:01 PST)
- Re: [AMBER] Problem in generating CCL4 solvent Box (Sun Feb 22 2015 - 13:16:54 PST)
- Re: [AMBER] Solvent Box Wrapping Issue (Sun Feb 22 2015 - 13:12:35 PST)
- Re: [AMBER] single strand DNA in hairpin conformation (Fri Feb 20 2015 - 08:57:34 PST)
- Re: [AMBER] Error while running tleap for the ligand containing two chlorine atoms (Fri Feb 20 2015 - 07:40:16 PST)
- Re: [AMBER] Error while running tleap for the ligand containing two chlorine atoms (Fri Feb 20 2015 - 07:38:47 PST)
- Re: [AMBER] Error while running tleap for the ligand containing two chlorine atoms (Fri Feb 20 2015 - 05:24:50 PST)
- Re: [AMBER] pmemd.cuda error cudaMemcpy GpuBuffer:: (Thu Feb 19 2015 - 05:03:06 PST)
- Re: [AMBER] problem with RMSD for small molecule (Thu Feb 19 2015 - 04:58:40 PST)
- Re: [AMBER] single strand DNA in hairpin conformation (Wed Feb 18 2015 - 12:27:24 PST)
- Re: [AMBER] Question regarding the calculation of binding constants (Wed Feb 18 2015 - 07:41:18 PST)
- Re: [AMBER] restraining the torsion (Wed Feb 18 2015 - 07:35:10 PST)
- Re: [AMBER] Simulations in CCl4 (Wed Feb 18 2015 - 06:13:54 PST)
- Re: [AMBER] Regarding AmberTool 14 installation (Tue Feb 17 2015 - 07:00:25 PST)
- Re: [AMBER] pbsa (Sun Feb 15 2015 - 14:40:17 PST)
- Re: [AMBER] assignment of Water molecules (Fri Feb 13 2015 - 09:25:36 PST)
- Re: [AMBER] alkynes in GAFF (Thu Feb 12 2015 - 04:27:32 PST)
- Re: [AMBER] single strand DNA in hairpin conformation (Thu Feb 12 2015 - 04:24:56 PST)
- Re: [AMBER] list of atomic coordinates involved in solvent accessible area (Wed Feb 11 2015 - 19:36:26 PST)
- Re: [AMBER] unexpected behaviour with antechamber (Wed Feb 11 2015 - 04:54:25 PST)
- Re: [AMBER] unexpected behaviour with antechamber (Mon Feb 09 2015 - 17:46:58 PST)
- Re: [AMBER] memory issue in mmpbsa_py_nabnmode (Mon Feb 09 2015 - 17:28:37 PST)
- Re: [AMBER] xleap syntax error (Thu Feb 05 2015 - 10:40:51 PST)
- Re: [AMBER] seek help (Wed Feb 04 2015 - 05:11:38 PST)
- Re: [AMBER] have not atom type (Wed Feb 04 2015 - 04:58:42 PST)
- Re: [AMBER] harmonic restraint file (Tue Feb 03 2015 - 05:14:52 PST)
- Re: [AMBER] error in equil.rst steps of AMBER (Mon Feb 02 2015 - 06:59:21 PST)
- Re: [AMBER] parameterization (Mon Feb 02 2015 - 06:52:18 PST)
- Re: [AMBER] Error: Unable to run flex; this is required for NAB and antechamber Please check your PATH, or install the program (Mon Feb 02 2015 - 05:15:12 PST)
- Re: [AMBER] reparametrize water molecule near metal site (Mon Feb 02 2015 - 05:05:22 PST)
- Re: [AMBER] missing atom of heme (Sun Feb 01 2015 - 05:48:41 PST)
David Case
- Re: [AMBER] Assignment of charges for Guanidine (Sat Feb 07 2015 - 18:03:46 PST)
- Re: [AMBER] vmd_box_dims.sh (Sat Feb 07 2015 - 17:54:09 PST)
Dhiraj Srivastava
- Re: [AMBER] cis peptide bond (Fri Feb 06 2015 - 09:45:17 PST)
- [AMBER] cis peptide bond (Fri Feb 06 2015 - 08:40:34 PST)
- Re: [AMBER] AmberTools14 installation (Mon Feb 02 2015 - 11:38:48 PST)
- Re: [AMBER] AmberTools14 installation (Mon Feb 02 2015 - 11:37:36 PST)
- [AMBER] AmberTools14 installation (Mon Feb 02 2015 - 11:25:25 PST)
Dr. Robert Molt Jr.
- Re: [AMBER] Average Internal Coordinates in cpptraj (Mon Feb 09 2015 - 08:50:17 PST)
- [AMBER] Average Internal Coordinates in cpptraj (Mon Feb 09 2015 - 08:37:52 PST)
Edward Kalkreuter
- [AMBER] Error: Restart File Corrupted (Fri Feb 13 2015 - 10:03:10 PST)
Emmanuel
- [AMBER] Output Forces Acting of Each Atom During MD Simulation using Amber14 (Sun Feb 08 2015 - 16:05:23 PST)
Evans, Shalton
- [AMBER] FATAL: Atom .R<GRA 1>.A<H31 197> does not have a type. (Thu Feb 26 2015 - 22:51:43 PST)
- Re: [AMBER] ERRORS AND FATAL ERRORS (Apparently died to faulty connections) (Fri Feb 13 2015 - 13:30:13 PST)
- [AMBER] ERRORS AND FATAL ERRORS (Apparently died to faulty connections) (Wed Feb 04 2015 - 22:22:39 PST)
Fatemeh Sadat Alavi
- Re: [AMBER] vlimit exceeded for step (Mon Feb 23 2015 - 04:06:55 PST)
- [AMBER] vlimit exceeded for step (Sat Feb 21 2015 - 03:51:15 PST)
- [AMBER] dont have atom type (Mon Feb 16 2015 - 04:44:10 PST)
- [AMBER] have not atom type (Tue Feb 03 2015 - 22:20:36 PST)
- [AMBER] missing atom of heme (Sun Feb 01 2015 - 00:14:31 PST)
Francesca Tessaro
- [AMBER] Cofactor parametrization (Thu Feb 26 2015 - 06:45:59 PST)
Fugui
- [AMBER] Problem with Ambertools14 (Sat Jan 31 2015 - 10:27:12 PST)
Garisekurthi Satheesh
- Re: [AMBER] Fwd: Amber tleap error (Mon Feb 23 2015 - 21:01:41 PST)
- [AMBER] Fwd: Amber tleap error (Sun Feb 22 2015 - 19:30:09 PST)
George Tzotzos
- Re: [AMBER] MMGBSA: calculation of deltaG of ligand binding at dimer interface (Thu Feb 26 2015 - 10:08:57 PST)
- Re: [AMBER] MMGBSA: calculation of deltaG of ligand binding at dimer interface (Thu Feb 26 2015 - 09:16:50 PST)
- [AMBER] MMGBSA: calculation of deltaG of ligand binding at dimer interface (Thu Feb 26 2015 - 07:46:45 PST)
- Re: [AMBER] cpptraj: H-bond clarification sought (Mon Feb 23 2015 - 10:40:16 PST)
- [AMBER] cpptraj: H-bond clarification sought (Mon Feb 23 2015 - 10:12:33 PST)
- [AMBER] atomicfluct issue (Mon Feb 23 2015 - 05:30:04 PST)
- Re: [AMBER] rms: Warning: [rms] Not all arguments handled: [ rmsd.agr ] (Sat Feb 21 2015 - 16:05:21 PST)
- Re: [AMBER] rms: Warning: [rms] Not all arguments handled: [ rmsd.agr ] (Sat Feb 21 2015 - 13:57:18 PST)
- [AMBER] rms: Warning: [rms] Not all arguments handled: [ rmsd.agr ] (Sat Feb 21 2015 - 13:14:45 PST)
- [AMBER] MMPBSA pairwise decomposition error (Tue Feb 17 2015 - 12:00:34 PST)
- [AMBER] MMGBSA question (Mon Feb 16 2015 - 11:53:26 PST)
- [AMBER] MMGBSA question (Mon Feb 16 2015 - 11:11:28 PST)
- Re: [AMBER] MMPBSA - standard deviation (again) (Thu Feb 12 2015 - 07:29:31 PST)
- [AMBER] MMPBSA - standard deviation (again) (Thu Feb 12 2015 - 06:29:04 PST)
Ghulam Mustafa
- [AMBER] LIPID14 and ff15SB (Fri Feb 20 2015 - 09:06:35 PST)
Gould, Ian R
- Re: [AMBER] Lipid14 POPE lipids (Fri Feb 20 2015 - 06:31:26 PST)
Gustavo Seabra
- Re: [AMBER] Help creating custom monosaccharide unit in Glycam (Fri Feb 20 2015 - 11:23:30 PST)
- Re: [AMBER] Help creating custom monosaccharide unit in Glycam (Thu Feb 19 2015 - 03:42:38 PST)
- [AMBER] Help creating custom monosaccharide unit in Glycam (Wed Feb 18 2015 - 10:54:40 PST)
Hadeer ELHabashy
- [AMBER] Strange md and RMSD behavior (Sat Feb 07 2015 - 13:22:43 PST)
- Re: [AMBER] Real time event with amber mds with shake (Fri Feb 06 2015 - 04:46:27 PST)
- Re: [AMBER] Real time event with amber mds with shake (Thu Feb 05 2015 - 10:44:16 PST)
- [AMBER] Real time event with amber mds with shake (Thu Feb 05 2015 - 03:49:28 PST)
- [AMBER] AMD stuck with v-limit exceeded error (Sun Feb 01 2015 - 02:56:00 PST)
- [AMBER] Create one larger averaged trajectory file ! (Sun Feb 01 2015 - 02:36:25 PST)
Hai Nguyen
- Re: [AMBER] Help calculating RMSD between two proteins (Thu Feb 19 2015 - 13:28:09 PST)
- Re: [AMBER] Help calculating RMSD between two proteins (Thu Feb 19 2015 - 11:55:20 PST)
Hannes Loeffler
- [AMBER] Announcement: release of FESetup 1.1 (Tue Feb 24 2015 - 07:48:25 PST)
- Re: [AMBER] RV: segmentation fault when running parmchk (Mon Feb 23 2015 - 02:59:33 PST)
- Re: [AMBER] Water diffusion - in 2D and 3D (Fri Feb 13 2015 - 02:20:55 PST)
- Re: [AMBER] unexpected behaviour with antechamber (Wed Feb 11 2015 - 02:18:34 PST)
- Re: [AMBER] unexpected behaviour with antechamber (Tue Feb 10 2015 - 01:24:30 PST)
- [AMBER] unexpected behaviour with antechamber (Mon Feb 09 2015 - 08:31:07 PST)
- Re: [AMBER] Error while running antechamber and tleap for silver salt of carboxylic acid (Wed Feb 04 2015 - 05:38:53 PST)
- Re: [AMBER] Error while running antechamber and tleap for silver salt of carboxylic acid (Wed Feb 04 2015 - 03:52:03 PST)
hannes.loeffler.stfc.ac.uk
- Re: [AMBER] Inability to use antechamber on Anion (Sat Feb 28 2015 - 00:19:57 PST)
- Re: [AMBER] Error while running tleap for the ligand containing two chlorine atoms (Fri Feb 20 2015 - 05:07:26 PST)
- Re: [AMBER] ANTECHAMBER: error in mol2 file (Fri Feb 20 2015 - 04:12:13 PST)
- Re: [AMBER] Error while running tleap for the ligand containing two chlorine atoms (Fri Feb 20 2015 - 03:39:04 PST)
- Re: [AMBER] Error while running tleap for the ligand containing two chlorine atoms (Fri Feb 20 2015 - 03:13:31 PST)
- Re: [AMBER] ANTECHAMBER: error in mol2 file (Fri Feb 20 2015 - 03:05:29 PST)
- Re: [AMBER] angles values in GAFF for alkynes (Fri Feb 13 2015 - 11:28:49 PST)
- Re: [AMBER] angles values in GAFF for alkynes (Fri Feb 13 2015 - 10:40:35 PST)
- Re: [AMBER] Water diffusion - in 2D and 3D (Fri Feb 13 2015 - 00:28:28 PST)
- Re: [AMBER] antechamber error (Wed Feb 11 2015 - 00:14:56 PST)
- Re: [AMBER] vmd_box_dims.sh (Sat Feb 07 2015 - 01:12:50 PST)
- Re: [AMBER] Constructing a single Zwitterion in xleap (Sun Feb 01 2015 - 07:37:00 PST)
Harald Lanig
- [AMBER] [MGMS-DS]: Molecular Modelling Workshop March 9-11, 2015 in Erlangen, Germany (Tue Feb 17 2015 - 06:10:03 PST)
Harmeet Kaur
- [AMBER] antechamber error (Tue Feb 10 2015 - 23:07:13 PST)
- [AMBER] no parameter for nicotine (Wed Feb 04 2015 - 02:07:40 PST)
Hector A. Baldoni
- [AMBER] SDPC and SAPC lipid bilayer (Fri Feb 27 2015 - 06:21:14 PST)
Houcemeddine Othman
- Re: [AMBER] bad atom type: OA (Wed Feb 04 2015 - 04:26:09 PST)
Ibrahim Said
- [AMBER] Create a unit of mixture (Mon Feb 23 2015 - 10:56:59 PST)
- [AMBER] assignment of Water molecules (Fri Feb 13 2015 - 04:13:47 PST)
- [AMBER] Number of molecules for md calculations (Wed Feb 11 2015 - 08:57:30 PST)
- Re: [AMBER] Assignment of charges for Guanidine (Sun Feb 08 2015 - 10:01:28 PST)
- Re: [AMBER] Assignment of charges for Guanidine (Sat Feb 07 2015 - 14:19:32 PST)
- Re: [AMBER] Assignment of charges for Guanidine (Sat Feb 07 2015 - 00:16:39 PST)
- Re: [AMBER] Assignment of charges for Guanidine (Fri Feb 06 2015 - 11:02:24 PST)
- [AMBER] Assignment of charges for Guanidine (Fri Feb 06 2015 - 07:54:14 PST)
- [AMBER] Create a 2M urea box (Mon Feb 02 2015 - 12:33:06 PST)
Iqbal, Muhammad Sajid
- [AMBER] list of atomic coordinates involved in solvent accessible area (Wed Feb 11 2015 - 14:26:51 PST)
Jacopo Sgrignani
- [AMBER] rmsavgcorr (Thu Feb 19 2015 - 07:46:17 PST)
James Starlight
- Re: [AMBER] Calculation of the number of internal waters during md simulation (Thu Feb 26 2015 - 07:12:17 PST)
- Re: [AMBER] On the collective dynamics in terms of NMA and PCA (Thu Feb 26 2015 - 03:04:34 PST)
- Re: [AMBER] Calculation of the number of internal waters during md simulation (Wed Feb 25 2015 - 07:00:31 PST)
- [AMBER] On the collective dynamics in terms of NMA and PCA (Tue Feb 24 2015 - 02:23:55 PST)
- Re: [AMBER] Distance/Angle distribution along the trajectory using cpptraj (Wed Feb 18 2015 - 02:53:15 PST)
- [AMBER] Distance/Angle distribution along the trajectory using cpptraj (Wed Feb 18 2015 - 01:51:28 PST)
- Re: [AMBER] Calculation of the number of internal waters during md simulation (Fri Feb 13 2015 - 01:50:54 PST)
- Re: [AMBER] Calculation of the number of internal waters during md simulation (Tue Feb 10 2015 - 10:36:06 PST)
- Re: [AMBER] On the crushing of the membrane protein simulation (Tue Feb 10 2015 - 09:31:00 PST)
- Re: [AMBER] Calculation of the number of internal waters during md simulation (Tue Feb 10 2015 - 09:23:24 PST)
- [AMBER] On the crushing of the membrane protein simulation (Tue Feb 10 2015 - 07:44:01 PST)
- Re: [AMBER] Calculation of the number of internal waters during md simulation (Tue Feb 10 2015 - 04:58:19 PST)
- Re: [AMBER] Analysis of the MMGBSA decomposition output (Fri Feb 06 2015 - 10:14:39 PST)
- Re: [AMBER] Analysis of the MMGBSA decomposition output (Fri Feb 06 2015 - 01:07:44 PST)
- Re: [AMBER] Calculation of the number of internal waters during md simulation (Fri Feb 06 2015 - 01:05:28 PST)
- Re: [AMBER] Calculation of the number of internal waters during md simulation (Fri Feb 06 2015 - 00:23:39 PST)
- Re: [AMBER] bash scripting for MD tasks (Thu Feb 05 2015 - 06:10:34 PST)
- Re: [AMBER] Calculation of the number of internal waters during md simulation (Thu Feb 05 2015 - 01:24:22 PST)
- Re: [AMBER] Calculation of the number of internal waters during md simulation (Wed Feb 04 2015 - 01:30:51 PST)
- Re: [AMBER] Issue during mmgbsa decomposition (Tue Feb 03 2015 - 12:38:31 PST)
- Re: [AMBER] Calculation of the number of internal waters during md simulation (Tue Feb 03 2015 - 08:38:02 PST)
- [AMBER] Calculation of the number of internal waters during md simulation (Tue Feb 03 2015 - 07:54:03 PST)
- Re: [AMBER] Issue during mmgbsa decomposition (Tue Feb 03 2015 - 07:38:36 PST)
- [AMBER] Analysis of the MMGBSA decomposition output (Tue Feb 03 2015 - 06:34:44 PST)
- Re: [AMBER] Issue during mmgbsa decomposition (Tue Feb 03 2015 - 00:09:11 PST)
- [AMBER] Issue during mmgbsa decomposition (Mon Feb 02 2015 - 04:26:49 PST)
Jason Swails
- Re: [AMBER] help in sdf (Sat Feb 28 2015 - 13:15:18 PST)
- Re: [AMBER] problem with running tutorial C1 (Sat Feb 28 2015 - 04:46:39 PST)
- Re: [AMBER] problem with running tutorial C1 (Sat Feb 28 2015 - 03:13:08 PST)
- Re: [AMBER] Center of mass restraints work on pmemd.MPI, but not on the GPU (Fri Feb 27 2015 - 14:00:06 PST)
- Re: [AMBER] Center of mass restraints work on pmemd.MPI, but not on the GPU (Fri Feb 27 2015 - 12:06:51 PST)
- Re: [AMBER] Parallel GPU calculation (Fri Feb 27 2015 - 06:59:02 PST)
- Re: [AMBER] Error: Unable to run flex; this is required for NAB and antechamber Please check your PATH, or install the program (Fri Feb 27 2015 - 05:27:36 PST)
- Re: [AMBER] Error: Unable to run flex; this is required for NAB and antechamber Please check your PATH, or install the program (Fri Feb 27 2015 - 05:15:02 PST)
- Re: [AMBER] Parallel GPU calculation (Fri Feb 27 2015 - 05:06:09 PST)
- Re: [AMBER] MMGBSA: calculation of deltaG of ligand binding at dimer interface (Thu Feb 26 2015 - 11:32:49 PST)
- Re: [AMBER] MMGBSA: calculation of deltaG of ligand binding at dimer interface (Thu Feb 26 2015 - 09:21:34 PST)
- Re: [AMBER] Cofactor parametrization (Thu Feb 26 2015 - 08:22:08 PST)
- Re: [AMBER] MMGBSA: calculation of deltaG of ligand binding at dimer interface (Thu Feb 26 2015 - 08:11:12 PST)
- Re: [AMBER] H-REMD failure on GPU (Thu Feb 26 2015 - 05:51:49 PST)
- Re: [AMBER] Closest residues to an atom in ptraj (Wed Feb 25 2015 - 05:17:01 PST)
- Re: [AMBER] On the collective dynamics in terms of NMA and PCA (Tue Feb 24 2015 - 18:02:32 PST)
- Re: [AMBER] Chamber problem (Tue Feb 24 2015 - 17:56:07 PST)
- Re: [AMBER] Bond Energy Term for a TIP3P Water (Tue Feb 24 2015 - 11:58:12 PST)
- Re: [AMBER] Steered MD using the jar=1 option (Tue Feb 24 2015 - 04:40:19 PST)
- Re: [AMBER] how to find out if a prmtop file was created with ff12 or ff14 (Mon Feb 23 2015 - 09:41:47 PST)
- Re: [AMBER] Error: Unable to run flex; this is required for NAB and antechamber Please check your PATH, or install the program (Mon Feb 23 2015 - 07:56:04 PST)
- Re: [AMBER] Error: Unable to run flex; this is required for NAB and antechamber Please check your PATH, or install the program (Mon Feb 23 2015 - 05:26:40 PST)
- Re: [AMBER] vlimit exceeded for step (Mon Feb 23 2015 - 05:22:21 PST)
- Re: [AMBER] Problem in generating CCL4 solvent Box (Mon Feb 23 2015 - 03:21:40 PST)
- Re: [AMBER] A tool to analyze amberesults (Sun Feb 22 2015 - 06:58:39 PST)
- Re: [AMBER] vlimit exceeded for step (Sat Feb 21 2015 - 12:30:30 PST)
- Re: [AMBER] Error while running tleap for the ligand containing two chlorine atoms (Sat Feb 21 2015 - 09:32:29 PST)
- Re: [AMBER] Error while running tleap for the ligand containing two chlorine atoms (Fri Feb 20 2015 - 07:48:24 PST)
- Re: [AMBER] Sander in background (Fri Feb 20 2015 - 05:42:52 PST)
- Re: [AMBER] Error while running tleap for the ligand containing two chlorine atoms (Fri Feb 20 2015 - 05:34:06 PST)
- Re: [AMBER] Error while running tleap for the ligand containing two chlorine atoms (Fri Feb 20 2015 - 05:08:12 PST)
- Re: [AMBER] Help calculating RMSD between two proteins (Thu Feb 19 2015 - 13:38:59 PST)
- Re: [AMBER] Bad atom type error in MMPBSA (Wed Feb 18 2015 - 14:09:11 PST)
- Re: [AMBER] Forces from Potential (Wed Feb 18 2015 - 09:39:34 PST)
- Re: [AMBER] memory issue in mmpbsa_py_nabnmode (Tue Feb 17 2015 - 18:58:18 PST)
- Re: [AMBER] memory issue in mmpbsa_py_nabnmode (Tue Feb 17 2015 - 16:15:37 PST)
- Re: [AMBER] memory issue in mmpbsa_py_nabnmode (Tue Feb 17 2015 - 13:21:43 PST)
- Re: [AMBER] memory issue in mmpbsa_py_nabnmode (Tue Feb 17 2015 - 10:18:56 PST)
- Re: [AMBER] memory issue in mmpbsa_py_nabnmode (Tue Feb 17 2015 - 10:17:35 PST)
- Re: [AMBER] Regarding AmberTool 14 installation (Tue Feb 17 2015 - 06:54:53 PST)
- Re: [AMBER] MMGBSA question (Mon Feb 16 2015 - 13:51:57 PST)
- Re: [AMBER] reweighing aMD trajectory (Mon Feb 16 2015 - 10:03:37 PST)
- Re: [AMBER] AMBER: MPI run issue (Mon Feb 16 2015 - 06:15:05 PST)
- Re: [AMBER] dont have atom type (Mon Feb 16 2015 - 05:32:49 PST)
- Re: [AMBER] pressure fluctuation problem (Mon Feb 16 2015 - 05:25:57 PST)
- Re: [AMBER] amber14 hangs on Python datetime module (Sun Feb 15 2015 - 13:28:50 PST)
- Re: [AMBER] pbsa (Sun Feb 15 2015 - 05:37:39 PST)
- Re: [AMBER] pressure fluctuation problem (Sun Feb 15 2015 - 05:35:20 PST)
- Re: [AMBER] ERRORS AND FATAL ERRORS (Apparently died to faulty connections) (Fri Feb 13 2015 - 13:58:18 PST)
- Re: [AMBER] d (Fri Feb 13 2015 - 13:46:37 PST)
- Re: [AMBER] hbond analysis (Fri Feb 13 2015 - 02:04:55 PST)
- Re: [AMBER] memory issue in mmpbsa_py_nabnmode (Thu Feb 12 2015 - 14:44:14 PST)
- Re: [AMBER] MMPBSA - standard deviation (again) (Thu Feb 12 2015 - 08:56:18 PST)
- Re: [AMBER] MMPBSA - standard deviation (again) (Thu Feb 12 2015 - 06:49:15 PST)
- Re: [AMBER] memory issue in mmpbsa_py_nabnmode (Thu Feb 12 2015 - 05:48:49 PST)
- Re: [AMBER] problem with nab (Wed Feb 11 2015 - 06:06:49 PST)
- Re: [AMBER] Density equilibration crash in cuda (Wed Feb 11 2015 - 04:41:16 PST)
- Re: [AMBER] Density equilibration crash in cuda (Wed Feb 11 2015 - 04:05:55 PST)
- Re: [AMBER] Fwd: MMPBSA (Wed Feb 11 2015 - 04:03:22 PST)
- Re: [AMBER] memory issue in mmpbsa_py_nabnmode (Mon Feb 09 2015 - 19:51:23 PST)
- Re: [AMBER] How to find out buried waters? (Mon Feb 09 2015 - 13:25:08 PST)
- Re: [AMBER] Inexperienced User Trying to Solve Simulation Blowup (Sun Feb 08 2015 - 20:16:24 PST)
- Re: [AMBER] Output Forces Acting of Each Atom During MD Simulation using Amber14 (Sun Feb 08 2015 - 18:00:41 PST)
- Re: [AMBER] Assignment of charges for Guanidine (Sun Feb 08 2015 - 13:15:08 PST)
- Re: [AMBER] Assignment of charges for Guanidine (Sat Feb 07 2015 - 16:03:16 PST)
- Re: [AMBER] Assignment of charges for Guanidine (Sat Feb 07 2015 - 05:23:20 PST)
- Re: [AMBER] Analysis of the MMGBSA decomposition output (Fri Feb 06 2015 - 17:28:31 PST)
- Re: [AMBER] Assignment of charges for Guanidine (Fri Feb 06 2015 - 11:19:06 PST)
- Re: [AMBER] Query regarding Dynamics Studies (Fri Feb 06 2015 - 06:53:11 PST)
- Re: [AMBER] Error while running MD for carboxylate anion (Fri Feb 06 2015 - 03:25:34 PST)
- Re: [AMBER] charmmlipid2amber.x (Fri Feb 06 2015 - 03:21:48 PST)
- Re: [AMBER] xleap syntax error (Thu Feb 05 2015 - 12:46:40 PST)
- Re: [AMBER] Real time event with amber mds with shake (Thu Feb 05 2015 - 11:33:26 PST)
- Re: [AMBER] Real time event with amber mds with shake (Thu Feb 05 2015 - 04:55:13 PST)
- Re: [AMBER] ERRORS AND FATAL ERRORS (Apparently died to faulty connections) (Thu Feb 05 2015 - 04:28:49 PST)
- Re: [AMBER] 回复：回复： seek help (Thu Feb 05 2015 - 04:25:11 PST)
- Re: [AMBER] 回复：回复： seek help (Wed Feb 04 2015 - 20:23:34 PST)
- Re: [AMBER] MD cis-azobenzene error (Wed Feb 04 2015 - 15:43:35 PST)
- Re: [AMBER] 回复： seek help (Wed Feb 04 2015 - 08:01:25 PST)
- Re: [AMBER] Amber14 hardware setup (Wed Feb 04 2015 - 05:30:00 PST)
- Re: [AMBER] REGARDING GAUSSIAN BASED SIDE CHAIN MODEL OPTIMIZATION (Wed Feb 04 2015 - 02:28:35 PST)
- Re: [AMBER] no parameter for nicotine (Wed Feb 04 2015 - 02:12:23 PST)
- Re: [AMBER] confusion in md run (Wed Feb 04 2015 - 02:00:49 PST)
- Re: [AMBER] ante-MMPBSA IndexError: list index out of range (Tue Feb 03 2015 - 12:23:53 PST)
- Re: [AMBER] restraintmask error (Tue Feb 03 2015 - 06:51:34 PST)
- Re: [AMBER] ante-MMPBSA IndexError: list index out of range (Mon Feb 02 2015 - 17:16:21 PST)
- Re: [AMBER] Create a 2M urea box (Mon Feb 02 2015 - 17:01:33 PST)
- Re: [AMBER] AmberTools14 installation (Mon Feb 02 2015 - 11:44:36 PST)
- Re: [AMBER] Error: Unable to run flex; this is required for NAB and antechamber Please check your PATH, or install the program (Mon Feb 02 2015 - 06:07:51 PST)
- Re: [AMBER] can not be a parameter fitting (Mon Feb 02 2015 - 05:28:22 PST)
- Re: [AMBER] parameterization (Mon Feb 02 2015 - 05:22:29 PST)
- Re: [AMBER] Error: Unable to run flex; this is required for NAB and antechamber Please check your PATH, or install the program (Mon Feb 02 2015 - 05:16:52 PST)
- Re: [AMBER] Constructing a single Zwitterion in xleap (Sun Feb 01 2015 - 04:55:02 PST)
- Re: [AMBER] Create one larger averaged trajectory file ! (Sun Feb 01 2015 - 03:35:03 PST)
Jochen Hub
- Re: [AMBER] New web server for setup of membrane simulation systems (Wed Feb 18 2015 - 02:22:22 PST)
- [AMBER] New web server for setup of membrane simulation systems (Sun Feb 08 2015 - 03:32:28 PST)
Jodi Ann Hadden
- [AMBER] Announcement: "Hands-On" Workshop on Computational Biophysics in Urbana, IL (April 6-10, 2015) (Mon Feb 16 2015 - 13:41:55 PST)
Jonathan Sheehan
- Re: [AMBER] Solvent Box Wrapping Issue (Sat Feb 21 2015 - 14:03:39 PST)
Jorgen Simonsen
- [AMBER] reparametrize water molecule near metal site (Sun Feb 01 2015 - 11:21:58 PST)
Jose Borreguero
- [AMBER] Unexpected behavior of trajout after invoking filter: Bug? (Tue Feb 24 2015 - 14:57:59 PST)
- Re: [AMBER] Can I use the presence of a particular hydrogen bond as a condition to filter out frames? (Tue Feb 24 2015 - 11:34:10 PST)
- Re: [AMBER] Can I use the presence of a particular hydrogen bond as a condition to filter out frames? (Tue Feb 24 2015 - 11:09:05 PST)
- [AMBER] Can I use the presence of a particular hydrogen bond as a condition to filter out frames? (Tue Feb 24 2015 - 10:16:18 PST)
- Re: [AMBER] Can cpptraj-hbond report the lifetimes of H-bonds between protein and water? (Tue Feb 17 2015 - 12:36:41 PST)
- [AMBER] Can cpptraj-hbond report the lifetimes of H-bonds between protein and water? (Tue Feb 17 2015 - 07:57:46 PST)
- Re: [AMBER] How to find out buried waters? (Mon Feb 09 2015 - 14:45:52 PST)
- [AMBER] How to find out buried waters? (Mon Feb 09 2015 - 12:40:35 PST)
Joseph Baker
- Re: [AMBER] Steered MD using the jar=1 option (Fri Feb 27 2015 - 08:59:52 PST)
- Re: [AMBER] Lipid14 POPE lipids (Fri Feb 27 2015 - 08:29:45 PST)
- Re: [AMBER] Steered MD using the jar=1 option (Thu Feb 26 2015 - 15:13:44 PST)
- Re: [AMBER] Steered MD using the jar=1 option (Mon Feb 23 2015 - 15:20:52 PST)
- Re: [AMBER] Steered MD using the jar=1 option (Mon Feb 23 2015 - 14:32:46 PST)
- [AMBER] Steered MD using the jar=1 option (Mon Feb 23 2015 - 14:07:08 PST)
- [AMBER] Lipid14 POPE lipids (Fri Feb 20 2015 - 04:42:09 PST)
Karl Kirschner
- Re: [AMBER] Constructing a single Zwitterion in xleap (Sun Feb 01 2015 - 07:13:04 PST)
Kenneth Huang
- Re: [AMBER] Help calculating RMSD between two proteins (Thu Feb 19 2015 - 11:00:03 PST)
- Re: [AMBER] Bad atom type error in MMPBSA (Thu Feb 19 2015 - 09:51:55 PST)
- [AMBER] Bad atom type error in MMPBSA (Wed Feb 18 2015 - 13:02:48 PST)
- Re: [AMBER] Analysis of the MMGBSA decomposition output (Fri Feb 06 2015 - 14:49:22 PST)
- Re: [AMBER] Analysis of the MMGBSA decomposition output (Thu Feb 05 2015 - 10:52:52 PST)
- Re: [AMBER] Issue during mmgbsa decomposition (Tue Feb 03 2015 - 11:24:09 PST)
- Re: [AMBER] ante-MMPBSA IndexError: list index out of range (Tue Feb 03 2015 - 10:30:55 PST)
- Re: [AMBER] Issue during mmgbsa decomposition (Tue Feb 03 2015 - 07:22:31 PST)
- [AMBER] ante-MMPBSA IndexError: list index out of range (Mon Feb 02 2015 - 11:57:15 PST)
Khanna, Tarun
- [AMBER] ired t1 relaxation time (Thu Feb 19 2015 - 10:56:57 PST)
Kornelius Zeth
- [AMBER] Question regarding the calculation of binding constants (Tue Feb 17 2015 - 07:17:06 PST)
Kshatresh Dutta Dubey
- Re: [AMBER] Density equilibration crash in cuda (Wed Feb 11 2015 - 04:09:57 PST)
- [AMBER] Density equilibration crash in cuda (Wed Feb 11 2015 - 03:36:33 PST)
Lachele Foley
- Re: [AMBER] Help creating custom monosaccharide unit in Glycam (Fri Feb 20 2015 - 10:39:34 PST)
- Re: [AMBER] Help creating custom monosaccharide unit in Glycam (Wed Feb 18 2015 - 19:16:23 PST)
- Re: [AMBER] d (Fri Feb 13 2015 - 22:51:08 PST)
Lara rajam
- [AMBER] restraining the torsion (Wed Feb 18 2015 - 07:03:09 PST)
- [AMBER] torsion restrain (Mon Feb 16 2015 - 07:16:20 PST)
Mahad Gatti Iou
- Re: [AMBER] FATAL: Atom .R<RU5 13>.A<P 29> does not have a type. (Thu Feb 05 2015 - 08:58:31 PST)
Mahmood Jasim
- Re: [AMBER] combining trajectories (Mon Feb 16 2015 - 08:39:28 PST)
- [AMBER] Umbrella Sampling (Fri Feb 13 2015 - 04:36:08 PST)
Marc van der Kamp
- Re: [AMBER] Error while running tleap for carboxylate anion (Thu Feb 05 2015 - 01:23:27 PST)
Marek Maly
- Re: [AMBER] memory issue in mmpbsa_py_nabnmode (Fri Feb 20 2015 - 06:48:51 PST)
- Re: [AMBER] memory issue in mmpbsa_py_nabnmode (Tue Feb 17 2015 - 18:18:22 PST)
- Re: [AMBER] memory issue in mmpbsa_py_nabnmode (Tue Feb 17 2015 - 13:42:17 PST)
- Re: [AMBER] memory issue in mmpbsa_py_nabnmode (Tue Feb 17 2015 - 12:09:52 PST)
- Re: [AMBER] memory issue in mmpbsa_py_nabnmode (Tue Feb 17 2015 - 07:30:02 PST)
- Re: [AMBER] memory issue in mmpbsa_py_nabnmode (Thu Feb 12 2015 - 15:00:29 PST)
- Re: [AMBER] memory issue in mmpbsa_py_nabnmode (Thu Feb 12 2015 - 14:14:51 PST)
- Re: [AMBER] memory issue in mmpbsa_py_nabnmode (Tue Feb 10 2015 - 07:49:44 PST)
- [AMBER] memory issue in mmpbsa_py_nabnmode (Mon Feb 09 2015 - 15:54:20 PST)
Martin Olsson
- [AMBER] Regarding ff02 force field and RESP method documentation (Mon Feb 23 2015 - 07:50:13 PST)
Maryam Hamzehee
- Re: [AMBER] problem with running tutorial C1 (Sat Feb 28 2015 - 04:27:14 PST)
- [AMBER] problem with running tutorial C1 (Fri Feb 27 2015 - 23:14:21 PST)
- [AMBER] Invitation for proposing a book chapter (Mon Feb 23 2015 - 23:20:20 PST)
- [AMBER] problem with RMSD for small molecule (Thu Feb 19 2015 - 01:45:06 PST)
mmaestre
- [AMBER] Center of mass restraints work on pmemd.MPI, but not on the GPU (Wed Feb 25 2015 - 20:19:51 PST)
- [AMBER] Problems with COM distance restraints plus positional restraints using pmemd.cuda (Tue Feb 17 2015 - 01:27:08 PST)
- [AMBER] Disentangling domains (Tue Feb 10 2015 - 01:17:04 PST)
mmaestre.gate.sinica.edu.tw
- Re: [AMBER] Create a 2M urea box (Mon Feb 02 2015 - 23:41:20 PST)
- Re: [AMBER] Create a 2M urea box (Mon Feb 02 2015 - 15:36:05 PST)
MOHD HOMAIDUR RAHMAN
- [AMBER] Regarding AmberTool 14 installation (Tue Feb 17 2015 - 00:08:40 PST)
Needham, Perri
- Re: [AMBER] Center of mass restraints work on pmemd.MPI, but not on the GPU (Fri Feb 27 2015 - 13:19:23 PST)
- Re: [AMBER] Center of mass restraints work on pmemd.MPI, but not on the GPU (Fri Feb 27 2015 - 11:44:43 PST)
Neha Gandhi
- [AMBER] aMD and scaled MD in amber 14 (Thu Feb 12 2015 - 04:59:24 PST)
Nhai
- Re: [AMBER] Distance/Angle distribution along the trajectory using cpptraj (Wed Feb 18 2015 - 02:50:50 PST)
Nicole Ippolito
- Re: [AMBER] Help calculating RMSD between two proteins (Thu Feb 19 2015 - 13:20:33 PST)
- [AMBER] Help calculating RMSD between two proteins (Thu Feb 19 2015 - 10:09:29 PST)
Niel Henriksen
- [AMBER] Restraint bugs after most recent patch (Thu Feb 05 2015 - 22:41:26 PST)
Nihal Korkmaz
- Re: [AMBER] Forcefield for DNA (Sun Feb 01 2015 - 11:25:18 PST)
Novosielski, Ryan
- Re: [AMBER] Parallel GPU calculation (Fri Feb 27 2015 - 06:59:00 PST)
- Re: [AMBER] amber14 hangs on Python datetime module (Sun Feb 15 2015 - 11:53:24 PST)
- Re: [AMBER] Xeon Phi (Thu Feb 05 2015 - 13:07:07 PST)
- Re: [AMBER] CUDA 5.0 vs 6.5 (Thu Feb 05 2015 - 12:59:46 PST)
- [AMBER] Xeon Phi (Wed Feb 04 2015 - 15:48:21 PST)
- Re: [AMBER] AmberTools14 installation (Mon Feb 02 2015 - 11:30:09 PST)
Parker de Waal
- Re: [AMBER] CUDA- Error pmemd Lipid Membrane (Thu Feb 26 2015 - 19:27:07 PST)
- Re: [AMBER] Distance/Angle distribution along the trajectory using cpptraj (Wed Feb 18 2015 - 05:08:44 PST)
Pengfei Li
- Re: [AMBER] REGARDING GAUSSIAN BASED SIDE CHAIN MODEL OPTIMIZATION (Tue Feb 03 2015 - 07:57:13 PST)
Petr Jurecka
- Re: [AMBER] Forcefield for DNA (Wed Feb 04 2015 - 06:34:55 PST)
pradeep pant
- Re: [AMBER] Problem in generating CCL4 solvent Box (Sun Feb 22 2015 - 23:05:52 PST)
- [AMBER] Problem in generating CCL4 solvent Box (Sun Feb 22 2015 - 10:02:44 PST)
- [AMBER] Fwd: Simulations in CCl4 (Wed Feb 18 2015 - 04:25:21 PST)
- [AMBER] Simulations in CCl4 (Tue Feb 17 2015 - 23:14:38 PST)
Pragya Priyadarshini
- Re: [AMBER] Could not find vdW (or other) parameters for type: Fe2+(Problem Solved) (Sun Feb 15 2015 - 23:18:42 PST)
- [AMBER] Could not find vdW (or other) parameters for type: Fe2+ (Sun Feb 15 2015 - 19:45:46 PST)
Ray Luo, Ph.D.
- Re: [AMBER] Fwd: MMPBSA (Wed Feb 11 2015 - 13:32:14 PST)
Rebeca García Fandiño
- Re: [AMBER] angles values in GAFF for alkynes (Fri Feb 13 2015 - 10:47:39 PST)
- [AMBER] angles values in GAFF for alkynes (Fri Feb 13 2015 - 10:19:12 PST)
- Re: [AMBER] alkynes in GAFF (Thu Feb 12 2015 - 13:51:40 PST)
- Re: [AMBER] alkynes in GAFF (Thu Feb 12 2015 - 04:56:46 PST)
- [AMBER] alkynes in GAFF (Thu Feb 12 2015 - 01:42:06 PST)
Robert Molt
- [AMBER] Inability to use antechamber on Anion (Fri Feb 27 2015 - 18:04:32 PST)
- [AMBER] Inexperienced User Trying to Solve Simulation Blowup (Sun Feb 08 2015 - 20:02:03 PST)
- [AMBER] Constructing a single Zwitterion in xleap (Sat Jan 31 2015 - 21:36:16 PST)
Robert Wohlhueter
- Re: [AMBER] amber14 hangs on Python datetime module (Sun Feb 15 2015 - 12:36:53 PST)
- Re: [AMBER] amber14 hangs on Python datetime module (Sun Feb 15 2015 - 12:34:05 PST)
- Re: [AMBER] amber14 hangs on Python datetime module (Sun Feb 15 2015 - 12:13:12 PST)
- [AMBER] amber14 hangs on Python datetime module (Sun Feb 15 2015 - 11:06:55 PST)
Robin Jain
- [AMBER] help in sdf (Sat Feb 28 2015 - 08:39:58 PST)
- [AMBER] confusion in md run (Wed Feb 04 2015 - 00:12:43 PST)
Romero, Raquel
- [AMBER] CUDA- Error pmemd Lipid Membrane (Thu Feb 26 2015 - 18:02:11 PST)
Ross Walker
- Re: [AMBER] GTX980 PERFORMANCE (Fri Feb 27 2015 - 09:05:53 PST)
- Re: [AMBER] Lipid14 POPE lipids (Fri Feb 27 2015 - 08:58:09 PST)
- Re: [AMBER] CUDA- Error pmemd Lipid Membrane (Thu Feb 26 2015 - 19:36:26 PST)
- Re: [AMBER] Center of mass restraints work on pmemd.MPI, but not on the GPU (Wed Feb 25 2015 - 20:29:53 PST)
- Re: [AMBER] Lipid14 POPE lipids (Fri Feb 20 2015 - 12:58:21 PST)
- [AMBER] Invitation to Attend Computational Chemical Biology Conference (Aug 6th to 9th 2015), Cairns, Australia (http://tinyurl.com/nyblv7o) (Tue Feb 17 2015 - 08:26:26 PST)
- Re: [AMBER] pmemd.cuda error cudaMemcpy GpuBuffer:: (Sat Feb 14 2015 - 10:38:53 PST)
- Re: [AMBER] pmemd.cuda error cudaMemcpy GpuBuffer:: (Sat Feb 14 2015 - 05:49:46 PST)
- Re: [AMBER] On the crushing of the membrane protein simulation (Tue Feb 10 2015 - 09:06:38 PST)
- Re: [AMBER] MD JOB was terminated before achieving the No. of steps (Fri Feb 06 2015 - 12:56:30 PST)
- Re: [AMBER] Restraint bugs after most recent patch (Fri Feb 06 2015 - 12:53:42 PST)
- Re: [AMBER] Xeon Phi (Thu Feb 05 2015 - 13:27:24 PST)
- Re: [AMBER] Xeon Phi (Thu Feb 05 2015 - 12:57:40 PST)
- Re: [AMBER] CUDA 5.0 vs 6.5 (Thu Feb 05 2015 - 12:54:30 PST)
- Re: [AMBER] Xeon Phi (Wed Feb 04 2015 - 16:42:23 PST)
- [AMBER] Second announcement: AMBER Workshop - Haifa Israel, Sun Apr 26th to 30th. (Tue Feb 03 2015 - 13:44:39 PST)
- Re: [AMBER] pmemd.cuda.MPI interruption error! (Mon Feb 02 2015 - 16:31:49 PST)
Ruchika Bhat
- Re: [AMBER] Query regarding Dynamics Studies (Fri Feb 06 2015 - 11:04:14 PST)
- [AMBER] Query regarding Dynamics Studies (Fri Feb 06 2015 - 05:03:26 PST)
Ryan Novosielski
- [AMBER] CUDA 5.0 vs 6.5 (Thu Feb 05 2015 - 12:48:03 PST)
- Re: [AMBER] Xeon Phi (Thu Feb 05 2015 - 12:45:40 PST)
Scott Brozell
- Re: [AMBER] REMD jobs crashing repeatedly on GPUs (Fri Feb 27 2015 - 09:33:03 PST)
- [AMBER] Announcement: Release of DOCK 6.7 (Thu Feb 12 2015 - 16:27:51 PST)
Shreeramesh
- Re: [AMBER] Error while running tleap for the ligand containing two chlorine atoms (Sat Feb 21 2015 - 07:41:08 PST)
- Re: [AMBER] Error while running tleap for the ligand containing two chlorine atoms (Sat Feb 21 2015 - 07:29:47 PST)
- Re: [AMBER] Error while running tleap for the ligand containing two chlorine atoms (Fri Feb 20 2015 - 04:33:05 PST)
- Re: [AMBER] Error while running tleap for the ligand containing two chlorine atoms (Fri Feb 20 2015 - 03:23:44 PST)
- [AMBER] Error while running tleap for the ligand containing two chlorine atoms (Fri Feb 20 2015 - 02:58:03 PST)
- [AMBER] MD JOB was terminated before achieving the No. of steps (Fri Feb 06 2015 - 01:28:53 PST)
- Re: [AMBER] Error while running MD for carboxylate anion (Fri Feb 06 2015 - 01:25:44 PST)
- [AMBER] Error while running tleap for carboxylate anion (Thu Feb 05 2015 - 01:18:37 PST)
- Re: [AMBER] Error while running antechamber and tleap for silver salt of carboxylic acid (Wed Feb 04 2015 - 04:25:24 PST)
- [AMBER] Error while running antechamber and tleap for silver salt of carboxylic acid (Wed Feb 04 2015 - 03:06:06 PST)
- [AMBER] error in equil.rst steps of AMBER (Mon Feb 02 2015 - 06:32:51 PST)
Shukla, Saurabh
- [AMBER] Chamber problem (Tue Feb 24 2015 - 17:24:05 PST)
Sofia Vasilakaki
- [AMBER] Amber14 hardware setup (Wed Feb 04 2015 - 04:59:49 PST)
Stefano Motta
- Re: [AMBER] Parallel GPU calculation (Fri Feb 27 2015 - 06:14:12 PST)
- [AMBER] Parallel GPU calculation (Fri Feb 27 2015 - 03:46:42 PST)
Swithin Hanosh
- [AMBER] REGARDING WARNINGS RETURNED DURING FORCE FIELD GENERATION (Tue Feb 24 2015 - 11:19:27 PST)
- [AMBER] REGARDING GAUSSIAN BASED SIDE CHAIN MODEL OPTIMIZATION (Wed Feb 04 2015 - 01:30:08 PST)
- [AMBER] REGARDING GAUSSIAN BASED SIDE CHAIN MODEL OPTIMIZATION (Tue Feb 03 2015 - 07:06:12 PST)
Sylvester Tumusiime
- [AMBER] csv file for DPC (Fri Feb 13 2015 - 12:41:39 PST)
Takuya Uto
- [AMBER] can not be a parameter fitting (Sun Feb 01 2015 - 21:54:36 PST)
Thomas Evangelidis
- Re: [AMBER] Error: Expected DCD block size of 48, got -1029941464 (Mon Feb 23 2015 - 09:16:24 PST)
- [AMBER] how to find out if a prmtop file was created with ff12 or ff14 (Mon Feb 23 2015 - 08:27:37 PST)
- Re: [AMBER] Error: Expected DCD block size of 48, got -1029941464 (Sat Feb 21 2015 - 16:04:48 PST)
- Re: [AMBER] Error: Expected DCD block size of 48, got -1029941464 (Sat Feb 21 2015 - 13:21:06 PST)
- [AMBER] Error: Expected DCD block size of 48, got -1029941464 (Sat Feb 21 2015 - 13:06:03 PST)
Urszula Uciechowska
- Re: [AMBER] single strand DNA in hairpin conformation (Fri Feb 20 2015 - 05:46:52 PST)
- Re: [AMBER] single strand DNA in hairpin conformation (Wed Feb 18 2015 - 08:55:42 PST)
- [AMBER] single strand DNA in hairpin conformation (Thu Feb 12 2015 - 01:13:02 PST)
- [AMBER] problem with nab (Wed Feb 11 2015 - 05:53:12 PST)
- [AMBER] restraintmask error (Tue Feb 03 2015 - 06:45:53 PST)
Valentina Romano
- [AMBER] A tool to analyze amberesults (Sun Feb 22 2015 - 06:56:15 PST)
- [AMBER] Sander in background (Fri Feb 20 2015 - 05:36:28 PST)
- Re: [AMBER] ANTECHAMBER: error in mol2 file (Fri Feb 20 2015 - 03:56:49 PST)
- [AMBER] ANTECHAMBER: error in mol2 file (Fri Feb 20 2015 - 01:59:45 PST)
Vijay Achari
- Re: [AMBER] solute-solvent hbond fraction value is more than 1.0 (Tue Feb 17 2015 - 20:37:34 PST)
- [AMBER] solute-solvent hbond fraction value is more than 1.0 (Mon Feb 16 2015 - 23:14:55 PST)
- Re: [AMBER] combining trajectories (Mon Feb 16 2015 - 21:12:58 PST)
- [AMBER] rotational diffusion (Fri Feb 13 2015 - 03:00:08 PST)
- Re: [AMBER] Water diffusion - in 2D and 3D (Fri Feb 13 2015 - 02:42:07 PST)
- Re: [AMBER] Water diffusion - in 2D and 3D (Fri Feb 13 2015 - 02:04:02 PST)
- [AMBER] Water diffusion - in 2D and 3D (Thu Feb 12 2015 - 22:11:24 PST)
- Re: [AMBER] calculating HB lifetime (Thu Feb 12 2015 - 07:39:18 PST)
- Re: [AMBER] calculating HB lifetime (Thu Feb 12 2015 - 07:37:13 PST)
- Re: [AMBER] calculating HB lifetime (Thu Feb 12 2015 - 07:28:08 PST)
- Re: [AMBER] calculating HB lifetime (Thu Feb 12 2015 - 07:19:12 PST)
- Re: [AMBER] calculating HB lifetime (Thu Feb 12 2015 - 01:19:13 PST)
- Re: [AMBER] calculating HB lifetime (Thu Feb 12 2015 - 00:09:58 PST)
- Re: [AMBER] calculating HB lifetime (Wed Feb 11 2015 - 17:32:23 PST)
- Re: [AMBER] calculating HB lifetime (Wed Feb 11 2015 - 09:35:50 PST)
- [AMBER] calculating HB lifetime (Wed Feb 11 2015 - 02:18:08 PST)
vijay kumar narsapuram
- Re: [AMBER] Error: Unable to run flex; this is required for NAB and antechamber Please check your PATH, or install the program (Fri Feb 27 2015 - 05:25:45 PST)
- Re: [AMBER] Error: Unable to run flex; this is required for NAB and antechamber Please check your PATH, or install the program (Fri Feb 27 2015 - 05:11:21 PST)
- Re: [AMBER] Error: Unable to run flex; this is required for NAB and antechamber Please check your PATH, or install the program (Mon Feb 23 2015 - 06:45:40 PST)
- Re: [AMBER] Error: Unable to run flex; this is required for NAB and antechamber Please check your PATH, or install the program (Mon Feb 23 2015 - 04:49:54 PST)
- Re: [AMBER] Error: Unable to run flex; this is required for NAB and antechamber Please check your PATH, or install the program (Mon Feb 02 2015 - 05:48:46 PST)
- Re: [AMBER] Error: Unable to run flex; this is required for NAB and antechamber Please check your PATH, or install the program (Mon Feb 02 2015 - 05:47:12 PST)
- Re: [AMBER] Error: Unable to run flex; this is required for NAB and antechamber Please check your PATH, or install the program (Sun Feb 01 2015 - 22:15:41 PST)
- [AMBER] Error: Unable to run flex; this is required for NAB and antechamber Please check your PATH, or install the program (Sun Feb 01 2015 - 12:59:16 PST)
Vlad Cojocaru
- Re: [AMBER] atomicfluct issue (Mon Feb 23 2015 - 05:56:42 PST)
- [AMBER] LAST CALL: Free Energy Workshop, Münster, March 9-11, 2015 (Tue Feb 03 2015 - 12:35:33 PST)
Wei Ye
- Re: [AMBER] FATAL: Atom .R<GRA 1>.A<H31 197> does not have a type. (Thu Feb 26 2015 - 22:59:18 PST)
wjli
- [AMBER] 回复： MCPB (Fri Feb 06 2015 - 02:01:10 PST)
zahra khatti
- [AMBER] pbsa (Sun Feb 15 2015 - 10:53:34 PST)
- Re: [AMBER] pbsa (Sun Feb 15 2015 - 09:44:13 PST)
- Re: [AMBER] pbsa (Sun Feb 15 2015 - 06:48:24 PST)
- [AMBER] pbsa (Sat Feb 14 2015 - 21:31:46 PST)
Zhang, Sixue
- Re: [AMBER] Bond Energy Term for a TIP3P Water (Tue Feb 24 2015 - 16:51:16 PST)
- Re: [AMBER] Bond Energy Term for a TIP3P Water (Tue Feb 24 2015 - 13:08:17 PST)
- Re: [AMBER] Bond Energy Term for a TIP3P Water (Tue Feb 24 2015 - 11:37:18 PST)
- [AMBER] Bond Energy Term for a TIP3P Water (Tue Feb 24 2015 - 11:30:55 PST)
- Re: [AMBER] Solvent Box Wrapping Issue (Sat Feb 21 2015 - 09:21:32 PST)
- [AMBER] Solvent Box Wrapping Issue (Fri Feb 20 2015 - 13:04:43 PST)
徐晓庶
- [AMBER] Question about hbond analysis (Sat Feb 14 2015 - 23:06:51 PST)
新生大侠
- [AMBER] 回复：回复：回复： seek help (Thu Feb 05 2015 - 06:09:07 PST)
- [AMBER] 回复：回复：回复： seek help (Wed Feb 04 2015 - 22:38:16 PST)
- [AMBER] 回复：回复： seek help (Wed Feb 04 2015 - 19:02:31 PST)
- [AMBER] 回复： seek help (Wed Feb 04 2015 - 06:55:13 PST)
- [AMBER] seek help (Wed Feb 04 2015 - 03:42:57 PST)
汪盛
- [AMBER] pmemd.cuda.MPI interruption error! (Mon Feb 02 2015 - 16:13:45 PST)
김준기
- [AMBER] d (Fri Feb 13 2015 - 07:26:27 PST)

Amber Archive Feb 2015 by author