Amber Archive Aug 2013: by author

372133720
- [AMBER] MMPBSA_decomp (Mon Aug 05 2013 - 18:30:02 PDT)
- [AMBER] Fw: Re: MMPBSA problem (Thu Aug 01 2013 - 05:57:41 PDT)
- [AMBER] MMPBSA problem (Thu Aug 01 2013 - 03:54:37 PDT)
- [AMBER] Fw: Re: MMPBSA problem (Wed Jul 31 2013 - 19:01:51 PDT)
Aditya Padhi
- [AMBER] Query regarding membrane-peptide simulation (Mon Aug 19 2013 - 03:28:16 PDT)
Adrian Roitberg
- Re: [AMBER] ARG as a titratable residue for constant pH simulations (Thu Aug 29 2013 - 07:35:50 PDT)
- Re: [AMBER] BOND, ANGLE and TORSION energies discrepancy between amber and gromacs (Fri Aug 09 2013 - 08:05:05 PDT)
Alexander Button
- Re: [AMBER] Problems with NAB (Wed Jul 31 2013 - 20:27:56 PDT)
- Re: [AMBER] Problems with NAB (Wed Jul 31 2013 - 19:03:54 PDT)
Andre C. Stiel
- [AMBER] parmed.py with closest command from ptraj (Tue Aug 06 2013 - 03:39:39 PDT)
Andreas Goetz
- Re: [AMBER] dftb3 (Wed Aug 07 2013 - 16:10:04 PDT)
- Re: [AMBER] Distance based mask for qmmask (Fri Aug 02 2013 - 10:43:32 PDT)
- Re: [AMBER] Distance based mask for qmmask (Thu Aug 01 2013 - 20:34:15 PDT)
aneesh cna
- [AMBER] Generating snapshots in amber trajectory format (Thu Aug 01 2013 - 03:48:03 PDT)
Angelica Parente
- Re: [AMBER] 2nd Announcement AMBER workshop in Brazil (Oct 7-11 2013) pre-registration open (Sun Aug 11 2013 - 22:23:27 PDT)
anu chandra
- Re: [AMBER] Number of contacts (Sun Aug 25 2013 - 23:20:34 PDT)
- [AMBER] Large difference in GB and PB values of binding free energy (Sun Aug 25 2013 - 23:04:01 PDT)
- [AMBER] Number of contacts (Fri Aug 23 2013 - 05:44:09 PDT)
- [AMBER] Hbond alaysis in CPPTRAJ (Thu Aug 15 2013 - 00:10:18 PDT)
- Re: [AMBER] Question regarding H-bond calculation (Tue Aug 13 2013 - 23:21:48 PDT)
- [AMBER] Question regarding H-bond calculation (Mon Aug 12 2013 - 23:37:54 PDT)
arundhati dutta
- Re: [AMBER] Pucker Command In Cpptraj (Mon Aug 26 2013 - 12:46:30 PDT)
- [AMBER] Pucker Command In Cpptraj (Mon Aug 26 2013 - 09:31:29 PDT)
- Re: [AMBER] About SNB range in statistics command in cpptraj (Mon Aug 26 2013 - 09:20:23 PDT)
- [AMBER] About SNB range in statistics command in cpptraj (Mon Aug 26 2013 - 07:58:22 PDT)
Asmita Gupta
- Re: [AMBER] Terminal pair fraying in nucleic acids (Fri Aug 02 2013 - 05:45:42 PDT)
- [AMBER] Terminal pair fraying in nucleic acids (Thu Aug 01 2013 - 22:46:03 PDT)
Atila Petrosian
- [AMBER] question about amber installation (Fri Aug 30 2013 - 05:22:17 PDT)
- [AMBER] How to insert a drug near center of lipids in the membrane? (Wed Aug 21 2013 - 01:45:04 PDT)
Ayesha Fatima
- Re: [AMBER] R.E.D server output files (Sat Aug 10 2013 - 19:33:56 PDT)
- [AMBER] R.E.D server output files (Tue Aug 06 2013 - 19:16:09 PDT)
Aylin Sahin
- [AMBER] problem with making a movie (Wed Aug 28 2013 - 23:04:27 PDT)
- [AMBER] Modelling the folding of the c-terminus of a protein (Mon Aug 12 2013 - 23:47:33 PDT)
Barnett, James W.
- Re: [AMBER] "All hydrogens" in antechamber (Mon Aug 26 2013 - 06:42:55 PDT)
- [AMBER] "All hydrogens" in antechamber (Sat Aug 24 2013 - 08:44:18 PDT)
BERGY
- [AMBER] Partial Charges in AMBE force field (Fri Aug 16 2013 - 23:07:53 PDT)
berin karaman
- Re: [AMBER] radii effect on PB_cavity surften_cavity offset (Fri Aug 02 2013 - 00:24:37 PDT)
- [AMBER] radii effect on PB_cavity surften_cavity offset (Thu Aug 01 2013 - 06:54:15 PDT)
- Re: [AMBER] igb8 SURFTEN SURFOFF (Thu Aug 01 2013 - 00:47:28 PDT)
Bharatham, Nagakumar
- [AMBER] rk2 and rk3 values in NMR restraints (Wed Aug 21 2013 - 14:31:17 PDT)
Bill Miller III
- Re: [AMBER] Problem in energy decomposition (Tue Aug 13 2013 - 20:57:54 PDT)
- Re: [AMBER] MMPBSA selection error (Fri Aug 09 2013 - 11:56:14 PDT)
- Re: [AMBER] Is there any problem with this input file? (Mon Aug 05 2013 - 07:47:27 PDT)
Bill Ross
- Re: [AMBER] RMSD calculation followed by superimposition (Wed Aug 21 2013 - 22:04:00 PDT)
Brian Radak
- Re: [AMBER] frcmod.ionsjc_*** file and water model (Thu Aug 29 2013 - 06:48:36 PDT)
- Re: [AMBER] HW-HW for TIP3P? (Mon Aug 26 2013 - 13:55:18 PDT)
- Re: [AMBER] RED: charge equivalencing with intramolecular charge constraints? (Fri Aug 23 2013 - 09:21:29 PDT)
- [AMBER] RED: charge equivalencing with intramolecular charge constraints? (Fri Aug 23 2013 - 08:08:21 PDT)
- Re: [AMBER] problems with calculation continuing (Mon Aug 19 2013 - 09:47:31 PDT)
- Re: [AMBER] Energy terms in mdout (Etot, EKtot, ...) (Fri Aug 09 2013 - 07:20:15 PDT)
- Re: [AMBER] Trajectory post-processing (Tue Aug 06 2013 - 14:06:38 PDT)
- Re: [AMBER] output nuclear force and hessian (Tue Aug 06 2013 - 07:25:43 PDT)
- Re: [AMBER] output nuclear force and hessian (Mon Aug 05 2013 - 12:20:19 PDT)
- Re: [AMBER] How to Calculate Energy (Fri Aug 02 2013 - 13:12:41 PDT)
Carlos Romero
- Re: [AMBER] amber11 installation error (Thu Aug 29 2013 - 12:47:58 PDT)
- Re: [AMBER] amber11 installation error (Thu Aug 29 2013 - 12:42:20 PDT)
- [AMBER] amber11 installation error (Thu Aug 29 2013 - 11:59:23 PDT)
case
- Re: [AMBER] problems with disulfide bond creation (Tue Aug 27 2013 - 19:03:27 PDT)
Catein Catherine
- Re: [AMBER] MM-GBSA igb=2 or igb=5? [Ref: Exploring Protein Native States and Large-Scale Conformational Changes With a Modified Generalized Born Model] (Wed Jul 31 2013 - 21:09:00 PDT)
CH NIMILITHA Nimilitha
- [AMBER] can't neutralize (Thu Aug 01 2013 - 04:06:27 PDT)
Chaitanya Murthy
- [AMBER] NAB transformation matrix conventions (rotation about x-axis is left handed?) (Mon Aug 26 2013 - 19:15:52 PDT)
Changqing Yan
- [AMBER] Nmode question (Mon Aug 05 2013 - 01:57:25 PDT)
- [AMBER] Is there any problem with this input file? (Fri Aug 02 2013 - 07:34:03 PDT)
- [AMBER] Jobs resubmitted when calculating entropy (Thu Aug 01 2013 - 03:02:50 PDT)
Chinthaka Ratnaweera
- [AMBER] Secondary Structure analysis (Wed Aug 07 2013 - 09:56:09 PDT)
Chris Forman
- Re: [AMBER] Hydroxylysine Parameters (Thu Aug 29 2013 - 05:36:19 PDT)
- Re: [AMBER] Hydroxylysine Parameters (Thu Aug 29 2013 - 05:33:45 PDT)
- [AMBER] Hydroxylysine Parameters (Tue Aug 27 2013 - 08:23:24 PDT)
Collins Nganou
- [AMBER] simulation of single strand DNA (Tue Aug 13 2013 - 09:19:19 PDT)
Daniel Roe
- Re: [AMBER] cpptraj removes velocities upon imaging (Sat Aug 31 2013 - 14:44:51 PDT)
- Re: [AMBER] cpptraj removes velocities upon imaging (Sat Aug 31 2013 - 04:14:32 PDT)
- Re: [AMBER] Number of contacts (Tue Aug 27 2013 - 09:57:24 PDT)
- Re: [AMBER] Pucker Command In Cpptraj (Mon Aug 26 2013 - 14:06:59 PDT)
- Re: [AMBER] Pucker Command In Cpptraj (Mon Aug 26 2013 - 12:42:36 PDT)
- Re: [AMBER] About SNB range in statistics command in cpptraj (Mon Aug 26 2013 - 08:51:09 PDT)
- Re: [AMBER] Problematic structure after minimization on GPU (Mon Aug 26 2013 - 08:15:31 PDT)
- Re: [AMBER] Number of contacts (Fri Aug 23 2013 - 08:35:30 PDT)
- Re: [AMBER] RMSD calculation followed by superimposition (Fri Aug 23 2013 - 08:30:51 PDT)
- Re: [AMBER] RMSD calculation followed by superimposition (Wed Aug 21 2013 - 22:02:37 PDT)
- Re: [AMBER] RMSD calculation followed by superimposition (Wed Aug 21 2013 - 21:59:09 PDT)
- Re: [AMBER] RMSD calculation followed by superimposition (Wed Aug 21 2013 - 21:22:05 PDT)
- Re: [AMBER] how to check for errors in a topology library file created with saveOff (Wed Aug 21 2013 - 12:01:45 PDT)
- Re: [AMBER] how to check for errors in a topology library file created with saveOff (Tue Aug 20 2013 - 20:22:50 PDT)
- Re: [AMBER] Two questions in one... (Mon Aug 19 2013 - 13:13:02 PDT)
- Re: [AMBER] Error: Bad topology file. Sum of ATOMS_PER_MOLECULE does not equal NATOM. (Mon Aug 19 2013 - 12:00:09 PDT)
- Re: [AMBER] Hbond alaysis in CPPTRAJ (Thu Aug 15 2013 - 07:37:52 PDT)
- Re: [AMBER] Problem with Amber tutorial A.15 (Wed Aug 14 2013 - 15:25:23 PDT)
- Re: [AMBER] Problem with Amber tutorial A.15 (Wed Aug 14 2013 - 09:05:58 PDT)
- Re: [AMBER] Question regarding H-bond calculation (Tue Aug 13 2013 - 07:24:24 PDT)
- Re: [AMBER] ptraj is not splitting LES trajectory (Sun Aug 11 2013 - 11:20:19 PDT)
- Re: [AMBER] Reading velocity trajectories (Sat Aug 10 2013 - 22:19:37 PDT)
- Re: [AMBER] Trajectory post-processing (Sat Aug 10 2013 - 14:09:38 PDT)
- Re: [AMBER] ptraj is not splitting LES trajectory (Fri Aug 09 2013 - 17:59:12 PDT)
- Re: [AMBER] Trajectory post-processing (Fri Aug 09 2013 - 08:28:32 PDT)
- Re: [AMBER] cpptraj: noxcol example, order of cmdline args (Fri Aug 09 2013 - 08:26:46 PDT)
- Re: [AMBER] cpptraj: noxcol example, order of cmdline args (Fri Aug 09 2013 - 08:01:17 PDT)
- Re: [AMBER] cpptraj: noxcol example, order of cmdline args (Fri Aug 09 2013 - 07:44:19 PDT)
- Re: [AMBER] Suggestions for using "distance" in cpptraj (Thu Aug 08 2013 - 14:29:24 PDT)
- Re: [AMBER] Distance between group of atoms using Ptraj (Thu Aug 08 2013 - 08:34:43 PDT)
- Re: [AMBER] Trajectory post-processing (Thu Aug 08 2013 - 08:27:08 PDT)
- Re: [AMBER] mask command issue (Wed Aug 07 2013 - 14:00:29 PDT)
- Re: [AMBER] mask command issue (Wed Aug 07 2013 - 10:59:43 PDT)
- Re: [AMBER] Secondary Structure analysis (Wed Aug 07 2013 - 10:16:50 PDT)
- Re: [AMBER] Auto-image "Could not determine atomic number from mass" (Wed Aug 07 2013 - 09:11:31 PDT)
- Re: [AMBER] mask command issue (Wed Aug 07 2013 - 08:26:33 PDT)
- Re: [AMBER] Trajectory post-processing (Tue Aug 06 2013 - 14:08:02 PDT)
- [AMBER] AmberTools update 15 for CPPTRAJ (Tue Aug 06 2013 - 09:14:42 PDT)
- Re: [AMBER] parmed.py with closest command from ptraj (Tue Aug 06 2013 - 05:51:54 PDT)
- Re: [AMBER] parmed.py with closest command from ptraj (Tue Aug 06 2013 - 05:50:33 PDT)
- Re: [AMBER] Auto-image "Could not determine atomic number from mass" (Mon Aug 05 2013 - 16:35:05 PDT)
- [AMBER] Auto-image "Could not determine atomic number from mass" (Mon Aug 05 2013 - 13:33:15 PDT)
- Re: [AMBER] Parameter file is not saved - AMBER! (Mon Aug 05 2013 - 09:16:47 PDT)
- Re: [AMBER] change coordinate (Sun Aug 04 2013 - 20:54:12 PDT)
- Re: [AMBER] Using ante-mmpbsa.py to create prmtops (Fri Aug 02 2013 - 11:00:33 PDT)
- Re: [AMBER] 10 ns explicit water NPT (Fri Aug 02 2013 - 10:32:30 PDT)
- Re: [AMBER] Using ante-mmpbsa.py to create prmtops (Fri Aug 02 2013 - 10:20:52 PDT)
- Re: [AMBER] 10 ns explicit water NPT (Fri Aug 02 2013 - 08:07:11 PDT)
- Re: [AMBER] Updating AmberTools1.5 (Thu Aug 01 2013 - 21:40:39 PDT)
- Re: [AMBER] SASA / AmberTools1.5 (Thu Aug 01 2013 - 21:38:10 PDT)
David A Case
- Re: [AMBER] TI input files in A9 tutorial and Amber12 manual (Fri Aug 30 2013 - 12:45:01 PDT)
- Re: [AMBER] setting up a covalently bonded ligand to enzyme with tleap (Wed Aug 28 2013 - 05:33:18 PDT)
- Re: [AMBER] Hydroxylysine Parameters (Tue Aug 27 2013 - 09:11:12 PDT)
- Re: [AMBER] antechamber bond type error (Tue Aug 27 2013 - 06:29:34 PDT)
- Re: [AMBER] AMBER: antechamber error : Cannot open CONNECT.TPL, exit (Tue Aug 27 2013 - 06:26:37 PDT)
- Re: [AMBER] Gaussian charges in xleap (Tue Aug 27 2013 - 06:24:06 PDT)
- Re: [AMBER] antechamber returns different results from same molecule structures (Tue Aug 27 2013 - 06:00:04 PDT)
- Re: [AMBER] PLP- L Histidinal Phosphate parameters (Wed Aug 21 2013 - 06:14:00 PDT)
- Re: [AMBER] Input files for Targeted MD using Amber (Tue Aug 20 2013 - 18:59:29 PDT)
- Re: [AMBER] AMBER minimization job (Mon Aug 19 2013 - 12:31:42 PDT)
- Re: [AMBER] Error using Antechamber (Mon Aug 19 2013 - 06:12:09 PDT)
- Re: [AMBER] Box info not found (Thu Aug 15 2013 - 18:03:48 PDT)
- Re: [AMBER] Cterm and Nterm caps (Thu Aug 15 2013 - 06:16:14 PDT)
- Re: [AMBER] Problem with xLeap : Segmentation fault (core dumped) (Wed Aug 14 2013 - 06:06:57 PDT)
- Re: [AMBER] Modelling the folding of the c-terminus of a protein (Wed Aug 14 2013 - 04:39:55 PDT)
- Re: [AMBER] Add potential energy term (Wed Aug 14 2013 - 04:38:04 PDT)
- Re: [AMBER] simulation of single strand DNA (Tue Aug 13 2013 - 11:59:31 PDT)
- Re: [AMBER] Magnesium charges using leaprc.ff99SB - metals move away (Mon Aug 12 2013 - 09:10:56 PDT)
- Re: [AMBER] Problem with Amber tutorial A.15 (Mon Aug 12 2013 - 07:04:13 PDT)
- Re: [AMBER] antechamber returns different results from same molecule structures (Mon Aug 12 2013 - 04:51:17 PDT)
- Re: [AMBER] Fw: output nuclear force and hessian (Sat Aug 10 2013 - 18:55:07 PDT)
- Re: [AMBER] DNA Phosphate error (Sat Aug 10 2013 - 06:40:26 PDT)
- Re: [AMBER] output nuclear force and hessian (Sat Aug 10 2013 - 06:30:54 PDT)
- Re: [AMBER] Problems running NAB scripts in the manual (Fri Aug 09 2013 - 10:22:53 PDT)
- Re: [AMBER] Magnesium charges using leaprc.ff99SB - metals move away (Fri Aug 09 2013 - 09:36:06 PDT)
- Re: [AMBER] TI with ifsc==2 (reposted) (Fri Aug 09 2013 - 08:30:57 PDT)
- Re: [AMBER] BOND, ANGLE and TORSION energies discrepancy between amber and gromacs (Fri Aug 09 2013 - 06:46:51 PDT)
- Re: [AMBER] ERROR in rms: KRMS_ reported Number of atoms less than 2 (Fri Aug 09 2013 - 06:44:00 PDT)
- Re: [AMBER] Why are sigma values of OPLS so big? (Thu Aug 08 2013 - 18:33:07 PDT)
- Re: [AMBER] Magnesium charges using leaprc.ff99SB - metals move away (Thu Aug 08 2013 - 18:20:54 PDT)
- Re: [AMBER] Distance between group of atoms using Ptraj (Thu Aug 08 2013 - 09:57:10 PDT)
- Re: [AMBER] pmemd.cuda.MPI problem (Wed Aug 07 2013 - 11:50:02 PDT)
- Re: [AMBER] output nuclear force and hessian (Tue Aug 06 2013 - 13:04:04 PDT)
- Re: [AMBER] Segmentation Fault (Tue Aug 06 2013 - 06:39:21 PDT)
- Re: [AMBER] Segmentation Fault (Tue Aug 06 2013 - 04:53:31 PDT)
- Re: [AMBER] Error when loading the opls dihedral information. (Tue Aug 06 2013 - 04:51:33 PDT)
- Re: [AMBER] Auto-image "Could not determine atomic number from mass" (Tue Aug 06 2013 - 04:49:25 PDT)
- Re: [AMBER] Parameter file is not saved - AMBER! (Mon Aug 05 2013 - 11:11:25 PDT)
- Re: [AMBER] Nmode question (Mon Aug 05 2013 - 11:08:08 PDT)
- Re: [AMBER] Nmode question (Mon Aug 05 2013 - 08:49:02 PDT)
- Re: [AMBER] ambpdb -ext ... but how? (Sun Aug 04 2013 - 18:01:05 PDT)
- Re: [AMBER] isothermal compressibility (Fri Aug 02 2013 - 18:27:47 PDT)
- Re: [AMBER] Terminal pair fraying in nucleic acids (Fri Aug 02 2013 - 10:10:48 PDT)
- Re: [AMBER] 10 ns explicit water NPT (Fri Aug 02 2013 - 05:26:37 PDT)
- Re: [AMBER] Terminal pair fraying in nucleic acids (Fri Aug 02 2013 - 05:24:31 PDT)
- Re: [AMBER] Charmmgui pdb file error (Thu Aug 01 2013 - 13:40:48 PDT)
- Re: [AMBER] Charmmgui pdb file error (Thu Aug 01 2013 - 06:44:55 PDT)
- Re: [AMBER] can't neutralize (Thu Aug 01 2013 - 04:56:15 PDT)
- Re: [AMBER] SASA / AmberTools1.5 (Thu Aug 01 2013 - 04:52:09 PDT)
- Re: [AMBER] igb8 SURFTEN SURFOFF (Thu Aug 01 2013 - 04:50:16 PDT)
David A. Case
- Re: [AMBER] nmr upper_bond criteria (Thu Aug 22 2013 - 19:12:52 PDT)
- Re: [AMBER] problem with ambertools test (Thu Aug 22 2013 - 19:06:54 PDT)
David Case
- Re: [AMBER] "All hydrogens" in antechamber (Sat Aug 24 2013 - 16:17:50 PDT)
- Re: [AMBER] Gaussian charges in xleap (Fri Aug 23 2013 - 07:22:45 PDT)
Dickson, Callum
- Re: [AMBER] DMPC GAFF lipid membrane is freezing at 303 K. (Thu Aug 22 2013 - 11:13:07 PDT)
dilrajl.bii.a-star.edu.sg
- [AMBER] Comparing Enthalpy change and energy decomposition values (Fri Aug 23 2013 - 03:41:59 PDT)
Divi/GMAIL
- Re: [AMBER] GTX-Titan / GTX780 Fix (Wed Aug 07 2013 - 17:53:09 PDT)
Dwight McGee
- Re: [AMBER] error when running binding energy in amber (Thu Aug 01 2013 - 20:03:28 PDT)
egeh00
- Re: [AMBER] Question about different SCEE&SCNB to specified atom pairs. (Tue Aug 20 2013 - 09:16:39 PDT)
- [AMBER] Question about different SCEE&SCNB to specified atom pairs. (Mon Aug 19 2013 - 21:45:21 PDT)
- [AMBER] Tutorial for specified SCEE and SCNB for different atom pairs? (Fri Aug 16 2013 - 21:31:58 PDT)
- [AMBER] Possibility of mixing OPLS and Glycam? (Mon Aug 12 2013 - 21:15:38 PDT)
- [AMBER] Difference between lower case and upper case in atomtype? (Sun Aug 11 2013 - 21:36:43 PDT)
- [AMBER] Puzzles about SCEE and SCNB? (Fri Aug 09 2013 - 14:54:33 PDT)
- [AMBER] Why are sigma values of OPLS so big? (Thu Aug 08 2013 - 14:10:36 PDT)
- [AMBER] Questions about improper dihedral scan? (Tue Aug 06 2013 - 15:44:21 PDT)
- [AMBER] Error when loading the opls dihedral information. (Mon Aug 05 2013 - 16:16:35 PDT)
Eric Berquist
- Re: [AMBER] cpptraj removes velocities upon imaging (Sat Aug 31 2013 - 07:34:38 PDT)
- [AMBER] cpptraj removes velocities upon imaging (Fri Aug 30 2013 - 12:47:03 PDT)
erik.laurini.di3.units.it
- [AMBER] reax forcefield (Wed Aug 07 2013 - 08:42:14 PDT)
ET
- Re: [AMBER] GTX-Titan / GTX780 Fix (Wed Aug 14 2013 - 08:07:12 PDT)
Fabrício Bracht
- [AMBER] Constant ph with replica exchange (Thu Aug 29 2013 - 14:00:39 PDT)
- Re: [AMBER] Distance based mask for qmmask (Fri Aug 02 2013 - 17:21:01 PDT)
- Re: [AMBER] Distance based mask for qmmask (Thu Aug 01 2013 - 21:26:22 PDT)
fatahiya
- [AMBER] SASA (Tue Aug 20 2013 - 01:27:57 PDT)
- [AMBER] Updating AmberTools1.5 (Thu Aug 01 2013 - 19:49:36 PDT)
- Re: [AMBER] SASA / AmberTools1.5 (Thu Aug 01 2013 - 19:23:13 PDT)
- [AMBER] SASA / AmberTools1.5 (Thu Aug 01 2013 - 02:44:52 PDT)
filip fratev
- Re: [AMBER] GTX-Titan / GTX780 Fix (Wed Aug 07 2013 - 10:30:35 PDT)
FyD
- Re: [AMBER] Gaussian charges in xleap (Thu Aug 29 2013 - 01:51:43 PDT)
- Re: [AMBER] Hydroxylysine Parameters (Thu Aug 29 2013 - 01:47:49 PDT)
- Re: [AMBER] RED: charge equivalencing with intramolecular charge constraints? (Sat Aug 24 2013 - 08:45:24 PDT)
- Re: [AMBER] RED: charge equivalencing with intramolecular charge constraints? (Fri Aug 23 2013 - 09:16:05 PDT)
- Re: [AMBER] Gaussian charges in xleap (Fri Aug 23 2013 - 08:47:51 PDT)
- Re: [AMBER] Gaussian charges in xleap (Thu Aug 22 2013 - 05:19:58 PDT)
- Re: [AMBER] how to check for errors in a topology library file created with saveOff (Thu Aug 22 2013 - 05:09:01 PDT)
- Re: [AMBER] how to check for errors in a topology library file created with saveOff (Wed Aug 21 2013 - 03:54:15 PDT)
- Re: [AMBER] PLP-L Histidinal Phosphate parameters (Wed Aug 21 2013 - 03:50:15 PDT)
- Re: [AMBER] Partial Charges in AMBE force field (Sun Aug 18 2013 - 08:29:35 PDT)
- Re: [AMBER] R.E.D server output files (Thu Aug 08 2013 - 03:18:43 PDT)
- Re: [AMBER] Resp charges (Thu Aug 08 2013 - 02:47:42 PDT)
Ganesh Kamath
- [AMBER] Reading velocity trajectories (Fri Aug 09 2013 - 18:05:53 PDT)
Gannett, Peter
- Re: [AMBER] Fw: Re: MMPBSA problem (Thu Aug 01 2013 - 06:21:30 PDT)
gargi borgohai
- [AMBER] Fwd: (Wed Aug 28 2013 - 05:55:21 PDT)
George Green
- Re: [AMBER] mmpbsa nonpolar contribution using stability calculations (Wed Aug 21 2013 - 01:31:24 PDT)
- Re: [AMBER] mmpbsa nonpolar contribution using stability calculations (Mon Aug 19 2013 - 03:07:51 PDT)
- Re: [AMBER] mmpbsa nonpolar contribution using stability calculations (Thu Aug 01 2013 - 13:44:14 PDT)
- Re: [AMBER] mmpbsa nonpolar contribution using stability calculations (Thu Aug 01 2013 - 08:53:37 PDT)
Giorgos Lamprinidis
- Re: [AMBER] Charmmgui pdb file error (Fri Aug 02 2013 - 00:22:13 PDT)
- Re: [AMBER] Charmmgui pdb file error (Thu Aug 01 2013 - 07:49:38 PDT)
- [AMBER] Charmmgui pdb file error (Thu Aug 01 2013 - 06:17:38 PDT)
glbala87.imtech.res.in
- [AMBER] antechamber bond type error (Tue Aug 27 2013 - 05:10:06 PDT)
- Re: [AMBER] AMBER: antechamber error : Cannot open CONNECT.TPL, exit (Tue Aug 27 2013 - 04:10:45 PDT)
Golshan Hejazi
- Re: [AMBER] BOND, ANGLE and TORSION energies discrepancy between amber and gromacs (Mon Aug 12 2013 - 06:32:20 PDT)
- Re: [AMBER] BOND, ANGLE and TORSION energies discrepancy between amber and gromacs (Fri Aug 09 2013 - 15:32:40 PDT)
- Re: [AMBER] BOND, ANGLE and TORSION energies discrepancy between amber and gromacs (Fri Aug 09 2013 - 15:01:29 PDT)
- Re: [AMBER] BOND, ANGLE and TORSION energies discrepancy between amber and gromacs (Fri Aug 09 2013 - 10:02:18 PDT)
- Re: [AMBER] BOND, ANGLE and TORSION energies discrepancy between amber and gromacs (Fri Aug 09 2013 - 07:53:40 PDT)
- Re: [AMBER] BOND, ANGLE and TORSION energies discrepancy between amber and gromacs (Fri Aug 09 2013 - 06:35:55 PDT)
- [AMBER] BOND, ANGLE and TORSION energies discrepancy between amber and gromacs (Thu Aug 08 2013 - 12:26:53 PDT)
Hailin Huang
- Re: [AMBER] Problem with xLeap : Segmentation fault (core dumped) (Wed Aug 14 2013 - 01:21:42 PDT)
- Re: [AMBER] Abnormal md output (Thu Aug 08 2013 - 14:37:59 PDT)
- [AMBER] Abnormal md output (Thu Aug 08 2013 - 11:38:47 PDT)
- Re: [AMBER] Auto-image "Could not determine atomic number from mass" (Wed Aug 07 2013 - 12:43:28 PDT)
- Re: [AMBER] Auto-image "Could not determine atomic number from mass" (Mon Aug 05 2013 - 14:09:40 PDT)
- [AMBER] Auto-image "Could not determine atomic number from mass" (Mon Aug 05 2013 - 12:41:33 PDT)
Hamed S. Hayatshahi
- [AMBER] TI input files in A9 tutorial and Amber12 manual (Fri Aug 30 2013 - 11:14:17 PDT)
- Re: [AMBER] Pucker Command In Cpptraj (Mon Aug 26 2013 - 11:55:54 PDT)
- Re: [AMBER] Resp charges (Mon Aug 05 2013 - 13:55:43 PDT)
HIMANSHU JOSHI
- [AMBER] xLeap : Undo option (Thu Aug 29 2013 - 11:10:22 PDT)
- Re: [AMBER] Gaussian charges in xleap (Tue Aug 27 2013 - 05:57:49 PDT)
- Re: [AMBER] Gaussian charges in xleap (Mon Aug 26 2013 - 22:04:34 PDT)
- Re: [AMBER] Gaussian charges in xleap (Fri Aug 23 2013 - 04:20:00 PDT)
- [AMBER] Gaussian charges in xleap (Wed Aug 21 2013 - 22:14:43 PDT)
- Re: [AMBER] Problem with xLeap : Segmentation fault (core dumped) (Wed Aug 14 2013 - 09:28:15 PDT)
- [AMBER] Problem with xLeap : Segmentation fault (core dumped) (Wed Aug 14 2013 - 00:55:54 PDT)
- Re: [AMBER] Distance between group of atoms using Ptraj (Thu Aug 08 2013 - 23:28:16 PDT)
- [AMBER] Distance between group of atoms using Ptraj (Thu Aug 08 2013 - 03:24:28 PDT)
Hiromasa WATANABE
- Re: [AMBER] antechamber returns different results from same molecule structures (Tue Aug 27 2013 - 17:57:28 PDT)
- Re: [AMBER] antechamber returns different results from same molecule structures (Tue Aug 27 2013 - 17:53:54 PDT)
- Re: [AMBER] antechamber returns different results from same molecule structures (Mon Aug 26 2013 - 20:14:46 PDT)
- Re: [AMBER] antechamber returns different results from same molecule structures (Sun Aug 18 2013 - 17:45:04 PDT)
- Re: [AMBER] antechamber returns different results from same molecule structures (Mon Aug 12 2013 - 22:33:16 PDT)
- [AMBER] antechamber returns different results from same molecule structures (Sun Aug 11 2013 - 19:36:06 PDT)
Hunter Brown
- Re: [AMBER] MMPBSA selection error (Fri Aug 09 2013 - 12:33:05 PDT)
- [AMBER] MMPBSA selection error (Fri Aug 09 2013 - 09:29:13 PDT)
- Re: [AMBER] Suggestions for using (Thu Aug 08 2013 - 14:44:30 PDT)
- [AMBER] Suggestions for using "distance" in cpptraj (Thu Aug 08 2013 - 13:44:57 PDT)
- Re: [AMBER] Using ante-mmpbsa.py to create prmtops (Fri Aug 02 2013 - 10:39:47 PDT)
- Re: [AMBER] Using ante-mmpbsa.py to create prmtops (Fri Aug 02 2013 - 10:17:34 PDT)
- Re: [AMBER] Using ante-mmpbsa.py to create prmtops (Thu Aug 01 2013 - 14:05:09 PDT)
- [AMBER] Using ante-mmpbsa.py to create prmtops (Thu Aug 01 2013 - 10:07:36 PDT)
Ilyas Yildirim
- Re: [AMBER] Chi torsions (Thu Aug 08 2013 - 14:11:50 PDT)
Indrajit Deb
- Re: [AMBER] How to Calculate Energy (Fri Aug 02 2013 - 14:21:47 PDT)
- [AMBER] How to Calculate Energy (Fri Aug 02 2013 - 12:18:24 PDT)
iqtcub
- Re: [AMBER] GTX-Titan / GTX780 Fix (Wed Aug 21 2013 - 01:14:06 PDT)
Ismail, Mohd F.
- Re: [AMBER] Diffusion constant's unit (Tue Aug 06 2013 - 22:26:32 PDT)
Jagur Lambix
- [AMBER] Residue decomposition: not possible with PB ? (Fri Aug 09 2013 - 16:04:06 PDT)
Jake Smith
- Re: [AMBER] Cpu busy looping? (Tue Aug 20 2013 - 17:38:37 PDT)
- Re: [AMBER] Cpu busy looping? (Tue Aug 20 2013 - 15:19:13 PDT)
- [AMBER] Cpu busy looping? (Tue Aug 20 2013 - 12:32:01 PDT)
James W. Snyder, Jr.
- Re: [AMBER] ptraj is not splitting LES trajectory (Sun Aug 11 2013 - 12:43:47 PDT)
- Re: [AMBER] ptraj is not splitting LES trajectory (Fri Aug 09 2013 - 18:09:17 PDT)
- [AMBER] ptraj is not splitting LES trajectory (Fri Aug 09 2013 - 17:02:21 PDT)
- Re: [AMBER] multiple heat baths in a single simulation (Wed Aug 07 2013 - 14:03:21 PDT)
- [AMBER] multiple heat baths in a single simulation (Wed Aug 07 2013 - 11:38:14 PDT)
Jan-Philip Gehrcke
- Re: [AMBER] mmP(G)BSA correlation time (Fri Aug 30 2013 - 00:56:49 PDT)
- Re: [AMBER] Problematic structure after minimization on GPU (Tue Aug 27 2013 - 02:13:11 PDT)
- Re: [AMBER] Problematic structure after minimization on GPU (Mon Aug 26 2013 - 07:48:52 PDT)
- [AMBER] Problematic structure after minimization on GPU (Mon Aug 26 2013 - 07:25:00 PDT)
- [AMBER] Problematic structure after minimization on GPU (Mon Aug 26 2013 - 04:52:27 PDT)
- Re: [AMBER] PMEMD Performance issue on AMD cluster (Wed Aug 21 2013 - 05:40:41 PDT)
- Re: [AMBER] Cpu busy looping? (Wed Aug 21 2013 - 04:56:34 PDT)
- Re: [AMBER] CUDA_VISIBLE_DEVICES and real instance IDs (Thu Aug 15 2013 - 12:21:09 PDT)
- Re: [AMBER] RMSD calculation followed by superimposition (Thu Aug 15 2013 - 01:27:07 PDT)
- Re: [AMBER] cpptraj: noxcol example, order of cmdline args (Fri Aug 09 2013 - 08:16:17 PDT)
- Re: [AMBER] cpptraj: noxcol example, order of cmdline args (Fri Aug 09 2013 - 03:44:30 PDT)
- [AMBER] cpptraj: noxcol example, order of cmdline args (Fri Aug 09 2013 - 03:05:56 PDT)
Jason Swails
- Re: [AMBER] Cannot download Amber12, bugfix.18.bz2 (Fri Aug 30 2013 - 20:03:40 PDT)
- Re: [AMBER] mmP(G)BSA correlation time (Fri Aug 30 2013 - 10:29:17 PDT)
- Re: [AMBER] question about amber installation (Fri Aug 30 2013 - 05:35:59 PDT)
- Re: [AMBER] Constant ph with replica exchange (Thu Aug 29 2013 - 14:37:03 PDT)
- Re: [AMBER] amber11 installation error (Thu Aug 29 2013 - 12:29:44 PDT)
- Re: [AMBER] Simmetry problem (Thu Aug 29 2013 - 04:54:44 PDT)
- Re: [AMBER] mpi4py building error during AmberTools 13 install (Wed Aug 28 2013 - 07:56:41 PDT)
- Re: [AMBER] Fwd: (Wed Aug 28 2013 - 06:00:27 PDT)
- Re: [AMBER] mmP(G)BSA correlation time (Wed Aug 28 2013 - 04:59:54 PDT)
- Re: [AMBER] Different SASA values in MM/PBSA and MM/GBSA? (Tue Aug 27 2013 - 05:38:40 PDT)
- Re: [AMBER] MMPBSA: AttributeError: 'list' object has no attribute 'stdev' (Sun Aug 25 2013 - 20:32:24 PDT)
- Re: [AMBER] σ in Amber and OPLS-AA? (Thu Aug 22 2013 - 19:16:52 PDT)
- Re: [AMBER] how to check for errors in a topology library file created with saveOff (Wed Aug 21 2013 - 08:29:43 PDT)
- Re: [AMBER] PMEMD Performance issue on AMD cluster (Wed Aug 21 2013 - 05:20:14 PDT)
- Re: [AMBER] nmr upper_bond criteria (Wed Aug 21 2013 - 05:03:48 PDT)
- Re: [AMBER] Cpu busy looping? (Tue Aug 20 2013 - 13:00:56 PDT)
- Re: [AMBER] Question about different SCEE&SCNB to specified atom pairs. (Tue Aug 20 2013 - 08:34:41 PDT)
- Re: [AMBER] SASA (Tue Aug 20 2013 - 06:12:30 PDT)
- Re: [AMBER] Error: Bad topology file. Sum of ATOMS_PER_MOLECULE does not equal NATOM. (Mon Aug 19 2013 - 10:02:28 PDT)
- Re: [AMBER] mmpbsa nonpolar contribution using stability calculations (Mon Aug 19 2013 - 04:30:53 PDT)
- Re: [AMBER] problem with ambertools test (Sun Aug 18 2013 - 18:07:31 PDT)
- Re: [AMBER] Error: Bad topology file. Sum of ATOMS_PER_MOLECULE does not equal NATOM. (Sun Aug 18 2013 - 18:03:58 PDT)
- Re: [AMBER] MMPBSA doubt (Fri Aug 16 2013 - 15:33:26 PDT)
- Re: [AMBER] Problem with Amber tutorial A.15 (Wed Aug 14 2013 - 09:17:33 PDT)
- Re: [AMBER] MMPBSA doubt (Wed Aug 14 2013 - 09:11:23 PDT)
- Re: [AMBER] Puzzles about SCEE and SCNB? (Fri Aug 09 2013 - 15:35:46 PDT)
- Re: [AMBER] MMPBSA selection error (Fri Aug 09 2013 - 14:26:12 PDT)
- Re: [AMBER] BOND, ANGLE and TORSION energies discrepancy between amber and gromacs (Fri Aug 09 2013 - 14:23:03 PDT)
- Re: [AMBER] Energy terms in mdout (Etot, EKtot, ...) (Fri Aug 09 2013 - 14:15:15 PDT)
- Re: [AMBER] pmemd.cuda.MPI problem (Wed Aug 07 2013 - 12:44:52 PDT)
- Re: [AMBER] output nuclear force and hessian (Wed Aug 07 2013 - 11:41:41 PDT)
- Re: [AMBER] pmemd.cuda.MPI problem (Wed Aug 07 2013 - 11:38:26 PDT)
- Re: [AMBER] Trajectory post-processing (Tue Aug 06 2013 - 17:13:09 PDT)
- Re: [AMBER] parmed.py with closest command from ptraj (Tue Aug 06 2013 - 11:47:21 PDT)
- Re: [AMBER] output nuclear force and hessian (Tue Aug 06 2013 - 11:45:09 PDT)
- Re: [AMBER] MMPBSA_decomp (Mon Aug 05 2013 - 22:44:29 PDT)
- Re: [AMBER] output nuclear force and hessian (Mon Aug 05 2013 - 22:41:56 PDT)
- Re: [AMBER] Using ante-mmpbsa.py to create prmtops (Sat Aug 03 2013 - 06:47:17 PDT)
- Re: [AMBER] mmpbsa nonpolar contribution using stability calculations (Thu Aug 01 2013 - 14:20:41 PDT)
- Re: [AMBER] Using ante-mmpbsa.py to create prmtops (Thu Aug 01 2013 - 14:16:21 PDT)
- Re: [AMBER] Using ante-mmpbsa.py to create prmtops (Thu Aug 01 2013 - 11:14:00 PDT)
- Re: [AMBER] Jobs resubmitted when calculating entropy (Thu Aug 01 2013 - 06:54:00 PDT)
- Re: [AMBER] Generating snapshots in amber trajectory format (Thu Aug 01 2013 - 06:42:32 PDT)
- Re: [AMBER] Fw: Re: MMPBSA problem (Thu Aug 01 2013 - 06:22:33 PDT)
- Re: [AMBER] MM-GBSA igb=2 or igb=5? [Ref: Exploring Protein Native States and Large-Scale Conformational Changes With a Modified Generalized Born Model] (Thu Aug 01 2013 - 06:19:57 PDT)
Jia Xu
- [AMBER] MTKPP/MCPB charge is not integer (Wed Aug 14 2013 - 11:25:58 PDT)
Jiri Sponer
- Re: [AMBER] Chi torsions (Fri Aug 09 2013 - 02:06:43 PDT)
John Gehman
- [AMBER] ambpdb -ext ... but how? (Sun Aug 04 2013 - 15:13:38 PDT)
John Travers
- Re: [AMBER] output nuclear force and hessian (Sat Aug 10 2013 - 15:38:05 PDT)
- [AMBER] Fw: output nuclear force and hessian (Sat Aug 10 2013 - 15:02:26 PDT)
- Re: [AMBER] output nuclear force and hessian (Fri Aug 09 2013 - 20:01:38 PDT)
- Re: [AMBER] output nuclear force and hessian (Wed Aug 07 2013 - 12:29:09 PDT)
- Re: [AMBER] output nuclear force and hessian (Tue Aug 06 2013 - 08:47:03 PDT)
- Re: [AMBER] output nuclear force and hessian (Tue Aug 06 2013 - 08:26:33 PDT)
- Re: [AMBER] output nuclear force and hessian (Mon Aug 05 2013 - 15:26:41 PDT)
- [AMBER] output nuclear force and hessian (Mon Aug 05 2013 - 11:51:53 PDT)
Jose Borreguero
- Re: [AMBER] how to check for errors in a topology library file created with saveOff (Wed Aug 21 2013 - 10:34:39 PDT)
- Re: [AMBER] how to check for errors in a topology library file created with saveOff (Wed Aug 21 2013 - 08:03:03 PDT)
- Re: [AMBER] how to check for errors in a topology library file created with saveOff (Wed Aug 21 2013 - 07:33:07 PDT)
- [AMBER] how to check for errors in a topology library file created with saveOff (Tue Aug 20 2013 - 16:05:19 PDT)
José Guilherme Vilhena Albuquerque d'Orey
- Re: [AMBER] Energy terms in mdout (Etot, EKtot, ...) (Sat Aug 10 2013 - 06:46:40 PDT)
- [AMBER] Energy terms in mdout (Etot, EKtot, ...) (Fri Aug 09 2013 - 03:23:00 PDT)
Julio Dominguez
- [AMBER] Phosphate (-1 and -2) parameterization and Wolf2Pack (Mon Aug 26 2013 - 20:06:40 PDT)
- Re: [AMBER] AMBER Digest, Vol 587, Issue 1 (Thu Aug 22 2013 - 19:43:17 PDT)
- Re: [AMBER] AMBER Digest, Vol 587, Issue 1 (Tue Aug 20 2013 - 19:12:18 PDT)
- [AMBER] Two questions in one... (Sun Aug 18 2013 - 20:43:52 PDT)
Jun Feng
- [AMBER] CHAMBER VDW energy in PBC (Fri Aug 30 2013 - 14:55:30 PDT)
- [AMBER] CHAMBER: dihe energy in c36 vs c22 (Fri Aug 30 2013 - 14:15:49 PDT)
Karl N. Kirschner
- Re: [AMBER] Phosphate (-1 and -2) parameterization and Wolf2Pack (Fri Aug 23 2013 - 06:39:23 PDT)
- [AMBER] Phosphate (-1 and -2) parameterization and Wolf2Pack (Fri Aug 23 2013 - 06:32:23 PDT)
- Re: [AMBER] AMBER Digest, Vol 587, Issue 1 (Wed Aug 21 2013 - 00:49:49 PDT)
- Re: [AMBER] Huge improper dihedral fitting coefficient. (Wed Aug 21 2013 - 00:48:15 PDT)
- Re: [AMBER] Two questions in one... (Mon Aug 19 2013 - 00:27:40 PDT)
Kepa K. Burusco
- Re: [AMBER] TI with ifsc==2 (reposted) (Fri Aug 09 2013 - 11:45:24 PDT)
- [AMBER] TI with ifsc==2 (reposted) (Fri Aug 09 2013 - 08:01:06 PDT)
kirtana S
- Re: [AMBER] isothermal compressibility (Fri Aug 02 2013 - 15:42:19 PDT)
Krati Sharma
- [AMBER] Parameter file is not saved - AMBER! (Mon Aug 05 2013 - 08:54:03 PDT)
Kshatresh Dutta Dubey
- Re: [AMBER] Large difference in GB and PB values of binding free energy (Sun Aug 25 2013 - 23:43:31 PDT)
- [AMBER] Problem in energy decomposition (Tue Aug 13 2013 - 07:45:31 PDT)
- Re: [AMBER] Question regarding H-bond calculation (Tue Aug 13 2013 - 01:05:01 PDT)
kurisaki
- Re: [AMBER] problems with disulfide bond creation (Tue Aug 27 2013 - 18:51:00 PDT)
Kyle Sutherland-Cash
- [AMBER] GpuBuffer::Download failed for kNLBuildNeighborListOrthogonal16_kernel (Wed Aug 07 2013 - 10:12:59 PDT)
- [AMBER] NMR restraints not working with pmemd.cuda.parallel (Wed Aug 07 2013 - 10:07:17 PDT)
Lachele Foley
- Re: [AMBER] glycam_in Xleap (Mon Aug 26 2013 - 12:17:58 PDT)
- Re: [AMBER] not able to build prmtop and inpcrd with glycam (Thu Aug 22 2013 - 12:10:41 PDT)
- Re: [AMBER] not able to build prmtop and inpcrd with glycam (Thu Aug 22 2013 - 12:03:42 PDT)
- Re: [AMBER] not able to build prmtop and inpcrd with glycam (Thu Aug 22 2013 - 11:56:24 PDT)
- Re: [AMBER] Possibility of mixing OPLS and Glycam? (Tue Aug 13 2013 - 09:04:23 PDT)
lara lara
- [AMBER] glycam_in Xleap (Mon Aug 26 2013 - 10:22:40 PDT)
- Re: [AMBER] not able to build prmtop and inpcrd with glycam (Thu Aug 22 2013 - 12:07:56 PDT)
- [AMBER] not able to build prmtop and inpcrd with glycam (Thu Aug 22 2013 - 11:58:09 PDT)
- [AMBER] not able to build prmtop and inpcrd with glycam (Thu Aug 22 2013 - 11:29:23 PDT)
madhu malar
- [AMBER] PLP- L Histidinal Phosphate parameters (Tue Aug 20 2013 - 23:50:30 PDT)
- [AMBER] PLP-L Histidinal Phosphate parameters (Tue Aug 20 2013 - 02:20:35 PDT)
Mahmoud Soliman
- [AMBER] setting up a covalently bonded ligand to enzyme with tleap (Wed Aug 28 2013 - 00:46:30 PDT)
Majid Taghdir
- [AMBER] problem with ambertools test (Sat Aug 17 2013 - 05:22:01 PDT)
Mallipeddi, Premalatha
- [AMBER] Thank you - Re: Magnesium charges using leaprc.ff99SB - metals move away (Wed Aug 14 2013 - 15:41:45 PDT)
- Re: [AMBER] Magnesium charges using leaprc.ff99SB - metals move away (Wed Aug 14 2013 - 08:38:18 PDT)
- Re: [AMBER] Magnesium charges using leaprc.ff99SB - metals move away (Mon Aug 12 2013 - 08:40:41 PDT)
- Re: [AMBER] Magnesium charges using leaprc.ff99SB - metals move away (Fri Aug 09 2013 - 08:40:52 PDT)
- [AMBER] Magnesium charges using leaprc.ff99SB - metals move away (Thu Aug 08 2013 - 14:06:42 PDT)
marawan hussain
- [AMBER] Simulating two hosts together (Thu Aug 29 2013 - 03:30:35 PDT)
Marek Maly
- Re: [AMBER] GTX-Titan / GTX780 Fix (Wed Aug 14 2013 - 15:23:17 PDT)
Mary Varughese
- [AMBER] total charge of the ligand (Fri Aug 23 2013 - 23:20:53 PDT)
- Re: [AMBER] MMPBSA doubt (Fri Aug 16 2013 - 20:34:24 PDT)
- Re: [AMBER] MMPBSA doubt (Thu Aug 15 2013 - 21:09:43 PDT)
- [AMBER] MMPBSA doubt (Wed Aug 14 2013 - 03:20:47 PDT)
Massimiliano Porrini
- Re: [AMBER] mask command issue (Wed Aug 07 2013 - 13:18:08 PDT)
- Re: [AMBER] mask command issue (Wed Aug 07 2013 - 09:30:11 PDT)
- [AMBER] mask command issue (Wed Aug 07 2013 - 07:05:49 PDT)
me, Nancy
- [AMBER] dftb3 (Wed Aug 07 2013 - 15:26:50 PDT)
Meij, Henk
- [AMBER] CUDA_VISIBLE_DEVICES and real instance IDs (Thu Aug 15 2013 - 11:47:39 PDT)
mish
- Re: [AMBER] Pucker Command In Cpptraj (Mon Aug 26 2013 - 13:14:15 PDT)
Moacyr Comar
- Re: [AMBER] ERROR: max pairlist cutoff must be less than unit cell max sphere radius (Tue Aug 20 2013 - 10:35:23 PDT)
- Re: [AMBER] Problem with Amber tutorial A.15 (Wed Aug 14 2013 - 11:08:36 PDT)
- Re: [AMBER] Problem with Amber tutorial A.15 (Wed Aug 14 2013 - 08:59:31 PDT)
- [AMBER] Problem with Amber tutorial A.15 (Mon Aug 12 2013 - 06:32:46 PDT)
MOHD HOMAIDUR RAHMAN
- Re: [AMBER] problem with making a movie (Thu Aug 29 2013 - 00:18:14 PDT)
moitrayee.mbu.iisc.ernet.in
- Re: [AMBER] RMSD calculation followed by superimposition (Thu Aug 22 2013 - 19:25:52 PDT)
- Re: [AMBER] RMSD calculation followed by superimposition (Wed Aug 21 2013 - 23:42:35 PDT)
- Re: [AMBER] RMSD calculation followed by superimposition (Wed Aug 21 2013 - 23:42:09 PDT)
- Re: [AMBER] RMSD calculation followed by superimposition (Wed Aug 21 2013 - 22:01:43 PDT)
- Re: [AMBER] RMSD calculation followed by superimposition (Wed Aug 21 2013 - 21:53:15 PDT)
- Re: [AMBER] RMSD calculation followed by superimposition (Wed Aug 21 2013 - 18:25:19 PDT)
- [AMBER] Cterm and Nterm caps (Wed Aug 14 2013 - 23:17:12 PDT)
- [AMBER] RMSD calculation followed by superimposition (Wed Aug 14 2013 - 19:34:39 PDT)
monica.imtech.res.in
- Re: [AMBER] PLP-L Histidinal Phosphate parameters (Tue Aug 20 2013 - 20:53:41 PDT)
Morteza Chehel Amirani
- [AMBER] Resp charges (Mon Aug 05 2013 - 12:03:07 PDT)
Mu Xia
- Re: [AMBER] Different SASA values in MM/PBSA and MM/GBSA? (Tue Aug 27 2013 - 06:32:46 PDT)
- [AMBER] Different SASA values in MM/PBSA and MM/GBSA? (Mon Aug 26 2013 - 20:46:29 PDT)
Nakashima, Yoshihisa
- [AMBER] Often, Amber BMT doesn't finish properly with Malti-GPGPU. (pmemd.cuda.MPI problem) (Fri Aug 16 2013 - 01:16:24 PDT)
nguyentb.bii.a-star.edu.sg
- Re: [AMBER] error when running binding energy in amber (Thu Aug 01 2013 - 20:18:17 PDT)
- [AMBER] error when running binding energy in amber (Thu Aug 01 2013 - 19:29:40 PDT)
- Re: [AMBER] error when running binding energy in amber (Thu Aug 01 2013 - 00:11:15 PDT)
Nicole Ippolito
- [AMBER] ARG as a titratable residue for constant pH simulations (Thu Aug 29 2013 - 07:31:23 PDT)
Oliver Grant
- Re: [AMBER] BOND, ANGLE and TORSION energies discrepancy between amber and gromacs (Sat Aug 17 2013 - 05:57:04 PDT)
- Re: [AMBER] BOND, ANGLE and TORSION energies discrepancy between amber and gromacs (Sat Aug 10 2013 - 02:26:18 PDT)
onetwo
- Re: [AMBER] Error using Antechamber (Mon Aug 19 2013 - 21:06:24 PDT)
- [AMBER] Error using Antechamber (Sat Aug 17 2013 - 07:33:26 PDT)
peter.stauffert.boehringer-ingelheim.com
- [AMBER] Cannot download Amber12, bugfix.18.bz2 (Fri Aug 30 2013 - 12:15:02 PDT)
Petr Jurecka
- Re: [AMBER] Chi torsions (Fri Aug 09 2013 - 07:20:25 PDT)
Prasanna Venkatesh D
- [AMBER] Forcefield for lipopeptides (Tue Aug 13 2013 - 00:24:04 PDT)
psu4.uic.edu
- Re: [AMBER] mmP(G)BSA correlation time (Fri Aug 30 2013 - 08:30:58 PDT)
- Re: [AMBER] mmP(G)BSA correlation time (Thu Aug 29 2013 - 20:19:56 PDT)
- [AMBER] mmP(G)BSA correlation time (Tue Aug 27 2013 - 16:57:16 PDT)
- [AMBER] mdout2pymbar.pl Use of uninitialized value in array element (Thu Aug 22 2013 - 15:45:09 PDT)
- Re: [AMBER] 2nd Announcement AMBER workshop in Brazil (Oct 7-11 2013) pre-registration open (Wed Aug 21 2013 - 19:38:08 PDT)
- [AMBER] which energy terms are included in TI DV/DL and why it fluctuate so wildly? (Mon Aug 12 2013 - 21:26:23 PDT)
Puspita Halder
- [AMBER] Question regarding principal component analysis (Wed Aug 28 2013 - 23:26:00 PDT)
Raman Parkesh
- Re: [AMBER] leap question (Sun Aug 25 2013 - 02:40:10 PDT)
Ray Luo, Ph.D.
- Re: [AMBER] radii effect on PB_cavity surften_cavity offset (Thu Aug 01 2013 - 20:36:09 PDT)
Rejwan
- Re: [AMBER] AMBER minimization job (Mon Aug 19 2013 - 13:58:41 PDT)
- Re: [AMBER] AMBER minimization job (Mon Aug 19 2013 - 13:00:39 PDT)
- [AMBER] AMBER minimization job (Mon Aug 19 2013 - 12:06:17 PDT)
- [AMBER] Box info not found (Thu Aug 15 2013 - 13:17:22 PDT)
Rodrigo Salazar
- [AMBER] problem installin amber9 in ubuntu 12.04 (Sat Aug 31 2013 - 20:00:32 PDT)
- [AMBER] Simmetry problem (Wed Aug 28 2013 - 18:51:20 PDT)
Roitberg,Adrian E
- Re: [AMBER] MMPBSA selection error (Fri Aug 09 2013 - 12:02:21 PDT)
Ross Walker
- Re: [AMBER] CHAMBER VDW energy in PBC (Fri Aug 30 2013 - 15:10:18 PDT)
- Re: [AMBER] CHAMBER: dihe energy in c36 vs c22 (Fri Aug 30 2013 - 15:03:47 PDT)
- Re: [AMBER] Problematic structure after minimization on GPU (Mon Aug 26 2013 - 08:15:02 PDT)
- Re: [AMBER] Problematic structure after minimization on GPU (Mon Aug 26 2013 - 07:18:59 PDT)
- Re: [AMBER] Density saturates at 0.97 after NPT (Thu Aug 22 2013 - 11:35:38 PDT)
- Re: [AMBER] 2nd Announcement AMBER workshop in Brazil (Oct 7-11 2013) pre-registration open (Wed Aug 21 2013 - 19:46:51 PDT)
- Re: [AMBER] GTX-Titan / GTX780 Fix (Wed Aug 21 2013 - 10:33:20 PDT)
- Re: [AMBER] DMPC GAFF lipid membrane is freezing at 303 K. (Wed Aug 21 2013 - 10:42:25 PDT)
- Re: [AMBER] Cpu busy looping? (Tue Aug 20 2013 - 15:35:13 PDT)
- Re: [AMBER] Cpu busy looping? (Tue Aug 20 2013 - 13:07:45 PDT)
- Re: [AMBER] ERROR: max pairlist cutoff must be less than unit cell max sphere radius (Tue Aug 20 2013 - 11:30:51 PDT)
- Re: [AMBER] Question about different SCEE&SCNB to specified atom pairs. (Mon Aug 19 2013 - 21:19:25 PDT)
- Re: [AMBER] AMBER minimization job (Mon Aug 19 2013 - 14:05:55 PDT)
- Re: [AMBER] AMBER minimization job (Mon Aug 19 2013 - 13:18:55 PDT)
- Re: [AMBER] AMBER minimization job (Mon Aug 19 2013 - 12:32:13 PDT)
- Re: [AMBER] Query regarding membrane-peptide simulation (Mon Aug 19 2013 - 08:41:59 PDT)
- Re: [AMBER] Tutorial for specified SCEE and SCNB for different atom pairs? (Fri Aug 16 2013 - 21:25:15 PDT)
- Re: [AMBER] Tutorial for specified SCEE and SCNB for different atom pairs? (Fri Aug 16 2013 - 21:12:39 PDT)
- Re: [AMBER] PARALLEL PERFORMANCE OF AMBER12 (Fri Aug 16 2013 - 09:52:53 PDT)
- Re: [AMBER] PARALLEL PERFORMANCE OF AMBER12 (Thu Aug 15 2013 - 22:33:05 PDT)
- Re: [AMBER] CUDA_VISIBLE_DEVICES and real instance IDs (Thu Aug 15 2013 - 13:50:48 PDT)
- Re: [AMBER] 2nd Announcement AMBER workshop in Brazil (Oct 7-11 2013) pre-registration open (Sun Aug 11 2013 - 23:01:01 PDT)
- Re: [AMBER] Difference between lower case and upper case in atomtype? (Sun Aug 11 2013 - 21:33:27 PDT)
- [AMBER] 2nd Announcement AMBER workshop in Brazil (Oct 7-11 2013) pre-registration open (Sun Aug 11 2013 - 15:35:49 PDT)
- Re: [AMBER] BOND, ANGLE and TORSION energies discrepancy between amber and gromacs (Fri Aug 09 2013 - 15:42:41 PDT)
- Re: [AMBER] BOND, ANGLE and TORSION energies discrepancy between amber and gromacs (Fri Aug 09 2013 - 14:54:37 PDT)
- Re: [AMBER] BOND, ANGLE and TORSION energies discrepancy between amber and gromacs (Thu Aug 08 2013 - 12:48:19 PDT)
- Re: [AMBER] Abnormal md output (Thu Aug 08 2013 - 12:02:59 PDT)
- Re: [AMBER] GTX-Titan / GTX780 Fix (Wed Aug 07 2013 - 18:21:47 PDT)
- Re: [AMBER] pmemd.cuda.MPI problem (Wed Aug 07 2013 - 13:02:50 PDT)
- Re: [AMBER] GTX-Titan / GTX780 Fix (Wed Aug 07 2013 - 10:52:51 PDT)
- Re: [AMBER] NMR restraints not working with pmemd.cuda.parallel (Wed Aug 07 2013 - 10:38:31 PDT)
- Re: [AMBER] reax forcefield (Wed Aug 07 2013 - 10:35:28 PDT)
- [AMBER] GTX-Titan / GTX780 Fix (Tue Aug 06 2013 - 10:41:04 PDT)
- [AMBER-Developers] GTX-Titan / GTX780 Fix (Mon Aug 05 2013 - 17:01:26 PDT)
- Re: [AMBER] Amber12 with CUDA5.0 test results (Mon Aug 05 2013 - 12:35:02 PDT)
Sangeetha B
- [AMBER] PMEMD Performance issue on AMD cluster (Tue Aug 20 2013 - 22:29:58 PDT)
sangita.imtech.res.in
- Re: [AMBER] nmr upper_bond criteria (Thu Aug 22 2013 - 04:57:35 PDT)
- [AMBER] nmr upper_bond criteria (Tue Aug 20 2013 - 22:27:53 PDT)
Sanjib Paul
- [AMBER] ERROR in rms: KRMS_ reported Number of atoms less than 2 (Fri Aug 09 2013 - 04:39:58 PDT)
Scott Le Grand
- Re: [AMBER] Problematic structure after minimization on GPU (Mon Aug 26 2013 - 10:05:01 PDT)
- Re: [AMBER] GpuBuffer::Download failed for kNLBuildNeighborListOrthogonal16_kernel (Fri Aug 09 2013 - 09:46:24 PDT)
- Re: [AMBER] GpuBuffer::Download failed for kNLBuildNeighborListOrthogonal16_kernel (Thu Aug 08 2013 - 20:10:14 PDT)
- Re: [AMBER] GpuBuffer::Download failed for kNLBuildNeighborListOrthogonal16_kernel (Thu Aug 08 2013 - 17:31:21 PDT)
- Re: [AMBER] BOND, ANGLE and TORSION energies discrepancy between amber and gromacs (Thu Aug 08 2013 - 16:36:27 PDT)
- Re: [AMBER] GTX-Titan / GTX780 Fix (Wed Aug 07 2013 - 10:46:57 PDT)
- Re: [AMBER] GpuBuffer::Download failed for kNLBuildNeighborListOrthogonal16_kernel (Wed Aug 07 2013 - 10:28:58 PDT)
Seongeun Yang
- [AMBER] frcmod.ionsjc_*** file and water model (Thu Aug 29 2013 - 04:52:08 PDT)
Soonmin Jang
- Re: [AMBER] sander option "-radii" (Tue Aug 06 2013 - 05:48:49 PDT)
- Re: [AMBER] Amber12 with CUDA5.0 test results (Tue Aug 06 2013 - 05:44:37 PDT)
- [AMBER] Amber12 with CUDA5.0 test results (Mon Aug 05 2013 - 12:06:24 PDT)
Sorensen, Jesper
- Re: [AMBER] Magnesium charges using leaprc.ff99SB - metals move away (Mon Aug 12 2013 - 14:50:28 PDT)
Sourav Purohit
- Re: [AMBER] Density saturates at 0.97 after NPT (Thu Aug 22 2013 - 11:50:50 PDT)
- [AMBER] Density saturates at 0.97 after NPT (Thu Aug 22 2013 - 10:59:58 PDT)
Souvik Sur
- Re: [AMBER] Segmentation Fault (Tue Aug 06 2013 - 05:59:28 PDT)
- [AMBER] Segmentation Fault (Mon Aug 05 2013 - 22:41:08 PDT)
steinbrt.rci.rutgers.edu
- Re: [AMBER] which energy terms are included in TI DV/DL and why it fluctuate so wildly? (Tue Aug 13 2013 - 01:35:50 PDT)
- Re: [AMBER] TI with ifsc==2 (reposted) (Fri Aug 09 2013 - 08:46:44 PDT)
Steven M. Graham
- Re: [AMBER] Chi torsions (Fri Aug 09 2013 - 12:49:02 PDT)
- [AMBER] Chi torsions (Thu Aug 08 2013 - 13:57:43 PDT)
- Re: [AMBER] Questions about improper dihedral scan? (Tue Aug 06 2013 - 18:27:53 PDT)
Subbarao Kanchi
- [AMBER] DMPC GAFF lipid membrane is freezing at 303 K. (Wed Aug 21 2013 - 06:55:27 PDT)
Sunny Chun
- [AMBER] Input files for Targeted MD using Amber (Tue Aug 20 2013 - 14:39:09 PDT)
sunyeping
- [AMBER] 答复: problems with disulfide bond creation (Wed Aug 28 2013 - 17:09:07 PDT)
- [AMBER] problems with disulfide bond creation (Tue Aug 27 2013 - 18:42:43 PDT)
- [AMBER] mpi4py building error during AmberTools 13 install (Tue Aug 27 2013 - 02:56:58 PDT)
Suri Moonsamy
- Re: [AMBER] setting up non-standard amino acid residues for MD simulation (Mon Aug 05 2013 - 02:22:43 PDT)
Thomas Evangelidis
- [AMBER] SLipids force field with AMBER12 (Wed Aug 21 2013 - 06:41:24 PDT)
- Re: [AMBER] Error: Bad topology file. Sum of ATOMS_PER_MOLECULE does not equal NATOM. (Mon Aug 19 2013 - 05:35:36 PDT)
- [AMBER] Error: Bad topology file. Sum of ATOMS_PER_MOLECULE does not equal NATOM. (Sun Aug 18 2013 - 16:17:50 PDT)
Uday Midya
- Re: [AMBER] PARALLEL PERFORMANCE OF AMBER12 (Fri Aug 16 2013 - 05:40:25 PDT)
- [AMBER] PARALLEL PERFORMANCE OF AMBER12 (Thu Aug 15 2013 - 21:53:16 PDT)
VanDyne_Aaron
- Re: [AMBER] Trajectory post-processing (Sat Aug 10 2013 - 17:52:44 PDT)
- Re: [AMBER] Trajectory post-processing (Thu Aug 08 2013 - 09:48:09 PDT)
- Re: [AMBER] Trajectory post-processing (Thu Aug 08 2013 - 07:39:01 PDT)
- Re: [AMBER] Trajectory post-processing (Tue Aug 06 2013 - 14:59:21 PDT)
- Re: [AMBER] Trajectory post-processing (Tue Aug 06 2013 - 14:57:27 PDT)
- [AMBER] Trajectory post-processing (Tue Aug 06 2013 - 13:50:55 PDT)
Victor Ma
- Re: [AMBER] pmemd.cuda.MPI problem (Wed Aug 07 2013 - 12:51:45 PDT)
- Re: [AMBER] pmemd.cuda.MPI problem (Wed Aug 07 2013 - 12:37:50 PDT)
- [AMBER] pmemd.cuda.MPI problem (Wed Aug 07 2013 - 09:59:24 PDT)
Vijay Manickam Achari
- Re: [AMBER] Diffusion constant's unit (Wed Aug 07 2013 - 00:47:15 PDT)
- [AMBER] Diffusion constant's unit (Tue Aug 06 2013 - 20:33:24 PDT)
- [AMBER] setbox command (Sun Aug 04 2013 - 21:10:53 PDT)
- [AMBER] change coordinate (Sun Aug 04 2013 - 20:28:22 PDT)
Wang Chern Hoe (Dr)
- [AMBER] leap question (Sun Aug 25 2013 - 00:56:49 PDT)
- Re: [AMBER] 10 ns explicit water NPT (Fri Aug 02 2013 - 16:24:31 PDT)
- Re: [AMBER] 10 ns explicit water NPT (Fri Aug 02 2013 - 08:32:47 PDT)
- Re: [AMBER] 10 ns explicit water NPT (Fri Aug 02 2013 - 07:54:22 PDT)
- [AMBER] 10 ns explicit water NPT (Fri Aug 02 2013 - 02:22:23 PDT)
William Cantara
- [AMBER] Add potential energy term (Tue Aug 13 2013 - 09:24:45 PDT)
wmsmith.uci.edu
- Re: [AMBER] mmpbsa nonpolar contribution using stability (Tue Aug 20 2013 - 09:19:47 PDT)
WuYunjian
- Re: [AMBER] ERROR: max pairlist cutoff must be less than unit cell max sphere radius (Wed Aug 21 2013 - 07:33:06 PDT)
- [AMBER] ERROR: max pairlist cutoff must be less than unit cell max sphere radius (Tue Aug 20 2013 - 09:13:56 PDT)
X Sun
- [AMBER] HW-HW for TIP3P? (Mon Aug 26 2013 - 14:37:10 PDT)
- [AMBER] Confused about Hydrogen bond and non-bond interaction. (Fri Aug 23 2013 - 16:50:14 PDT)
- [AMBER] σ in Amber and OPLS-AA? (Thu Aug 22 2013 - 16:53:27 PDT)
- [AMBER] Geometricmean sigma in AMBER? (Tue Aug 20 2013 - 12:51:02 PDT)
- [AMBER] Huge improper dihedral fitting coefficient. (Tue Aug 20 2013 - 12:47:29 PDT)
Xioling Chuang
- Re: [AMBER] AmberTools13 test: possible FAILURE (Mon Aug 26 2013 - 21:15:27 PDT)
- [AMBER] AmberTools13 test: possible FAILURE (Mon Aug 26 2013 - 19:29:59 PDT)
- Re: [AMBER] MMPBSA: AttributeError: 'list' object has no attribute 'stdev' (Mon Aug 26 2013 - 00:37:49 PDT)
- [AMBER] MMPBSA: AttributeError: 'list' object has no attribute 'stdev' (Sun Aug 25 2013 - 19:23:51 PDT)
Yeng-Tseng Wang
- Re: [AMBER] reax forcefield (Wed Aug 07 2013 - 09:45:23 PDT)
ymei
- Re: [AMBER] no CMAP information written out by chamber (Fri Aug 16 2013 - 16:31:27 PDT)
- [AMBER] no CMAP information written out by chamber (Fri Aug 16 2013 - 10:47:53 PDT)
- Re: [AMBER] Resp charges (Mon Aug 05 2013 - 12:11:38 PDT)
Карлов Дмитрий
- [AMBER] problems with calculation continuing (Mon Aug 19 2013 - 09:11:52 PDT)

Amber Archive Aug 2013 by author