Amber Archive Aug 2015: by author

Abelak, Kavin
- Re: [AMBER] Trying to perform a heating MD in increments (Tue Aug 04 2015 - 03:13:19 PDT)
achim.sandmann.chemie.stud.uni-erlangen.de
- Re: [AMBER] Non-equilibrium pulling with plane-point restraints (Fri Aug 28 2015 - 01:20:03 PDT)
- Re: [AMBER] Non-equilibrium pulling with plane-point restraints (Thu Aug 27 2015 - 00:46:14 PDT)
Adrian Roitberg
- Re: [AMBER] hydrogen mass repartitioning visualization in chimera (Thu Aug 20 2015 - 17:15:04 PDT)
- Re: [AMBER] the better box size for calculating host-guest interaction energies (Thu Aug 20 2015 - 09:41:52 PDT)
- Re: [AMBER] NPT equilibration failed (Tue Aug 18 2015 - 06:02:38 PDT)
- Re: [AMBER] About the QMMM simulation with LIO software (Mon Aug 17 2015 - 11:10:36 PDT)
- Re: [AMBER] RMSD and average value of interatomic distance? (Sat Aug 15 2015 - 07:15:34 PDT)
- Re: [AMBER] Overflow of the Fortran format used to store coordinates in the inpcrd/restart files. (Tue Aug 11 2015 - 11:46:44 PDT)
- Re: [AMBER] issue with 4 fs hydrogen mass repartitioning taking more time than a standard 2 fs simulation in AMBER14 (Wed Aug 05 2015 - 16:34:10 PDT)
- Re: [AMBER] [cpptraj] Kullback Leibler Divergence cutoff choice (Wed Aug 05 2015 - 09:09:45 PDT)
Albert
- [AMBER] CL topology (Wed Aug 19 2015 - 00:04:44 PDT)
- Re: [AMBER] NPT equilibration failed (Tue Aug 18 2015 - 06:09:08 PDT)
- [AMBER] NPT equilibration failed (Tue Aug 18 2015 - 05:58:56 PDT)
Amber mail
- Re: [AMBER] The protein is Leaving the water box! (Fri Aug 14 2015 - 05:11:25 PDT)
- [AMBER] The protein is Leaving the water box! (Thu Aug 13 2015 - 17:36:59 PDT)
- Re: [AMBER] cpptraj frames clustering limit (Wed Aug 12 2015 - 06:55:03 PDT)
- Re: [AMBER] Overflow of the Fortran format used to store coordinates in the inpcrd/restart files. (Wed Aug 12 2015 - 06:34:40 PDT)
- Re: [AMBER] Overflow of the Fortran format used to store coordinates in the inpcrd/restart files. (Tue Aug 11 2015 - 13:53:05 PDT)
- Re: [AMBER] Overflow of the Fortran format used to store coordinates in the inpcrd/restart files. (Tue Aug 11 2015 - 10:33:45 PDT)
- [AMBER] Overflow of the Fortran format used to store coordinates in the inpcrd/restart files. (Tue Aug 11 2015 - 10:18:16 PDT)
- Re: [AMBER] cpptraj - RMSD (Sun Aug 09 2015 - 13:50:33 PDT)
- [AMBER] cpptraj - RMSD (Sat Aug 08 2015 - 23:51:02 PDT)
- Re: [AMBER] Trying to perform a heating MD in increments (Tue Aug 04 2015 - 07:02:03 PDT)
- [AMBER] Trying to perform a heating MD in increments (Tue Aug 04 2015 - 01:39:02 PDT)
anilkumarsahoo.physics.iisc.ernet.in
- Re: [AMBER] Problem In Performing MMPBSA Calculation for System Containing Lipids (Tue Aug 25 2015 - 17:04:47 PDT)
- [AMBER] Problem In Performing MMPBSA Calculation for System Containing Lipids (Tue Aug 25 2015 - 04:29:38 PDT)
anu chandra
- Re: [AMBER] Total interaction energy between monomeric units of a dimer (Wed Aug 26 2015 - 10:04:15 PDT)
- Re: [AMBER] Solvent accessible surface area (SASA) calculation in CPPTRJ (Fri Aug 21 2015 - 08:58:51 PDT)
- [AMBER] Solvent accessible surface area (SASA) calculation in CPPTRJ (Thu Aug 20 2015 - 09:35:31 PDT)
- Re: [AMBER] Total interaction energy between monomeric units of a dimer (Thu Aug 20 2015 - 04:04:10 PDT)
- Re: [AMBER] Total interaction energy between monomeric units of a dimer (Tue Aug 18 2015 - 07:17:19 PDT)
- [AMBER] Total interaction energy between monomeric units of a dimer (Tue Aug 18 2015 - 04:55:46 PDT)
- [AMBER] A query about MMPBSA.py calcualtion (Sun Aug 16 2015 - 06:45:50 PDT)
- [AMBER] PCA analysis (Tue Aug 04 2015 - 15:55:05 PDT)
Ara Abramyan
- Re: [AMBER] Using MMPBSA.py with CHARMM force field (Fri Aug 21 2015 - 08:47:48 PDT)
- [AMBER] Using MMPBSA.py with CHARMM force field (Thu Aug 20 2015 - 13:43:11 PDT)
Arjun Sharma
- Re: [AMBER] cpin error (Fri Aug 28 2015 - 07:00:23 PDT)
- Re: [AMBER] Cpin error (Thu Aug 27 2015 - 08:31:18 PDT)
- [AMBER] cpin error (Tue Aug 25 2015 - 16:45:04 PDT)
bharat lakhani
- Re: [AMBER] MM-PBSA atom types (Wed Aug 05 2015 - 11:32:41 PDT)
- Re: [AMBER] MM-PBSA atom types (Tue Aug 04 2015 - 08:40:42 PDT)
- Re: [AMBER] MM-PBSA atom types (Mon Aug 03 2015 - 15:50:47 PDT)
- [AMBER] MM-PBSA atom types (Mon Aug 03 2015 - 15:24:53 PDT)
- [AMBER] MM-PBSA free energy calculation with keeping x-ray water (Mon Aug 03 2015 - 12:45:26 PDT)
Bill Ross
- Re: [AMBER] What is the best way to study a dynamics route of a molecule to enter a protein (Thu Aug 27 2015 - 16:47:45 PDT)
- Re: [AMBER] how to add lipid (Tue Aug 25 2015 - 13:13:22 PDT)
- Re: [AMBER] how to add lipid (Tue Aug 25 2015 - 01:36:57 PDT)
- Re: [AMBER] how to add lipid (Mon Aug 24 2015 - 12:20:41 PDT)
- Re: [AMBER] help in density equilibration (Sun Aug 23 2015 - 23:21:39 PDT)
- Re: [AMBER] how to add lipid (Sun Aug 23 2015 - 23:15:09 PDT)
- Re: [AMBER] tleap ask for bond to zinc ion (Sun Aug 23 2015 - 14:15:46 PDT)
- Re: [AMBER] how to add lipid (Sun Aug 23 2015 - 14:05:43 PDT)
- Re: [AMBER] adding NaCl (Wed Aug 19 2015 - 01:37:32 PDT)
- Re: [AMBER] Big potential difference between conformation in MD simulation and optimized conformation in Gaussian. (Mon Aug 17 2015 - 13:09:34 PDT)
- Re: [AMBER] the better box size (Fri Aug 14 2015 - 12:18:17 PDT)
Brittany Boykin
- [AMBER] AMBER Autoimage Warning (Mon Aug 24 2015 - 09:42:04 PDT)
- [AMBER] Autoimage Warning (Fri Aug 21 2015 - 08:10:12 PDT)
Carlos Simmerling
- Re: [AMBER] mismatch base pair from nab (Tue Aug 25 2015 - 06:20:10 PDT)
- Re: [AMBER] mismatch base pair from nab (Tue Aug 25 2015 - 04:54:29 PDT)
- [AMBER] awards applications open for ACS Division of Computers in Chemistry (Fri Aug 07 2015 - 08:33:37 PDT)
CHAMI F.
- [AMBER] parmch2 versus parmchk (Fri Aug 07 2015 - 06:00:23 PDT)
Charles Lin
- Re: [AMBER] how to add lipid (Thu Aug 27 2015 - 10:22:14 PDT)
- Re: [AMBER] how to add lipid (Tue Aug 25 2015 - 10:10:15 PDT)
Chinh Su Tran To
- [AMBER] ****** in results? (Sun Aug 16 2015 - 23:51:48 PDT)
cieplak.cgl.ucsf.edu
- Re: [AMBER] RESP fitting (Wed Aug 19 2015 - 13:48:16 PDT)
Damiano Spadoni
- Re: [AMBER] hpc error (Fri Aug 28 2015 - 04:37:17 PDT)
- [AMBER] hpc error (Tue Aug 18 2015 - 06:43:23 PDT)
Daniel Roe
- Re: [AMBER] closest command in cpptraj (Wed Aug 26 2015 - 07:48:44 PDT)
- Re: [AMBER] Regarding printing of trajectory (Tue Aug 25 2015 - 07:34:16 PDT)
- Re: [AMBER] Problem In Performing MMPBSA Calculation for System Containing Lipids (Tue Aug 25 2015 - 06:26:16 PDT)
- Re: [AMBER] closest command in cpptraj (Tue Aug 25 2015 - 06:23:48 PDT)
- Re: [AMBER] AMBER Autoimage Warning (Mon Aug 24 2015 - 10:42:42 PDT)
- Re: [AMBER] Regarding No of Hydrogen bonds (vs) Residue wise (Mon Aug 24 2015 - 07:40:28 PDT)
- Re: [AMBER] closest command in cpptraj (Fri Aug 21 2015 - 14:46:05 PDT)
- Re: [AMBER] cpptraj RMSD stats (Tue Aug 18 2015 - 08:34:46 PDT)
- Re: [AMBER] cpptraj perress RMSD (Tue Aug 18 2015 - 07:53:51 PDT)
- Re: [AMBER] cpptraj RMSD stats (Tue Aug 18 2015 - 06:50:20 PDT)
- Re: [AMBER] Total interaction energy between monomeric units of a dimer (Tue Aug 18 2015 - 06:05:49 PDT)
- Re: [AMBER] cpptraj cluster in MPI (Mon Aug 17 2015 - 20:12:01 PDT)
- Re: [AMBER] ImportError: No module named mcpb.gene_model_files (Mon Aug 17 2015 - 08:24:12 PDT)
- Re: [AMBER] saveamberparm (Mon Aug 17 2015 - 08:17:23 PDT)
- Re: [AMBER] RMSD and average value of interatomic distance? (Sat Aug 15 2015 - 08:13:50 PDT)
- Re: [AMBER] help in rdf (Fri Aug 14 2015 - 08:47:07 PDT)
- Re: [AMBER] cpptraj frames clustering limit (Thu Aug 13 2015 - 11:43:25 PDT)
- Re: [AMBER] Warning: ieee_inexact is signaling PMEMD Terminated Abnormally! (Wed Aug 12 2015 - 09:58:05 PDT)
- Re: [AMBER] Warning: ieee_inexact is signaling PMEMD Terminated Abnormally! (Wed Aug 12 2015 - 08:18:21 PDT)
- Re: [AMBER] cpptraj frames clustering limit (Wed Aug 12 2015 - 08:06:15 PDT)
- Re: [AMBER] "mask" command failure (Tue Aug 11 2015 - 12:25:24 PDT)
- Re: [AMBER] Overflow of the Fortran format used to store coordinates in the inpcrd/restart files. (Tue Aug 11 2015 - 12:03:09 PDT)
- Re: [AMBER] "mask" command failure (Mon Aug 10 2015 - 10:16:13 PDT)
- Re: [AMBER] cpptraj gist: Eww energies (Mon Aug 10 2015 - 10:12:57 PDT)
- Re: [AMBER] Problem with cpptraj autoimage command (Fri Aug 07 2015 - 06:18:33 PDT)
- Re: [AMBER] "mask" command failure (Thu Aug 06 2015 - 19:51:49 PDT)
- Re: [AMBER] "mask" command failure (Thu Aug 06 2015 - 19:42:45 PDT)
- Re: [AMBER] PCA: comparing PCs from different trajectories (Thu Aug 06 2015 - 13:06:45 PDT)
- Re: [AMBER] Problem with cpptraj autoimage command (Thu Aug 06 2015 - 07:29:35 PDT)
- Re: [AMBER] large .mdcrd splitting (Thu Aug 06 2015 - 04:39:35 PDT)
- Re: [AMBER] could not open mdcrd file (Thu Aug 06 2015 - 04:32:49 PDT)
- Re: [AMBER] PCA: comparing PCs from different trajectories (Wed Aug 05 2015 - 11:18:55 PDT)
- Re: [AMBER] [cpptraj] Kullback Leibler Divergence cutoff choice (Wed Aug 05 2015 - 10:31:31 PDT)
- Re: [AMBER] PCA: comparing PCs from different trajectories (Wed Aug 05 2015 - 10:16:24 PDT)
- Re: [AMBER] .mdcrd to .trr conversion problem (Wed Aug 05 2015 - 09:09:13 PDT)
- Re: [AMBER] PCA analysis (Tue Aug 04 2015 - 19:10:47 PDT)
- Re: [AMBER] PMEMD: Warning: ieee_inexact is signaling (Mon Aug 03 2015 - 12:59:58 PDT)
- Re: [AMBER] PCA: generate histogram (Mon Aug 03 2015 - 07:47:48 PDT)
- Re: [AMBER] PCA: generate histogram (Mon Aug 03 2015 - 07:01:30 PDT)
- Re: [AMBER] PCA: generate histogram (Mon Aug 03 2015 - 06:14:52 PDT)
David A Case
- Re: [AMBER] cyclic peptides (Sun Aug 30 2015 - 18:13:33 PDT)
- Re: [AMBER] Segmentation Fault with pmemd (Sun Aug 30 2015 - 12:46:12 PDT)
- Re: [AMBER] Segmentation Fault with pmemd (Sat Aug 29 2015 - 04:42:34 PDT)
- Re: [AMBER] How do I study the dimerisation energy (i.e. energy required to form a dimer from two monomeric units) using AMBER? (Sat Aug 29 2015 - 04:38:01 PDT)
- Re: [AMBER] Confusion in running QM/MMGBSA (Fri Aug 28 2015 - 18:34:08 PDT)
- Re: [AMBER] What is the best way to study a dynamics route of a molecule to enter a protein (Fri Aug 28 2015 - 10:23:58 PDT)
- Re: [AMBER] hpc error (Fri Aug 28 2015 - 05:20:16 PDT)
- Re: [AMBER] What is the best way to study a dynamics route of a molecule to enter a protein (Fri Aug 28 2015 - 05:11:22 PDT)
- Re: [AMBER] Molsurf: some questions on usage (Fri Aug 28 2015 - 05:03:18 PDT)
- Re: [AMBER] Problem In Performing MMPBSA Calculation for System Containing Lipids (Wed Aug 26 2015 - 05:33:02 PDT)
- Re: [AMBER] What is the best way to study a dynamics route of a molecule to enter a protein (Wed Aug 26 2015 - 05:26:19 PDT)
- Re: [AMBER] mismatch base pair from nab (Tue Aug 25 2015 - 12:57:41 PDT)
- Re: [AMBER] Regarding printing of trajectory (Tue Aug 25 2015 - 05:20:19 PDT)
- Re: [AMBER] how to neutralized my system with Na+ ions (Tue Aug 25 2015 - 05:15:12 PDT)
- Re: [AMBER] upgrading to AT15 (from AT14) (Mon Aug 24 2015 - 05:52:05 PDT)
- Re: [AMBER] help in density equilibration (Mon Aug 24 2015 - 05:47:41 PDT)
- Re: [AMBER] tleap ask for bond to zinc ion (Mon Aug 24 2015 - 05:34:04 PDT)
- Re: [AMBER] Solvent accessible surface area (SASA) calculation in CPPTRJ (Fri Aug 21 2015 - 10:36:59 PDT)
- Re: [AMBER] ImportError: No module named mcpb.gene_model_files (Fri Aug 21 2015 - 10:33:41 PDT)
- Re: [AMBER] Using MMPBSA.py with CHARMM force field (Fri Aug 21 2015 - 08:10:27 PDT)
- Re: [AMBER] upgrading to AT15 (from AT14) (Fri Aug 21 2015 - 04:58:44 PDT)
- Re: [AMBER] the better box size for calculating host-guest interaction energies (Thu Aug 20 2015 - 08:51:23 PDT)
- Re: [AMBER] Total interaction energy between monomeric units of a dimer (Thu Aug 20 2015 - 05:00:55 PDT)
- Re: [AMBER] xleap numbering in residues (Thu Aug 20 2015 - 04:54:43 PDT)
- Re: [AMBER] Total interaction energy between monomeric units of a dimer (Wed Aug 19 2015 - 09:22:16 PDT)
- Re: [AMBER] RESP fitting (Wed Aug 19 2015 - 08:03:07 PDT)
- Re: [AMBER] Help needed regarding simulating Lipopolysaccharide (Wed Aug 19 2015 - 07:53:11 PDT)
- Re: [AMBER] upgrading to AT15 (from AT14) (Tue Aug 18 2015 - 10:48:51 PDT)
- Re: [AMBER] hpc error (Tue Aug 18 2015 - 07:12:59 PDT)
- Re: [AMBER] acpype (Tue Aug 18 2015 - 06:28:25 PDT)
- Re: [AMBER] saveamberparm (Mon Aug 17 2015 - 08:34:19 PDT)
- Re: [AMBER] STOP PMEMD Terminated Abnormally! (Mon Aug 17 2015 - 04:51:55 PDT)
- Re: [AMBER] Help needed regarding simulating Lipopolysaccharide (Mon Aug 17 2015 - 04:49:21 PDT)
- Re: [AMBER] ****** in results? (Mon Aug 17 2015 - 04:38:03 PDT)
- Re: [AMBER] cg in GAFF: amb2gmx.pl vs virtualchemistry - LJ well depth (Wed Aug 12 2015 - 18:16:16 PDT)
- Re: [AMBER] acetylate and ammoniate (Wed Aug 12 2015 - 08:39:54 PDT)
- Re: [AMBER] FW: Regarding AMBER14 Error (Tue Aug 11 2015 - 04:42:16 PDT)
- Re: [AMBER] FW: Regarding AMBER 14 (Tue Aug 11 2015 - 04:41:18 PDT)
- Re: [AMBER] cpptraj - RMSD (Sun Aug 09 2015 - 05:02:44 PDT)
- Re: [AMBER] Automated restart (Sat Aug 08 2015 - 05:42:16 PDT)
- Re: [AMBER] Thermodynamic integration goes wrong in lambda =0 while lambda = 1 is ok!! (Thu Aug 06 2015 - 09:55:44 PDT)
- Re: [AMBER] large .mdcrd splitting (Thu Aug 06 2015 - 05:38:20 PDT)
- Re: [AMBER] Thermodynamic integration goes wrong in lambda =0 while lambda = 1 is ok!! (Thu Aug 06 2015 - 05:35:01 PDT)
- Re: [AMBER] antechamber error (Wed Aug 05 2015 - 09:19:09 PDT)
- Re: [AMBER] ired analysis: No modes data specified (Tue Aug 04 2015 - 06:44:13 PDT)
- Re: [AMBER] How to construct the Ala3 peptide shown in this picture? (Tue Aug 04 2015 - 06:06:35 PDT)
- Re: [AMBER] Antechamber for boronic acid derivatives? (Mon Aug 03 2015 - 04:56:36 PDT)
- Re: [AMBER] Implicit solvent simulation is unexpectedly slow (Sun Aug 02 2015 - 05:30:43 PDT)
Debodyuti Dutta
- [AMBER] MMPBSA.py problem (Tue Aug 04 2015 - 03:16:45 PDT)
diane lynch
- Re: [AMBER] [Solved] amber14 gpu webpage lists cuda 7.0 as supported (Wed Aug 12 2015 - 19:02:36 PDT)
- Re: [AMBER] amber14 gpu webpage lists cuda 7.0 as supported (Wed Aug 12 2015 - 19:01:56 PDT)
Dow Hurst
- [AMBER] [Solved] amber14 gpu webpage lists cuda 7.0 as supported (Wed Aug 12 2015 - 18:59:31 PDT)
- [AMBER] amber14 gpu webpage lists cuda 7.0 as supported (Wed Aug 12 2015 - 18:53:11 PDT)
Edward Kalkreuter
- [AMBER] RED Server for Altered Amino Acid (Wed Aug 05 2015 - 19:56:11 PDT)
Eg eh
- [AMBER] Big potential difference between conformation in MD simulation and optimized conformation in Gaussian. (Mon Aug 17 2015 - 12:08:44 PDT)
Eiros Zamora, Juan
- Re: [AMBER] PCA: comparing PCs from different trajectories (Thu Aug 06 2015 - 09:32:48 PDT)
- Re: [AMBER] [cpptraj] Kullback Leibler Divergence cutoff choice (Wed Aug 05 2015 - 09:23:44 PDT)
- [AMBER] [cpptraj] Kullback Leibler Divergence cutoff choice (Wed Aug 05 2015 - 09:01:18 PDT)
Eleftherios A P Lambros
- Re: [AMBER] MCPB.py mismatch error (Mon Aug 03 2015 - 13:39:05 PDT)
Eugene Radchenko
- Re: [AMBER] Automated restart (Sat Aug 08 2015 - 11:25:27 PDT)
- [AMBER] Automated restart (Sat Aug 08 2015 - 03:40:50 PDT)
- Re: [AMBER] cudaMemcpy GpuBuffer::Download failed - hardwareorsoftware? (Sun Aug 02 2015 - 23:56:46 PDT)
- Re: [AMBER] cudaMemcpy GpuBuffer::Download failed - hardware orsoftware? (Sun Aug 02 2015 - 01:52:04 PDT)
- [AMBER] cudaMemcpy GpuBuffer::Download failed - hardware or software? (Sat Aug 01 2015 - 13:30:14 PDT)
Garisekurthi Satheesh
- Re: [AMBER] Regarding No of Hydrogen bonds (vs) Residue wise (Mon Aug 24 2015 - 11:22:15 PDT)
- [AMBER] Regarding No of Hydrogen bonds (vs) Residue wise (Sun Aug 23 2015 - 21:15:03 PDT)
Gaurao Dhoke
- Re: [AMBER] cpptraj frames clustering limit (Thu Aug 13 2015 - 01:28:01 PDT)
- [AMBER] cpptraj frames clustering limit (Wed Aug 12 2015 - 06:46:07 PDT)
George Green
- Re: [AMBER] hydrogen mass repartitioning visualization in chimera (Fri Aug 21 2015 - 06:49:33 PDT)
- Re: [AMBER] hydrogen mass repartitioning visualization in chimera (Thu Aug 20 2015 - 18:03:12 PDT)
- Re: [AMBER] hydrogen mass repartitioning visualization in chimera (Thu Aug 20 2015 - 17:31:22 PDT)
- Re: [AMBER] hydrogen mass repartitioning visualization in chimera (Thu Aug 20 2015 - 17:18:42 PDT)
- [AMBER] hydrogen mass repartitioning visualization in chimera (Thu Aug 20 2015 - 16:49:14 PDT)
- Re: [AMBER] issue with 4 fs hydrogen mass repartitioning taking more time than a standard 2 fs simulation in AMBER14 (Wed Aug 05 2015 - 17:27:23 PDT)
- [AMBER] issue with 4 fs hydrogen mass repartitioning taking more time than a standard 2 fs simulation in AMBER14 (Wed Aug 05 2015 - 16:28:31 PDT)
George Tzotzos
- [AMBER] Molsurf: some questions on usage (Thu Aug 27 2015 - 08:05:44 PDT)
- Re: [AMBER] Solvent accessible surface area (SASA) calculation in CPPTRJ (Mon Aug 24 2015 - 12:03:56 PDT)
- Re: [AMBER] Solvent accessible surface area (SASA) calculation in CPPTRJ (Mon Aug 24 2015 - 09:29:15 PDT)
- Re: [AMBER] Total interaction energy between monomeric units of a dimer (Wed Aug 19 2015 - 08:57:09 PDT)
- Re: [AMBER] cpptraj perress RMSD (Tue Aug 18 2015 - 09:57:17 PDT)
- Re: [AMBER] cpptraj RMSD stats (Tue Aug 18 2015 - 08:18:22 PDT)
- [AMBER] cpptraj perress RMSD (Tue Aug 18 2015 - 07:47:36 PDT)
- [AMBER] cpptraj RMSD stats (Tue Aug 18 2015 - 06:43:52 PDT)
- Re: [AMBER] converting amber files (Tue Aug 18 2015 - 05:23:27 PDT)
- Re: [AMBER] mmpbsa.py: Error (Mon Aug 10 2015 - 12:56:12 PDT)
- Re: [AMBER] mmpbsa.py: Error (Mon Aug 10 2015 - 12:00:39 PDT)
- Re: [AMBER] mmpbsa.py: Error (Mon Aug 10 2015 - 10:37:10 PDT)
- Re: [AMBER] mmpbsa.py: Error (Mon Aug 10 2015 - 10:23:09 PDT)
- [AMBER] mmpbsa.py: Error (Mon Aug 10 2015 - 09:49:29 PDT)
- Re: [AMBER] PCA: comparing PCs from different trajectories (Thu Aug 06 2015 - 07:18:08 PDT)
- Re: [AMBER] PCA: comparing PCs from different trajectories (Wed Aug 05 2015 - 10:39:05 PDT)
- [AMBER] PCA: comparing PCs from different trajectories (Wed Aug 05 2015 - 01:24:45 PDT)
- [AMBER] Installation of AmberTools 15. Overriding earlier installation (Mon Aug 03 2015 - 12:26:25 PDT)
- Re: [AMBER] PCA: generate histogram (Mon Aug 03 2015 - 07:04:28 PDT)
- Re: [AMBER] PCA: generate histogram (Mon Aug 03 2015 - 06:48:32 PDT)
- [AMBER] PCA: generate histogram (Mon Aug 03 2015 - 03:46:55 PDT)
Gerald Monard
- Re: [AMBER] Job submission script for SGE (Fri Aug 14 2015 - 04:46:34 PDT)
Gould, Ian R
- Re: [AMBER] NaN with pmemd.cuda (Tue Aug 04 2015 - 22:14:27 PDT)
Hai Nguyen
- Re: [AMBER] how to neutralized my system with Na+ ions (Tue Aug 25 2015 - 10:19:14 PDT)
- Re: [AMBER] closest command in cpptraj (Mon Aug 24 2015 - 14:31:31 PDT)
- Re: [AMBER] Regarding No of Hydrogen bonds (vs) Residue wise (Mon Aug 24 2015 - 10:26:12 PDT)
- Re: [AMBER] cpptraj - RMSD (Sun Aug 09 2015 - 16:01:51 PDT)
- Re: [AMBER] cpptraj - RMSD (Sun Aug 09 2015 - 14:15:51 PDT)
- Re: [AMBER] "mask" command failure (Thu Aug 06 2015 - 19:46:59 PDT)
- Re: [AMBER] "mask" command failure (Thu Aug 06 2015 - 17:26:45 PDT)
- Re: [AMBER] large .mdcrd splitting (Thu Aug 06 2015 - 10:44:54 PDT)
- Re: [AMBER] .mdcrd to .trr conversion problem (Wed Aug 05 2015 - 08:48:51 PDT)
- Re: [AMBER] .mdcrd to .trr conversion problem (Wed Aug 05 2015 - 08:47:37 PDT)
- Re: [AMBER] Regarding DNA forcefield in Amber14 (Wed Aug 05 2015 - 05:48:22 PDT)
- Re: [AMBER] Bad Atom type during running MMPBSA with cobalt metal ion (Tue Aug 04 2015 - 22:54:57 PDT)
- Re: [AMBER] algorithm for clustering solvent molecules? (Mon Aug 03 2015 - 14:43:39 PDT)
- Re: [AMBER] algorithm for clustering solvent molecules? (Mon Aug 03 2015 - 13:48:24 PDT)
Harmeet Kaur
- [AMBER] Imaging and connectivity error (Thu Aug 13 2015 - 04:27:24 PDT)
Hector A. Baldoni
- Re: [AMBER] Total interaction energy between monomeric units of a dimer (Thu Aug 20 2015 - 06:21:15 PDT)
- Re: [AMBER] Total interaction energy between monomeric units of a dimer (Thu Aug 20 2015 - 05:09:43 PDT)
Himansu
- [AMBER] Job submission script for SGE (Thu Aug 13 2015 - 16:50:59 PDT)
- [AMBER] AMBER 14 installation Problem (Tue Aug 11 2015 - 03:23:45 PDT)
Investigador Química
- Re: [AMBER] the better box size for calculating host-guest interaction energies (Sat Aug 22 2015 - 13:38:37 PDT)
- Re: [AMBER] the better box size for calculating host-guest interaction energies (Sat Aug 22 2015 - 13:35:50 PDT)
- Re: [AMBER] the better box size for calculating host-guest interaction energies (Sat Aug 22 2015 - 13:34:10 PDT)
- Re: [AMBER] the better box size for calculating host-guest interaction energies (Thu Aug 20 2015 - 07:09:12 PDT)
- Re: [AMBER] the better box size for calculating host-guest interaction energies (Wed Aug 19 2015 - 07:43:41 PDT)
- [AMBER] the better box size (Fri Aug 14 2015 - 10:45:56 PDT)
Iqbal, Muhammad Sajid
- [AMBER] Draw a cube around the molecules (Mon Aug 31 2015 - 11:56:19 PDT)
Jacob Monroe
- Re: [AMBER] Non-equilibrium pulling with plane-point restraints (Mon Aug 31 2015 - 16:29:59 PDT)
- Re: [AMBER] Non-equilibrium pulling with plane-point restraints (Thu Aug 27 2015 - 11:02:29 PDT)
- [AMBER] Non-equilibrium pulling with plane-point restraints (Tue Aug 25 2015 - 10:45:22 PDT)
Jason Swails
- Re: [AMBER] Draw a cube around the molecules (Mon Aug 31 2015 - 12:04:14 PDT)
- Re: [AMBER] Segmentation Fault with pmemd (Sat Aug 29 2015 - 04:22:42 PDT)
- Re: [AMBER] Confusion in running QM/MMGBSA (Sat Aug 29 2015 - 04:09:28 PDT)
- Re: [AMBER] cpin error (Fri Aug 28 2015 - 07:22:29 PDT)
- Re: [AMBER] how to add lipid (Fri Aug 28 2015 - 06:34:35 PDT)
- Re: [AMBER] Cpin error (Thu Aug 27 2015 - 09:16:14 PDT)
- Re: [AMBER] Total interaction energy between monomeric units of a dimer (Wed Aug 26 2015 - 10:21:49 PDT)
- Re: [AMBER] cpin error (Wed Aug 26 2015 - 06:43:08 PDT)
- Re: [AMBER] Problem In Performing MMPBSA Calculation for System Containing Lipids (Wed Aug 26 2015 - 05:41:47 PDT)
- Re: [AMBER] how to neutralized my system with Na+ ions (Tue Aug 25 2015 - 10:12:34 PDT)
- Re: [AMBER] how to neutralized my system with Na+ ions (Tue Aug 25 2015 - 07:16:01 PDT)
- Re: [AMBER] Solvent accessible surface area (SASA) calculation in CPPTRJ (Mon Aug 24 2015 - 12:23:21 PDT)
- Re: [AMBER] how to add lipid (Mon Aug 24 2015 - 10:41:52 PDT)
- Re: [AMBER] how to add lipid (Mon Aug 24 2015 - 10:41:06 PDT)
- Re: [AMBER] AMBER Autoimage Warning (Mon Aug 24 2015 - 10:38:00 PDT)
- Re: [AMBER] Solvent accessible surface area (SASA) calculation in CPPTRJ (Mon Aug 24 2015 - 10:02:33 PDT)
- Re: [AMBER] Using MMPBSA.py with CHARMM force field (Fri Aug 21 2015 - 10:42:17 PDT)
- Re: [AMBER] Autoimage Warning (Fri Aug 21 2015 - 08:29:38 PDT)
- Re: [AMBER] ImportError: No module named mcpb.gene_model_files (Fri Aug 21 2015 - 08:27:38 PDT)
- Re: [AMBER] Using MMPBSA.py with CHARMM force field (Fri Aug 21 2015 - 06:40:41 PDT)
- Re: [AMBER] hydrogen mass repartitioning visualization in chimera (Fri Aug 21 2015 - 06:36:37 PDT)
- Re: [AMBER] Solvent accessible surface area (SASA) calculation in CPPTRJ (Thu Aug 20 2015 - 11:25:46 PDT)
- Re: [AMBER] the better box size for calculating host-guest interaction energies (Thu Aug 20 2015 - 07:32:34 PDT)
- Re: [AMBER] Total interaction energy between monomeric units of a dimer (Thu Aug 20 2015 - 06:12:14 PDT)
- Re: [AMBER] the better box size for calculating host-guest interaction energies (Wed Aug 19 2015 - 08:18:06 PDT)
- Re: [AMBER] CL topology (Wed Aug 19 2015 - 04:42:02 PDT)
- Re: [AMBER] adding NaCl (Wed Aug 19 2015 - 04:16:42 PDT)
- Re: [AMBER] upgrading to AT15 (from AT14) (Tue Aug 18 2015 - 10:25:55 PDT)
- Re: [AMBER] converting amber files (Tue Aug 18 2015 - 07:42:52 PDT)
- Re: [AMBER] converting amber files (Tue Aug 18 2015 - 06:27:30 PDT)
- Re: [AMBER] Total interaction energy between monomeric units of a dimer (Tue Aug 18 2015 - 06:08:12 PDT)
- Re: [AMBER] converting amber files (Tue Aug 18 2015 - 05:57:11 PDT)
- Re: [AMBER] Big potential difference between conformation in MD simulation and optimized conformation in Gaussian. (Mon Aug 17 2015 - 13:18:36 PDT)
- Re: [AMBER] calculation of rmsd with cpptraj (Mon Aug 17 2015 - 13:03:23 PDT)
- Re: [AMBER] STOP PMEMD Terminated Abnormally! (Mon Aug 17 2015 - 09:49:38 PDT)
- Re: [AMBER] About the QMMM simulation with LIO software (Mon Aug 17 2015 - 09:48:00 PDT)
- Re: [AMBER] A query about MMPBSA.py calcualtion (Sun Aug 16 2015 - 17:36:22 PDT)
- Re: [AMBER] About the QMMM simulation with LIO software (Sat Aug 15 2015 - 10:22:09 PDT)
- Re: [AMBER] AMBER Digest, Vol 1311, Issue 1 (Sat Aug 15 2015 - 06:21:17 PDT)
- Re: [AMBER] RMSD and average value of interatomic distance? (Sat Aug 15 2015 - 05:45:33 PDT)
- Re: [AMBER] the better box size (Fri Aug 14 2015 - 11:12:20 PDT)
- Re: [AMBER] The protein is Leaving the water box! (Fri Aug 14 2015 - 06:00:11 PDT)
- Re: [AMBER] Job submission script for SGE (Fri Aug 14 2015 - 04:46:27 PDT)
- Re: [AMBER] The protein is Leaving the water box! (Fri Aug 14 2015 - 04:38:36 PDT)
- Re: [AMBER] Imaging and connectivity error (Thu Aug 13 2015 - 07:06:29 PDT)
- Re: [AMBER] pH-REMD theory (Thu Aug 13 2015 - 05:43:41 PDT)
- Re: [AMBER] acetylate and ammoniate (Thu Aug 13 2015 - 04:23:38 PDT)
- Re: [AMBER] cpptraj frames clustering limit (Wed Aug 12 2015 - 06:59:58 PDT)
- Re: [AMBER] Overflow of the Fortran format used to store coordinates in the inpcrd/restart files. (Wed Aug 12 2015 - 06:53:47 PDT)
- Re: [AMBER] acetylate and ammoniate (Wed Aug 12 2015 - 06:10:30 PDT)
- Re: [AMBER] FW: Regarding AMBER 14 (Wed Aug 12 2015 - 04:00:56 PDT)
- Re: [AMBER] using chamber to convert psf to prmtop (Tue Aug 11 2015 - 15:02:15 PDT)
- Re: [AMBER] Overflow of the Fortran format used to store coordinates in the inpcrd/restart files. (Tue Aug 11 2015 - 15:00:03 PDT)
- Re: [AMBER] Overflow of the Fortran format used to store coordinates in the inpcrd/restart files. (Tue Aug 11 2015 - 10:26:27 PDT)
- Re: [AMBER] PB Bomb in pb_aaradi(): No radius assigned for atom (Tue Aug 11 2015 - 08:44:55 PDT)
- Re: [AMBER] PB Bomb in pb_aaradi(): No radius assigned for atom (Tue Aug 11 2015 - 07:43:55 PDT)
- Re: [AMBER] SPAM (Tue Aug 11 2015 - 06:39:24 PDT)
- Re: [AMBER] FW: Regarding AMBER 14 (Tue Aug 11 2015 - 06:31:22 PDT)
- Re: [AMBER] FW: Regarding AMBER 14 (Tue Aug 11 2015 - 06:10:54 PDT)
- Re: [AMBER] PB Bomb in pb_aaradi(): No radius assigned for atom (Tue Aug 11 2015 - 06:04:03 PDT)
- Re: [AMBER] PB Bomb in pb_aaradi(): No radius assigned for atom (Tue Aug 11 2015 - 04:53:13 PDT)
- Re: [AMBER] mmpbsa.py: Error (Mon Aug 10 2015 - 13:11:23 PDT)
- Re: [AMBER] mmpbsa.py: Error (Mon Aug 10 2015 - 10:22:13 PDT)
- Re: [AMBER] cpptraj gist: Eww energies (Mon Aug 10 2015 - 08:21:59 PDT)
- Re: [AMBER] Automated restart (Sat Aug 08 2015 - 12:03:53 PDT)
- Re: [AMBER] "mask" command failure (Thu Aug 06 2015 - 23:21:08 PDT)
- Re: [AMBER] Problem with cpptraj autoimage command (Thu Aug 06 2015 - 06:19:53 PDT)
- Re: [AMBER] NaN with pmemd.cuda (Wed Aug 05 2015 - 17:10:32 PDT)
- Re: [AMBER] issue with 4 fs hydrogen mass repartitioning taking more time than a standard 2 fs simulation in AMBER14 (Wed Aug 05 2015 - 17:03:14 PDT)
- Re: [AMBER] MM-PBSA atom types (Tue Aug 04 2015 - 09:09:18 PDT)
- Re: [AMBER] MMPBSA.py problem (Tue Aug 04 2015 - 06:22:10 PDT)
- Re: [AMBER] Trying to perform a heating MD in increments (Tue Aug 04 2015 - 05:55:30 PDT)
- Re: [AMBER] Bad Atom type during running MMPBSA with cobalt metal ion (Tue Aug 04 2015 - 05:52:14 PDT)
- Re: [AMBER] How to construct the Ala3 peptide shown in this picture? (Tue Aug 04 2015 - 05:50:16 PDT)
- Re: [AMBER] MM-PBSA atom types (Mon Aug 03 2015 - 15:37:59 PDT)
- Re: [AMBER] Installation of AmberTools 15. Overriding earlier installation (Mon Aug 03 2015 - 12:35:50 PDT)
- Re: [AMBER] algorithm for clustering solvent molecules? (Mon Aug 03 2015 - 12:31:21 PDT)
- Re: [AMBER] algorithm for clustering solvent molecules? (Mon Aug 03 2015 - 10:17:09 PDT)
- Re: [AMBER] FW: PMEMD: Warning: ieee_inexact is signaling (Mon Aug 03 2015 - 08:19:11 PDT)
- Re: [AMBER] algorithm for clustering solvent molecules? (Mon Aug 03 2015 - 07:00:18 PDT)
- Re: [AMBER] Does the "contacts" command of cpptraj implement imaging? (Mon Aug 03 2015 - 06:07:30 PDT)
Jorgen Simonsen
- [AMBER] tleap ask for bond to zinc ion (Sun Aug 23 2015 - 08:49:01 PDT)
Jose Borreguero
- Re: [AMBER] algorithm for clustering solvent molecules? (Mon Aug 03 2015 - 15:07:23 PDT)
- Re: [AMBER] algorithm for clustering solvent molecules? (Mon Aug 03 2015 - 14:35:57 PDT)
- Re: [AMBER] algorithm for clustering solvent molecules? (Mon Aug 03 2015 - 12:21:09 PDT)
- Re: [AMBER] algorithm for clustering solvent molecules? (Mon Aug 03 2015 - 09:57:08 PDT)
- Re: [AMBER] Does the "contacts" command of cpptraj implement imaging? (Mon Aug 03 2015 - 09:53:04 PDT)
- [AMBER] Does the "contacts" command of cpptraj implement imaging? (Sun Aug 02 2015 - 15:47:19 PDT)
- [AMBER] algorithm for clustering solvent molecules? (Sat Aug 01 2015 - 18:23:42 PDT)
Joseph Baker
- Re: [AMBER] closest command in cpptraj (Tue Aug 25 2015 - 19:21:50 PDT)
- Re: [AMBER] closest command in cpptraj (Mon Aug 24 2015 - 14:05:48 PDT)
- Re: [AMBER] closest command in cpptraj (Mon Aug 24 2015 - 12:34:57 PDT)
- Re: [AMBER] closest command in cpptraj (Mon Aug 24 2015 - 07:17:22 PDT)
- [AMBER] closest command in cpptraj (Fri Aug 21 2015 - 12:31:26 PDT)
- Re: [AMBER] NaN with pmemd.cuda (Thu Aug 06 2015 - 11:59:32 PDT)
- Re: [AMBER] NaN with pmemd.cuda (Wed Aug 05 2015 - 19:41:55 PDT)
- Re: [AMBER] NaN with pmemd.cuda (Wed Aug 05 2015 - 12:00:58 PDT)
- [AMBER] NaN with pmemd.cuda (Tue Aug 04 2015 - 21:43:22 PDT)
Karolina Markowska
- Re: [AMBER] Does it mean the card is damaged? (Mon Aug 31 2015 - 01:37:44 PDT)
- Re: [AMBER] Does it mean the card is damaged? (Fri Aug 28 2015 - 01:04:13 PDT)
- [AMBER] Does it mean the card is damaged? (Thu Aug 27 2015 - 01:40:19 PDT)
- Re: [AMBER] Problem with cpptraj autoimage command (Fri Aug 07 2015 - 13:48:25 PDT)
- Re: [AMBER] Problem with cpptraj autoimage command (Fri Aug 07 2015 - 02:35:48 PDT)
- [AMBER] Problem with cpptraj autoimage command (Thu Aug 06 2015 - 04:35:59 PDT)
Kasprzak, Wojciech (NIH/NCI) [C]
- Re: [AMBER] how to neutralized my system with Na+ ions (Tue Aug 25 2015 - 05:43:08 PDT)
- [AMBER] Problem with using the 12-6-4 LJ-Type Nonbonded Model in a an RNA-Mg system (Thu Aug 20 2015 - 13:08:09 PDT)
Kenneth Huang
- Re: [AMBER] converting amber files (Tue Aug 18 2015 - 07:22:38 PDT)
- Re: [AMBER] cpptraj cluster in MPI (Mon Aug 17 2015 - 19:55:16 PDT)
- Re: [AMBER] FW: Regarding AMBER 14 (Tue Aug 11 2015 - 06:05:07 PDT)
- [AMBER] mmpbsa.py: Error (Mon Aug 10 2015 - 12:30:00 PDT)
- Re: [AMBER] mmpbsa.py: Error (Mon Aug 10 2015 - 11:43:10 PDT)
- Re: [AMBER] mmpbsa.py: Error (Mon Aug 10 2015 - 10:23:36 PDT)
- Re: [AMBER] MMPBSA error using pbsa2 (Sun Aug 09 2015 - 12:09:17 PDT)
- Re: [AMBER] MM-PBSA atom types (Tue Aug 04 2015 - 09:09:13 PDT)
- Re: [AMBER] MM-PBSA free energy calculation with keeping x-ray water (Mon Aug 03 2015 - 12:57:14 PDT)
Khabiri, Morteza
- [AMBER] Thermodynamic integration and segmentation fault (Mon Aug 31 2015 - 06:40:15 PDT)
- [AMBER] dynlmb and TI (Thu Aug 13 2015 - 11:36:11 PDT)
- Re: [AMBER] Warning: ieee_inexact is signaling PMEMD Terminated Abnormally! (Wed Aug 12 2015 - 11:06:34 PDT)
- Re: [AMBER] Warning: ieee_inexact is signaling PMEMD Terminated Abnormally! (Wed Aug 12 2015 - 09:43:14 PDT)
- [AMBER] Warning: ieee_inexact is signaling PMEMD Terminated Abnormally! (Wed Aug 12 2015 - 06:36:57 PDT)
- [AMBER] Thermodynamic integration goes wrong in lambda =0 while lambda = 1 is ok!! (Thu Aug 06 2015 - 07:43:17 PDT)
- [AMBER] Thermodynamic integration goes wrong in lambda =0 while lambda = 1 is ok!! (Wed Aug 05 2015 - 18:34:39 PDT)
- Re: [AMBER] PMEMD: Warning: ieee_inexact is signaling (Mon Aug 03 2015 - 12:40:14 PDT)
- [AMBER] FW: PMEMD: Warning: ieee_inexact is signaling (Mon Aug 03 2015 - 06:26:01 PDT)
KK R
- [AMBER] using chamber to convert psf to prmtop (Tue Aug 11 2015 - 13:08:42 PDT)
koushik kasavajhala
- Re: [AMBER] NaN with pmemd.cuda (Wed Aug 05 2015 - 20:29:57 PDT)
Krantzman, Kristin D
- Re: [AMBER] calculation of rmsd with cpptraj (Mon Aug 17 2015 - 13:15:08 PDT)
- [AMBER] calculation of rmsd with cpptraj (Mon Aug 17 2015 - 12:53:05 PDT)
Kris Feher
- Re: [AMBER] ired analysis: No modes data specified (Tue Aug 04 2015 - 10:07:04 PDT)
- [AMBER] ired analysis: No modes data specified (Tue Aug 04 2015 - 05:23:53 PDT)
Lachele Foley
- Re: [AMBER] Help needed regarding simulating Lipopolysaccharide (Mon Aug 17 2015 - 08:30:24 PDT)
Lara rajam
- [AMBER] cyclic peptides (Sun Aug 30 2015 - 17:26:27 PDT)
- [AMBER] xleap numbering in residues (Wed Aug 19 2015 - 18:32:00 PDT)
- Re: [AMBER] cpptraj cluster in MPI (Mon Aug 17 2015 - 20:03:55 PDT)
- [AMBER] cpptraj cluster in MPI (Mon Aug 17 2015 - 19:43:09 PDT)
- [AMBER] antechamber error (Wed Aug 05 2015 - 07:27:08 PDT)
Lijuan Yu
- Re: [AMBER] Macromolecular crowding force-field and parameters (Wed Aug 12 2015 - 21:15:55 PDT)
lipengfei_mail
- [AMBER] How to construct the Ala3 peptide shown in this picture? (Tue Aug 04 2015 - 05:12:38 PDT)
Lorenzo Gontrani
- Re: [AMBER] Draw a cube around the molecules (Mon Aug 31 2015 - 12:02:58 PDT)
Lucas A. Defelipe
- [AMBER] Charge-dependent exchange-dispersion corrections (Thu Aug 27 2015 - 07:46:23 PDT)
Mahad Gatti Iou
- Re: [AMBER] Regarding DNA forcefield in Amber14 (Wed Aug 05 2015 - 05:59:51 PDT)
- Re: [AMBER] Regarding DNA forcefield in Amber14 (Wed Aug 05 2015 - 05:47:30 PDT)
Mahmood Jasim
- Re: [AMBER] RESP fitting (Thu Aug 20 2015 - 08:43:57 PDT)
- [AMBER] RESP fitting (Wed Aug 19 2015 - 05:46:21 PDT)
Marawan Hussien
- [AMBER] Immediate Postdoctoral Position Opening In Computational Chemistry And Computer-Aided Drug Design (CADD) (Mon Aug 17 2015 - 20:26:39 PDT)
- [AMBER] Immediate PhD Opening In Computational Structural Biology Of Membrane Proteins (Mon Aug 17 2015 - 20:25:18 PDT)
Marcelo Andrade Chagas
- Re: [AMBER] tleap ask for bond to zinc ion (Mon Aug 24 2015 - 10:33:00 PDT)
- Re: [AMBER] ImportError: No module named mcpb.gene_model_files (Fri Aug 21 2015 - 08:43:50 PDT)
- Re: [AMBER] ImportError: No module named mcpb.gene_model_files (Fri Aug 21 2015 - 08:15:12 PDT)
- Re: [AMBER] ImportError: No module named mcpb.gene_model_files (Mon Aug 17 2015 - 09:05:36 PDT)
- Re: [AMBER] ImportError: No module named mcpb.gene_model_files (Mon Aug 17 2015 - 04:57:53 PDT)
- [AMBER] ImportError: No module named mcpb.gene_model_files (Thu Aug 13 2015 - 12:14:22 PDT)
Martina Devi
- [AMBER] job submission in RED (Mon Aug 31 2015 - 03:34:40 PDT)
- Re: [AMBER] mismatch base pair from nab (Sat Aug 29 2015 - 05:39:10 PDT)
- Re: [AMBER] how to neutralized my system with Na+ ions (Tue Aug 25 2015 - 09:25:44 PDT)
- Re: [AMBER] how to neutralized my system with Na+ ions (Tue Aug 25 2015 - 07:33:43 PDT)
- Re: [AMBER] how to neutralized my system with Na+ ions (Tue Aug 25 2015 - 06:57:52 PDT)
- Re: [AMBER] mismatch base pair from nab (Tue Aug 25 2015 - 05:59:38 PDT)
- [AMBER] mismatch base pair from nab (Tue Aug 25 2015 - 04:49:01 PDT)
- [AMBER] how to neutralized my system with Na+ ions (Mon Aug 24 2015 - 23:53:54 PDT)
Massimiliano Porrini
- Re: [AMBER] upgrading to AT15 (from AT14) (Mon Aug 24 2015 - 03:28:46 PDT)
- Re: [AMBER] upgrading to AT15 (from AT14) (Fri Aug 21 2015 - 02:46:05 PDT)
- [AMBER] upgrading to AT15 (from AT14) (Tue Aug 18 2015 - 09:47:00 PDT)
Michael Shokhen
- Re: [AMBER] RMSD and average value of interatomic distance? (Sat Aug 15 2015 - 08:31:34 PDT)
- Re: [AMBER] RMSD and average value of interatomic distance? (Sat Aug 15 2015 - 07:49:14 PDT)
- Re: [AMBER] RMSD and average value of interatomic distance? (Sat Aug 15 2015 - 07:12:58 PDT)
- [AMBER] RMSD and average value of interatomic distance? (Sat Aug 15 2015 - 00:30:26 PDT)
- Re: [AMBER] Antechamber for boronic acid derivatives? (Tue Aug 04 2015 - 04:26:06 PDT)
mohammad r
- Re: [AMBER] how to add lipid (Fri Aug 28 2015 - 07:26:49 PDT)
- Re: [AMBER] how to add lipid (Fri Aug 28 2015 - 00:09:54 PDT)
- Re: [AMBER] how to add lipid (Wed Aug 26 2015 - 07:31:13 PDT)
- Re: [AMBER] how to add lipid (Wed Aug 26 2015 - 07:17:22 PDT)
- Re: [AMBER] how to add lipid (Tue Aug 25 2015 - 03:43:31 PDT)
- Re: [AMBER] how to add lipid (Tue Aug 25 2015 - 03:28:23 PDT)
- Re: [AMBER] how to add lipid (Mon Aug 24 2015 - 23:14:45 PDT)
- Re: [AMBER] how to add lipid (Mon Aug 24 2015 - 21:43:28 PDT)
- Re: [AMBER] how to add lipid (Mon Aug 24 2015 - 10:44:33 PDT)
- Re: [AMBER] how to add lipid (Mon Aug 24 2015 - 10:28:48 PDT)
- Re: [AMBER] how to add lipid (Mon Aug 24 2015 - 09:53:35 PDT)
- Re: [AMBER] how to add lipid (Mon Aug 24 2015 - 00:07:42 PDT)
- Re: [AMBER] how to add lipid (Sun Aug 23 2015 - 21:38:44 PDT)
- [AMBER] how to add lipid (Sun Aug 23 2015 - 06:47:36 PDT)
- [AMBER] adding lipid (Sun Aug 23 2015 - 06:41:32 PDT)
- Re: [AMBER] adding NaCl (Wed Aug 19 2015 - 01:45:14 PDT)
- [AMBER] adding NaCl (Wed Aug 19 2015 - 00:25:07 PDT)
- Re: [AMBER] upgrading to AT15 (from AT14) (Tue Aug 18 2015 - 23:10:09 PDT)
- [AMBER] adding NaCl (Tue Aug 18 2015 - 22:44:23 PDT)
- [AMBER] adding NaCl (Tue Aug 18 2015 - 21:32:47 PDT)
- Re: [AMBER] converting amber files (Tue Aug 18 2015 - 08:03:07 PDT)
- Re: [AMBER] acpype (Tue Aug 18 2015 - 07:04:12 PDT)
- Re: [AMBER] converting amber files (Tue Aug 18 2015 - 06:49:37 PDT)
- Re: [AMBER] converting amber files (Tue Aug 18 2015 - 06:10:12 PDT)
- [AMBER] converting amber files (Tue Aug 18 2015 - 05:12:49 PDT)
- [AMBER] ancpype problem (Tue Aug 18 2015 - 02:00:36 PDT)
- [AMBER] acpype (Tue Aug 18 2015 - 01:17:59 PDT)
- [AMBER] acpype (Mon Aug 17 2015 - 23:58:54 PDT)
- Re: [AMBER] saveamberparm (Mon Aug 17 2015 - 13:20:40 PDT)
- [AMBER] saveamberparm (Mon Aug 17 2015 - 07:14:26 PDT)
- Re: [AMBER] acetylate and ammoniate (Thu Aug 13 2015 - 00:06:16 PDT)
- Re: [AMBER] acetylate and ammoniate (Wed Aug 12 2015 - 08:04:20 PDT)
- [AMBER] acetylate and ammoniate (Wed Aug 12 2015 - 05:23:39 PDT)
mohammad roostaie
- [AMBER] how to add lipid (Sun Aug 23 2015 - 07:08:02 PDT)
Mohammad Salem
- Re: [AMBER] What is the best way to study a dynamics route of a molecule to enter a protein (Thu Aug 27 2015 - 15:44:10 PDT)
Mohd Farid Ismail
- [AMBER] Looking for suggestion for analysis (Thu Aug 27 2015 - 19:42:17 PDT)
MOHD HOMAIDUR RAHMAN
- [AMBER] Confusion in running QM/MMGBSA (Fri Aug 28 2015 - 12:08:49 PDT)
- Re: [AMBER] Regarding printing of trajectory (Tue Aug 25 2015 - 11:11:30 PDT)
- Re: [AMBER] Regarding printing of trajectory (Tue Aug 25 2015 - 07:22:11 PDT)
- [AMBER] Regarding printing of trajectory (Tue Aug 25 2015 - 00:11:55 PDT)
- Re: [AMBER] Bad Atom type during running MMPBSA with cobalt metal ion (Tue Aug 04 2015 - 22:51:41 PDT)
- [AMBER] Bad Atom type during running MMPBSA with cobalt metal ion (Mon Aug 03 2015 - 23:23:36 PDT)
Mrinda Jones
- Re: [AMBER] Help needed regarding simulating Lipopolysaccharide (Wed Aug 19 2015 - 00:20:11 PDT)
- Re: [AMBER] Help needed regarding simulating Lipopolysaccharide (Mon Aug 17 2015 - 05:43:25 PDT)
- [AMBER] Help needed regarding simulating Lipopolysaccharide (Mon Aug 17 2015 - 03:41:39 PDT)
Nguyen, Crystal
- Re: [AMBER] GIST vs. 3D-RISM (Wed Aug 12 2015 - 11:01:26 PDT)
- Re: [AMBER] cpptraj gist: Eww energies (Mon Aug 10 2015 - 08:42:30 PDT)
Nhai
- Re: [AMBER] ImportError: No module named scipy.optimize (Mon Aug 24 2015 - 21:23:44 PDT)
- Re: [AMBER] hydrogen mass repartitioning visualization in chimera (Thu Aug 20 2015 - 17:32:47 PDT)
- Re: [AMBER] Regarding DNA forcefield in Amber14 (Wed Aug 05 2015 - 06:07:45 PDT)
Parker de Waal
- [AMBER] Error: an illegal memory access was encountered launching kernel kClearForces (Sat Aug 22 2015 - 13:58:21 PDT)
Pragya Priyadarshini
- Re: [AMBER] STOP PMEMD Terminated Abnormally! (Mon Aug 17 2015 - 21:15:12 PDT)
- Re: [AMBER] STOP PMEMD Terminated Abnormally! (Mon Aug 17 2015 - 07:24:53 PDT)
- [AMBER] STOP PMEMD Terminated Abnormally! (Mon Aug 17 2015 - 04:14:11 PDT)
- [AMBER] Regarding DNA forcefield in Amber14 (Wed Aug 05 2015 - 00:35:34 PDT)
praSanna kuMar naYak
- Re: [AMBER] FW: Regarding AMBER 14 (Wed Aug 12 2015 - 04:26:51 PDT)
- Re: [AMBER] FW: Regarding AMBER 14 (Wed Aug 12 2015 - 00:04:10 PDT)
- Re: [AMBER] FW: Regarding AMBER 14 (Tue Aug 11 2015 - 06:23:25 PDT)
- Re: [AMBER] FW: Regarding AMBER 14 (Tue Aug 11 2015 - 04:59:48 PDT)
- [AMBER] FW: Regarding AMBER14 Error (Tue Aug 11 2015 - 01:47:52 PDT)
- [AMBER] FW: Regarding AMBER 14 (Tue Aug 11 2015 - 01:47:38 PDT)
psu4.uic.edu
- Re: [AMBER] MMPBSA.py problem (Tue Aug 04 2015 - 10:46:09 PDT)
Ray Luo, Ph.D.
- Re: [AMBER] MMPBSA error using pbsa2 (Sun Aug 09 2015 - 22:11:25 PDT)
- Re: [AMBER] MMPBSA error using pbsa2 (Fri Aug 07 2015 - 20:59:12 PDT)
Repic Matej
- Re: [AMBER] Draw a cube around the molecules (Mon Aug 31 2015 - 15:46:32 PDT)
- Re: [AMBER] how to add lipid (Thu Aug 27 2015 - 14:16:18 PDT)
richa anand
- [AMBER] Force-field and parameters (Wed Aug 12 2015 - 21:32:06 PDT)
- [AMBER] Macromolecular crowding force-field and parameters (Tue Aug 11 2015 - 20:55:40 PDT)
Robin Jain
- [AMBER] help in density equilibration (Sun Aug 23 2015 - 21:00:17 PDT)
- [AMBER] help in density equilibration (Fri Aug 21 2015 - 22:30:39 PDT)
- Re: [AMBER] AMBER Digest, Vol 1311, Issue 1 (Sat Aug 15 2015 - 01:58:47 PDT)
- [AMBER] help in rdf (Fri Aug 14 2015 - 00:59:12 PDT)
Ross Walker
- Re: [AMBER] Does it mean the card is damaged? (Mon Aug 31 2015 - 08:56:48 PDT)
- Re: [AMBER] Does it mean the card is damaged? (Thu Aug 27 2015 - 08:06:09 PDT)
- Re: [AMBER] Error: an illegal memory access was encountered launching kernel kClearForces (Mon Aug 24 2015 - 08:53:49 PDT)
- Re: [AMBER] NaN with pmemd.cuda (Thu Aug 06 2015 - 00:46:39 PDT)
- Re: [AMBER] cudaMemcpy GpuBuffer::Download failed - hardwareorsoftware? (Mon Aug 03 2015 - 12:54:35 PDT)
- Re: [AMBER] cudaMemcpy GpuBuffer::Download failed - hardware orsoftware? (Sun Aug 02 2015 - 20:22:45 PDT)
Ruchika Bhat
- [AMBER] MMPBSA_Ras-Raf complex tutorial (Wed Aug 05 2015 - 06:48:17 PDT)
Sangita Kachhap
- Re: [AMBER] PB Bomb in pb_aaradi(): No radius assigned for atom (Tue Aug 11 2015 - 09:13:30 PDT)
- Re: [AMBER] PB Bomb in pb_aaradi(): No radius assigned for atom (Tue Aug 11 2015 - 08:08:37 PDT)
- Re: [AMBER] PB Bomb in pb_aaradi(): No radius assigned for atom (Tue Aug 11 2015 - 07:15:08 PDT)
- Re: [AMBER] PB Bomb in pb_aaradi(): No radius assigned for atom (Tue Aug 11 2015 - 05:09:01 PDT)
- [AMBER] PB Bomb in pb_aaradi(): No radius assigned for atom (Tue Aug 11 2015 - 03:05:20 PDT)
Sarah Graham
- [AMBER] SPAM (Thu Aug 06 2015 - 11:06:23 PDT)
Scott Le Grand
- Re: [AMBER] NaN with pmemd.cuda (Fri Aug 07 2015 - 01:26:10 PDT)
Sharapa
- [AMBER] cg in GAFF: amb2gmx.pl vs virtualchemistry - LJ well depth (Wed Aug 12 2015 - 15:01:40 PDT)
shenna shearin
- Re: [AMBER] MMPBSA error using pbsa2 (Sun Aug 09 2015 - 04:38:24 PDT)
- [AMBER] MMPBSA error using pbsa2 (Fri Aug 07 2015 - 17:33:56 PDT)
Steven Ramsey
- Re: [AMBER] cpptraj gist: Eww energies (Mon Aug 10 2015 - 09:35:00 PDT)
Suchetana Gupta
- [AMBER] How do I study the dimerisation energy (i.e. energy required to form a dimer from two monomeric units) using AMBER? (Sat Aug 29 2015 - 00:15:11 PDT)
Suman Chakrabarty
- Re: [AMBER] acpype (Tue Aug 18 2015 - 07:30:17 PDT)
Sushi Shilpa
- [AMBER] ImportError: No module named scipy.optimize (Mon Aug 24 2015 - 21:07:25 PDT)
Thomas Cheatham
- Re: [AMBER] Regarding DNA forcefield in Amber14 (Thu Aug 06 2015 - 18:31:22 PDT)
Thomas Fox
- [AMBER] GIST vs. 3D-RISM (Wed Aug 12 2015 - 08:36:45 PDT)
- Re: [AMBER] cpptraj gist: Eww energies (Wed Aug 12 2015 - 08:31:09 PDT)
- [AMBER] cpptraj gist: Eww energies (Mon Aug 10 2015 - 02:49:21 PDT)
Tom Kurtzman
- Re: [AMBER] cpptraj gist: Eww energies (Mon Aug 10 2015 - 10:54:49 PDT)
- Re: [AMBER] cpptraj gist: Eww energies (Mon Aug 10 2015 - 07:59:44 PDT)
Tyler Luchko (Lists)
- Re: [AMBER] GIST vs. 3D-RISM (Wed Aug 12 2015 - 14:30:25 PDT)
Ucisik, Melek Nihan
- Re: [AMBER] "mask" command failure (Tue Aug 11 2015 - 08:20:38 PDT)
- Re: [AMBER] "mask" command failure (Sun Aug 09 2015 - 13:37:06 PDT)
- Re: [AMBER] "mask" command failure (Fri Aug 07 2015 - 09:20:54 PDT)
- [AMBER] "mask" command failure (Thu Aug 06 2015 - 14:26:40 PDT)
Urszula Uciechowska
- Re: [AMBER] error running mmpbsa.pl (Mon Aug 17 2015 - 02:27:03 PDT)
- [AMBER] error running mmpbsa.pl (Mon Aug 17 2015 - 02:12:40 PDT)
- [AMBER] MMPBSA.py error (Thu Aug 13 2015 - 03:59:19 PDT)
Vahid Kshani
- Re: [AMBER] could not open mdcrd file (Fri Aug 07 2015 - 00:05:55 PDT)
- [AMBER] could not open mdcrd file (Thu Aug 06 2015 - 04:22:21 PDT)
Vishal Nemaysh
- [AMBER] large .mdcrd splitting (Thu Aug 06 2015 - 00:49:02 PDT)
- [AMBER] .mdcrd to .trr conversion problem (Wed Aug 05 2015 - 08:41:51 PDT)
Vlad Cojocaru
- Re: [AMBER] Regarding DNA forcefield in Amber14 (Fri Aug 07 2015 - 00:55:30 PDT)
- Re: [AMBER] Regarding DNA forcefield in Amber14 (Wed Aug 05 2015 - 06:03:05 PDT)
- Re: [AMBER] Regarding DNA forcefield in Amber14 (Wed Aug 05 2015 - 01:40:11 PDT)
- Re: [AMBER] Regarding DNA forcefield in Amber14 (Wed Aug 05 2015 - 01:25:06 PDT)
Wenyu Qian
- Re: [AMBER] What is the best way to study a dynamics route of a molecule to enter a protein (Fri Aug 28 2015 - 07:55:45 PDT)
- [AMBER] What is the best way to study a dynamics route of a molecule to enter a protein (Tue Aug 25 2015 - 15:04:08 PDT)
whb
- [AMBER] pH-REMD theory (Wed Aug 12 2015 - 23:58:47 PDT)
Yeng-Tseng Wang
- Re: [AMBER] About the QMMM simulation with LIO software (Tue Aug 18 2015 - 01:08:05 PDT)
- Re: [AMBER] About the QMMM simulation with LIO software (Tue Aug 18 2015 - 00:59:56 PDT)
- Re: [AMBER] About the QMMM simulation with LIO software (Mon Aug 17 2015 - 09:21:22 PDT)
- [AMBER] About the QMMM simulation with LIO software (Sat Aug 15 2015 - 09:58:47 PDT)
Ying-Chieh Sun
- Re: [AMBER] Thermodynamic integration goes wrong in lambda =0 while lambda = 1 is ok!! (Wed Aug 05 2015 - 20:29:23 PDT)
Ziheng Wang
- Re: [AMBER] Segmentation Fault with pmemd (Sun Aug 30 2015 - 07:26:15 PDT)
- [AMBER] Segmentation Fault with pmemd (Sat Aug 29 2015 - 01:02:03 PDT)
浅井賢
- Re: [AMBER] Implicit solvent simulation is unexpectedly slow (Sun Aug 02 2015 - 06:59:57 PDT)
- [AMBER] Implicit solvent simulation is unexpectedly slow (Sun Aug 02 2015 - 01:21:43 PDT)

Amber Archive Aug 2015 by author