Amber Archive Feb 2013 by author
619 messages
:
Starting
Thu Jan 31 2013 - 16:30:03 PST,
Ending
Thu Feb 28 2013 - 19:00:03 PST
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Adam Mepham
[AMBER] pka calculation energy by residue
(Sat Feb 16 2013 - 15:46:28 PST)
[AMBER] idecomp output frequency
(Wed Feb 13 2013 - 17:56:20 PST)
[AMBER] Issues with idecomp
(Mon Feb 11 2013 - 14:17:30 PST)
[AMBER] Issues with idecomp
(Sat Feb 09 2013 - 20:55:19 PST)
Adrian Roitberg
Re: [AMBER] remd exchange acceptance
(Thu Feb 28 2013 - 04:37:40 PST)
Ahmed Ayoub
[AMBER] Calculating Hydrogen bond energy
(Fri Feb 22 2013 - 23:55:01 PST)
Alessandro Contini
Re: [AMBER] problem in running MMPBSA
(Sun Feb 24 2013 - 00:29:28 PST)
Re: [AMBER] problem in running MMPBSA
(Wed Feb 20 2013 - 00:50:17 PST)
Amparo Garcia Lopez
Re: [AMBER] Error analysing an RNA trajectory with anal
(Thu Feb 28 2013 - 07:55:42 PST)
Re: [AMBER] Error analysing an RNA trajectory with anal
(Thu Feb 28 2013 - 02:42:04 PST)
[AMBER] Error analysing an RNA trajectory with anal
(Wed Feb 27 2013 - 10:44:50 PST)
aneesh cna
Re: [AMBER] Error with MMPBSA calculation
(Mon Feb 18 2013 - 21:11:16 PST)
[AMBER] Error with MMPBSA calculation
(Mon Feb 18 2013 - 01:21:56 PST)
[AMBER] A doubt about averaging time in dynamic cross-correlation analysis
(Sat Feb 02 2013 - 02:17:42 PST)
Re: [AMBER] Fwd: Regarding the problem with ligand conformation
(Fri Feb 01 2013 - 01:05:58 PST)
Anne Kichler
[AMBER] pseudoatom
(Mon Feb 25 2013 - 03:32:41 PST)
[AMBER] simulation MD - basic questions
(Thu Feb 07 2013 - 02:54:17 PST)
Anselm Horn
[AMBER] Details about FF12SB
(Fri Feb 08 2013 - 10:54:21 PST)
Re: [AMBER] NaN error in restart file
(Fri Feb 08 2013 - 04:05:24 PST)
Aparna P
Re: [AMBER] regarding frcmod preparation
(Fri Feb 22 2013 - 06:16:13 PST)
[AMBER] regarding frcmod preparation
(Fri Feb 22 2013 - 03:07:46 PST)
Aron Broom
Re: [AMBER] GTX 680 vs GTX Titan
(Thu Feb 28 2013 - 08:24:00 PST)
Re: [AMBER] MMGBSA/MMPBSA Decomposition Analysis
(Wed Feb 27 2013 - 16:44:51 PST)
Re: [AMBER] Problem related to the bfactor calculation
(Mon Feb 25 2013 - 23:08:29 PST)
Re: [AMBER] Question regarding wham and umbrella sampling
(Mon Feb 25 2013 - 14:52:37 PST)
Re: [AMBER] Question regarding wham and umbrella sampling
(Mon Feb 25 2013 - 13:06:59 PST)
Re: [AMBER] GTX Titan was finally released
(Sat Feb 23 2013 - 12:12:49 PST)
Re: [AMBER] GTX Titan was finally released
(Fri Feb 22 2013 - 20:03:16 PST)
Re: [AMBER] GTX Titan was finally released
(Tue Feb 19 2013 - 15:01:20 PST)
Re: [AMBER] MM PBSA and entropy decomposition
(Sun Feb 17 2013 - 04:09:47 PST)
Re: [AMBER] MM PBSA and entropy decomposition
(Sat Feb 16 2013 - 13:05:12 PST)
[AMBER] MM PBSA and entropy decomposition
(Sat Feb 16 2013 - 10:06:30 PST)
Re: [AMBER] A general question about umbrella sampling
(Tue Feb 12 2013 - 13:16:01 PST)
Asmita Gupta
[AMBER] randomizeions with cpptraj
(Wed Feb 20 2013 - 02:56:43 PST)
Re: [AMBER] density calculation in radial cpptraj
(Wed Feb 06 2013 - 00:21:23 PST)
Re: [AMBER] density calculation in radial cpptraj
(Tue Feb 05 2013 - 09:01:53 PST)
Re: [AMBER] density calculation in radial cpptraj
(Mon Feb 04 2013 - 08:17:20 PST)
[AMBER] density calculation in radial cpptraj
(Mon Feb 04 2013 - 02:08:24 PST)
Ayesha Fatima
Re: [AMBER] problems starting amber
(Wed Feb 13 2013 - 19:51:31 PST)
[AMBER] problems starting amber
(Wed Feb 13 2013 - 19:00:02 PST)
BALA SUBRAMANI G L
[AMBER] phosporylated residue connectivity problem
(Tue Feb 05 2013 - 01:15:14 PST)
Barbault Florent
[AMBER] simulation of a nucleic acid linked on a gold surface
(Wed Feb 13 2013 - 11:54:18 PST)
Beale, John
[AMBER] aMD
(Thu Feb 28 2013 - 05:27:17 PST)
BERGY
Re: [AMBER] problem reading CHARMM lipid parameters into chamber
(Wed Feb 20 2013 - 20:49:22 PST)
[AMBER] Fwd:
(Tue Feb 05 2013 - 07:07:04 PST)
Re: [AMBER] (no subject)
(Tue Feb 05 2013 - 07:05:31 PST)
Bill Ross
Re: [AMBER] possibility to increase max . num. of bonded atoms ?
(Wed Feb 27 2013 - 11:18:19 PST)
Re: [AMBER] adding rings using sequence command
(Tue Feb 26 2013 - 23:00:26 PST)
Re: [AMBER] possibility to increase max . num. of bonded atoms ?
(Mon Feb 25 2013 - 17:44:46 PST)
Re: [AMBER] amber error about protein containing heme
(Sat Feb 23 2013 - 12:04:49 PST)
Re: [AMBER] Amber 11 Installment problem
(Sat Feb 23 2013 - 11:54:15 PST)
Re: [AMBER] Amber 11 Installment problem
(Wed Feb 20 2013 - 19:36:17 PST)
Brian Radak
Re: [AMBER] Question regarding wham and umbrella sampling
(Mon Feb 25 2013 - 13:07:00 PST)
Re: [AMBER] qmshake=1 did not prevent bonds from being broken
(Wed Feb 20 2013 - 11:08:07 PST)
Re: [AMBER] qmshake=1 did not prevent bonds from being broken
(Wed Feb 20 2013 - 06:08:08 PST)
Re: [AMBER] Error running large number of trajectories with multisander
(Mon Feb 11 2013 - 10:48:07 PST)
[AMBER] Error running large number of trajectories with multisander
(Mon Feb 11 2013 - 07:42:21 PST)
Re: [AMBER] Problem related to the umbrella sampling
(Fri Feb 08 2013 - 10:07:02 PST)
Re: [AMBER] Problem related with umbrella sampling
(Fri Feb 08 2013 - 06:13:54 PST)
Re: [AMBER] Problems with ti using DFTB for zinc bound hydroxyl
(Mon Feb 04 2013 - 11:51:45 PST)
Re: [AMBER] Problems with ti using DFTB for zinc bound hydroxyl
(Mon Feb 04 2013 - 10:52:26 PST)
Re: [AMBER] Problems with ti using DFTB for zinc bound hydroxyl
(Sun Feb 03 2013 - 09:19:00 PST)
Re: [AMBER] Problems with ti using DFTB for zinc bound hydroxyl
(Sat Feb 02 2013 - 13:03:35 PST)
[AMBER] Error initiating H-REMD
(Fri Feb 01 2013 - 15:52:32 PST)
Carlos Simmerling
Re: [AMBER] Query about checking of convergence in REMD
(Wed Feb 06 2013 - 04:32:35 PST)
Re: [AMBER] igb=7 & 8 CalcError: "pathway" failed with prmtop "protein".prmtop
(Sat Feb 02 2013 - 19:08:22 PST)
case
Re: [AMBER] PROBLEMS IN SETTING UP PHOSPHORYLATED SIMULATION MODELS
(Tue Feb 19 2013 - 16:51:24 PST)
Re: [AMBER] What algorithm does ptraj use for solvation of eigen-value problem.
(Sat Feb 16 2013 - 07:03:54 PST)
Re: [AMBER] Wrong Annotation of PREPIN generated by RESIDUEGEN
(Sun Feb 10 2013 - 09:43:54 PST)
Re: [AMBER] Steered Molecular Dynamics
(Sun Feb 10 2013 - 09:41:12 PST)
Cassandra Churchill
Re: [AMBER] ptraj RMSD- spikes in RMSD and co-ordinates at 0.000
(Thu Feb 07 2013 - 09:46:09 PST)
[AMBER] ptraj RMSD- spikes in RMSD and co-ordinates at 0.000
(Wed Feb 06 2013 - 09:58:18 PST)
CHAMI F.
Re: [AMBER] bond angle fitting
(Wed Feb 27 2013 - 04:30:42 PST)
[AMBER] bond angle fitting
(Tue Feb 26 2013 - 11:17:09 PST)
Changqing Yan
Re: [AMBER] Amber 11 Installment problem
(Thu Feb 21 2013 - 19:12:45 PST)
[AMBER] Amber 11 Installment problem
(Wed Feb 20 2013 - 19:14:31 PST)
[AMBER] Problem related to different version of amber
(Tue Feb 19 2013 - 23:42:18 PST)
Charles Do
Re: [AMBER] Kepler GTX680 MD Workstation
(Tue Feb 19 2013 - 19:38:15 PST)
[AMBER] Kepler GTX680 MD Workstation
(Tue Feb 19 2013 - 19:12:31 PST)
Re: [AMBER] xleap problem using savemol2
(Tue Feb 19 2013 - 06:54:32 PST)
[AMBER] xleap problem using savemol2
(Mon Feb 18 2013 - 10:44:38 PST)
Cheng Wang
Re: [AMBER] NPT with pmemd.amoeba.MPI Density alway decreasing
(Wed Feb 27 2013 - 11:16:51 PST)
[AMBER] NPT with pmemd.amoeba.MPI Density alway decreasing
(Tue Feb 26 2013 - 15:30:56 PST)
Chinthaka Ratnaweera
Re: [AMBER] rmsd of Ethanol
(Tue Feb 05 2013 - 10:52:38 PST)
[AMBER] rmsd of Ethanol
(Tue Feb 05 2013 - 08:37:37 PST)
Chris Chris
Re: [AMBER] PMEMD amd mmpbsa.py mpi
(Sat Feb 09 2013 - 22:42:54 PST)
Re: [AMBER] PMEMD amd mmpbsa.py mpi
(Fri Feb 08 2013 - 17:09:26 PST)
[AMBER] PMEMD amd mmpbsa.py mpi
(Fri Feb 08 2013 - 16:08:44 PST)
colvin
Re: [AMBER] dihedral distribution plot
(Tue Feb 26 2013 - 17:32:02 PST)
[AMBER] dihedral distribution plot
(Sun Feb 24 2013 - 21:33:06 PST)
Daniel Roe
Re: [AMBER] Error analysing an RNA trajectory with anal
(Wed Feb 27 2013 - 12:08:59 PST)
Re: [AMBER] Problem related to the bfactor calculation
(Tue Feb 26 2013 - 13:30:22 PST)
Re: [AMBER] PBSA vs MMPBSA.py
(Mon Feb 25 2013 - 07:18:25 PST)
Re: [AMBER] ligand moving out of protein incorrect imaging of trajectory using image and center commands with amber 10
(Fri Feb 22 2013 - 14:17:14 PST)
Re: [AMBER] ligand moving out of protein incorrect imaging of trajectory using image and center commands with amber 10
(Fri Feb 22 2013 - 12:19:08 PST)
Re: [AMBER] Problem with xleap/tleap
(Wed Feb 20 2013 - 10:22:18 PST)
Re: [AMBER] Dumping of center of mass coordinates of protein domain
(Tue Feb 19 2013 - 10:25:33 PST)
Re: [AMBER] PCA analysis query
(Mon Feb 18 2013 - 08:29:03 PST)
Re: [AMBER] atomic pair correlation function through PCA
(Mon Feb 18 2013 - 08:19:49 PST)
Re: [AMBER] the position of counterion
(Sun Feb 17 2013 - 11:42:28 PST)
Re: [AMBER] What algorithm does ptraj use for solvation of eigen-value problem.
(Fri Feb 15 2013 - 23:55:10 PST)
Re: [AMBER] What algorithm does ptraj use for solvation of eigen-value problem.
(Fri Feb 15 2013 - 07:43:18 PST)
Re: [AMBER] VIBRATIONAL FREQUANCY USING NMODE
(Wed Feb 13 2013 - 13:24:18 PST)
Re: [AMBER] Cannot open the input file: XYZ.pdb in rpdb(), exit
(Wed Feb 13 2013 - 11:04:30 PST)
Re: [AMBER] Error running large number of trajectories with multisander
(Mon Feb 11 2013 - 11:35:09 PST)
Re: [AMBER] Error running large number of trajectories with multisander
(Mon Feb 11 2013 - 10:30:42 PST)
Re: [AMBER] Using cpptraj to trim a range of water residues while maintaining a periodic box
(Sun Feb 10 2013 - 18:58:03 PST)
Re: [AMBER] Issues with idecomp
(Sun Feb 10 2013 - 10:11:21 PST)
Re: [AMBER] problem using autoimage from cpptraj
(Sat Feb 09 2013 - 18:01:37 PST)
Re: [AMBER] problem using autoimage from cpptraj
(Fri Feb 08 2013 - 20:57:17 PST)
Re: [AMBER] problem with strip water some distance away from peptide
(Fri Feb 08 2013 - 15:08:59 PST)
Re: [AMBER] change starting time of simulation
(Fri Feb 08 2013 - 07:43:08 PST)
Re: [AMBER] change starting time of simulation
(Fri Feb 08 2013 - 07:40:59 PST)
Re: [AMBER] restart file with *********** problem
(Fri Feb 08 2013 - 07:36:36 PST)
Re: [AMBER] problem with strip water some distance away from peptide
(Thu Feb 07 2013 - 17:24:02 PST)
Re: [AMBER] ptraj RMSD- spikes in RMSD and co-ordinates at 0.000
(Wed Feb 06 2013 - 10:34:20 PST)
Re: [AMBER] hbond analysis acceptor atoms
(Wed Feb 06 2013 - 09:32:39 PST)
Re: [AMBER] Hbond analysis in ptraj
(Wed Feb 06 2013 - 09:30:31 PST)
Re: [AMBER] density calculation in radial cpptraj
(Wed Feb 06 2013 - 08:43:50 PST)
Re: [AMBER] rmsd of Ethanol
(Tue Feb 05 2013 - 14:03:56 PST)
Re: [AMBER] active site rmsd (residue 5A around bound ligand) ???
(Tue Feb 05 2013 - 13:58:47 PST)
Re: [AMBER] rmsd of Ethanol
(Tue Feb 05 2013 - 10:13:58 PST)
Re: [AMBER] density calculation in radial cpptraj
(Tue Feb 05 2013 - 10:08:14 PST)
Re: [AMBER] active site rmsd (residue 5A around bound ligand) ???
(Tue Feb 05 2013 - 09:20:19 PST)
Re: [AMBER] AMBER pmemd and pmemd.cuda, not restart files after minimization - fort.16 file instead
(Tue Feb 05 2013 - 08:20:50 PST)
Re: [AMBER] active site rmsd (residue 5A around bound ligand) ???
(Tue Feb 05 2013 - 07:37:15 PST)
Re: [AMBER] Hbond analysis in ptraj
(Tue Feb 05 2013 - 07:27:02 PST)
Re: [AMBER] AMBER-Tools cpptraj residue numbering incorrect
(Mon Feb 04 2013 - 12:18:14 PST)
Re: [AMBER] AMBER-Tools cpptraj residue numbering incorrect
(Mon Feb 04 2013 - 10:52:03 PST)
Re: [AMBER] igb=7 & 8 CalcError: "pathway" failed with prmtop "protein".prmtop
(Mon Feb 04 2013 - 07:46:52 PST)
Re: [AMBER] density calculation in radial cpptraj
(Mon Feb 04 2013 - 07:36:28 PST)
Re: [AMBER] AMBER pmemd and pmemd.cuda, not restart files after minimization - fort.16 file instead
(Mon Feb 04 2013 - 07:30:11 PST)
Re: [AMBER] scaling problem in RADIAL of CPPTRAJ
(Fri Feb 01 2013 - 09:41:03 PST)
Re: [AMBER] scaling problem in RADIAL of CPPTRAJ
(Fri Feb 01 2013 - 08:02:56 PST)
Re: [AMBER] Query regarding cpptraj multiple input in a single file
(Fri Feb 01 2013 - 07:29:48 PST)
Daniel Sindhikara
Re: [AMBER] remd exchange acceptance
(Thu Feb 28 2013 - 02:02:36 PST)
Re: [AMBER] problems starting amber
(Wed Feb 13 2013 - 19:22:34 PST)
Re: [AMBER] problems with NAB
(Thu Feb 07 2013 - 00:03:15 PST)
Date, Mihir
[AMBER] atomic pair correlation function through PCA
(Sun Feb 17 2013 - 20:35:26 PST)
[AMBER] protein-protein binding free energy
(Fri Feb 01 2013 - 15:14:33 PST)
David A Case
Re: [AMBER] possibility to increase max . num. of bonded atoms ?
(Wed Feb 27 2013 - 12:25:27 PST)
Re: [AMBER] force field file
(Tue Feb 26 2013 - 05:51:10 PST)
Re: [AMBER] MMPBSA problem
(Tue Feb 26 2013 - 05:48:04 PST)
Re: [AMBER] possibility to increase max . num. of bonded atoms ?
(Sun Feb 24 2013 - 07:22:22 PST)
Re: [AMBER] Calculating Hydrogen bond energy
(Sat Feb 23 2013 - 06:05:26 PST)
Re: [AMBER] crgmask and qmmm region compatibility
(Thu Feb 21 2013 - 09:39:18 PST)
Re: [AMBER] glucose
(Wed Feb 20 2013 - 08:41:37 PST)
Re: [AMBER] randomizeions with cpptraj
(Wed Feb 20 2013 - 04:44:45 PST)
Re: [AMBER] PROBLEMS IN SETTING UP PHOSPHORYLATED SIMULATION MODELS
(Wed Feb 20 2013 - 04:39:46 PST)
Re: [AMBER] GTX Titan was finally released
(Tue Feb 19 2013 - 13:39:12 PST)
Re: [AMBER] How to calculate the vibrational frequancy
(Tue Feb 19 2013 - 09:50:54 PST)
Re: [AMBER] PROBLEMS IN SETTING UP PHOSPHORYLATED SIMULATION MODELS
(Tue Feb 19 2013 - 04:45:09 PST)
Re: [AMBER] Sander error - Segmentation fault (core dumped)
(Fri Feb 15 2013 - 11:51:49 PST)
[AMBER] test
(Fri Feb 15 2013 - 08:13:33 PST)
Re: [AMBER] Cannot open the input file: XYZ.pdb in rpdb(), exit
(Thu Feb 14 2013 - 05:38:45 PST)
Re: [AMBER] Cannot open the input file: XYZ.pdb in rpdb(), exit
(Wed Feb 13 2013 - 11:44:59 PST)
Re: [AMBER] Inquiry from beginner
(Mon Feb 11 2013 - 05:16:13 PST)
Re: [AMBER] Wrong Annotation of PREPIN generated by RESIDUEGEN
(Mon Feb 11 2013 - 05:12:28 PST)
Re: [AMBER] xleap could not find the type Cl-
(Sat Feb 09 2013 - 06:49:20 PST)
Re: [AMBER] problem with 3-ring system in antechamber
(Fri Feb 08 2013 - 12:20:40 PST)
Re: [AMBER] problem with 3-ring system in antechamber
(Fri Feb 08 2013 - 10:53:32 PST)
Re: [AMBER] problem with 3-ring system in antechamber
(Fri Feb 08 2013 - 08:41:19 PST)
Re: [AMBER] NMA(n-methylacetamide)
(Fri Feb 08 2013 - 05:21:59 PST)
Re: [AMBER] change starting time of simulation
(Fri Feb 08 2013 - 05:19:01 PST)
Re: [AMBER] missing parameter of B in .frcmod
(Fri Feb 08 2013 - 05:15:33 PST)
Re: [AMBER] AMBER pmemd and pmemd.cuda, not restart files after minimization - fort.16 file instead
(Wed Feb 06 2013 - 05:14:54 PST)
Re: [AMBER] espgen cannot deal with Gaussian 09 log file
(Wed Feb 06 2013 - 04:53:55 PST)
Re: [AMBER] setting certain atoms as static
(Wed Feb 06 2013 - 04:51:18 PST)
Re: [AMBER] topology file issue with entropy calculation
(Tue Feb 05 2013 - 04:46:28 PST)
Re: [AMBER] ERROR: the best APS is not zero, bonds involved by this atom are frozen
(Tue Feb 05 2013 - 04:44:39 PST)
Re: [AMBER] ERROR: the best APS is not zero, bonds involved by this atom are frozen
(Mon Feb 04 2013 - 08:45:30 PST)
Re: [AMBER] density calculation in radial cpptraj
(Mon Feb 04 2013 - 08:37:28 PST)
Re: [AMBER] amber11 installation test files
(Mon Feb 04 2013 - 05:32:12 PST)
Re: [AMBER] AMBER 10 install issue
(Sun Feb 03 2013 - 14:36:17 PST)
Re: [AMBER] protein-protein binding free energy
(Fri Feb 01 2013 - 18:40:43 PST)
Re: [AMBER] Problem using solvatebox for large, linear peptide
(Fri Feb 01 2013 - 18:36:20 PST)
Re: [AMBER] Problem using solvatebox for large, linear peptide
(Fri Feb 01 2013 - 13:14:27 PST)
Re: [AMBER] Can we model the solvent implicitly outside a solvent shell (irregular shape)
(Fri Feb 01 2013 - 05:03:19 PST)
Debayan Chakraborty
[AMBER] Can we model the solvent implicitly outside a solvent shell (irregular shape)
(Thu Jan 31 2013 - 19:29:49 PST)
DEBOSTUTI GHOSHDASTIDAR
Re: [AMBER] Using OPLS force field parameters in Amber MD run
(Thu Feb 21 2013 - 05:39:48 PST)
[AMBER] Using OPLS force field parameters in Amber MD run
(Wed Feb 20 2013 - 23:13:56 PST)
[AMBER] Application of mmpbsa
(Sun Feb 10 2013 - 21:46:31 PST)
Re: [AMBER] hbond analysis acceptor atoms
(Wed Feb 06 2013 - 21:51:26 PST)
[AMBER] hbond analysis acceptor atoms
(Wed Feb 06 2013 - 09:08:50 PST)
Re: [AMBER] Hbond analysis in ptraj
(Tue Feb 05 2013 - 22:00:54 PST)
[AMBER] Hbond analysis in ptraj
(Tue Feb 05 2013 - 05:07:17 PST)
Do Yong Kim
Re: [AMBER] problem with strip water some distance away from peptide
(Fri Feb 08 2013 - 15:06:39 PST)
[AMBER] problem with strip water some distance away from peptide
(Thu Feb 07 2013 - 16:03:16 PST)
Dr. M. Venkata Satish Kumar
[AMBER] restart file with *********** problem
(Fri Feb 08 2013 - 00:18:19 PST)
Dwight McGee
Re: [AMBER] mmpbsa_py_nabnmode for single macromolecule
(Wed Feb 20 2013 - 08:17:54 PST)
Elise Duboué-Dijon
Re: [AMBER] Problem to run sander with more than 60 atom types
(Thu Feb 28 2013 - 09:11:57 PST)
Re: [AMBER] Problem to run sander with more than 60 atom types
(Thu Feb 28 2013 - 08:51:03 PST)
Re: [AMBER] Problem to run sander with more than 60 atom types
(Thu Feb 28 2013 - 06:24:10 PST)
eneas.usal.es
[AMBER] PBSA vs MMPBSA.py
(Sun Feb 24 2013 - 23:57:12 PST)
esmaeel azadian
[AMBER] Error in RNA simulation
(Mon Feb 25 2013 - 04:25:14 PST)
ET
Re: [AMBER] mmgbsa minimisation failing with error in trajene()
(Mon Feb 25 2013 - 14:45:13 PST)
[AMBER] mmgbsa minimisation failing with error in trajene()
(Mon Feb 25 2013 - 04:42:14 PST)
Re: [AMBER] ligand moving out of protein incorrect imaging of trajectory using image and center commands with amber 10
(Fri Feb 22 2013 - 14:38:29 PST)
Re: [AMBER] ligand moving out of protein incorrect imaging of trajectory using image and center commands with amber 10
(Fri Feb 22 2013 - 13:45:20 PST)
[AMBER] ligand moving out of protein incorrect imaging of trajectory using image and center commands with amber 10
(Fri Feb 22 2013 - 10:10:20 PST)
Fabrício Bracht
Re: [AMBER] TI without ifsc = 1 crashes
(Tue Feb 26 2013 - 16:02:59 PST)
[AMBER] TI without ifsc = 1 crashes
(Tue Feb 26 2013 - 15:02:32 PST)
Re: [AMBER] Question regarding wham and umbrella sampling
(Mon Feb 25 2013 - 13:29:13 PST)
[AMBER] Question regarding wham and umbrella sampling
(Mon Feb 25 2013 - 12:09:23 PST)
[AMBER] crgmask and qmmm region compatibility
(Thu Feb 21 2013 - 06:44:02 PST)
Re: [AMBER] qmshake=1 did not prevent bonds from being broken
(Wed Feb 20 2013 - 13:30:03 PST)
Re: [AMBER] qmshake=1 did not prevent bonds from being broken
(Wed Feb 20 2013 - 10:56:33 PST)
[AMBER] qmshake=1 did not prevent bonds from being broken
(Tue Feb 19 2013 - 14:32:49 PST)
Re: [AMBER] Problems with ti using DFTB for zinc bound hydroxyl
(Mon Feb 04 2013 - 12:00:32 PST)
Re: [AMBER] Problems with ti using DFTB for zinc bound hydroxyl
(Mon Feb 04 2013 - 11:21:10 PST)
Re: [AMBER] Problems with ti using DFTB for zinc bound hydroxyl
(Mon Feb 04 2013 - 10:31:16 PST)
Re: [AMBER] Problems with ti using DFTB for zinc bound hydroxyl
(Sat Feb 02 2013 - 17:33:53 PST)
[AMBER] Problems with ti using DFTB for zinc bound hydroxyl
(Sat Feb 02 2013 - 11:35:04 PST)
filip fratev
Re: [AMBER] GTX 680 vs GTX Titan
(Thu Feb 28 2013 - 08:09:51 PST)
Re: [AMBER] GTX Titan was finally released
(Wed Feb 27 2013 - 11:21:17 PST)
Re: [AMBER] GTX Titan was finally released
(Mon Feb 25 2013 - 14:39:04 PST)
Re: [AMBER] GTX Titan was finally released
(Sat Feb 23 2013 - 11:33:34 PST)
Re: [AMBER] GTX Titan was finally released
(Fri Feb 22 2013 - 17:28:18 PST)
Re: [AMBER] GTX Titan was finally released
(Tue Feb 19 2013 - 11:59:39 PST)
[AMBER] GTX Titan was finally released
(Tue Feb 19 2013 - 08:40:12 PST)
Filippo Pullara
[AMBER] Amber 12 and CUDA 5.0 K20 vs GTX 680: GTX 680 is two time faster than K20
(Fri Feb 08 2013 - 13:05:21 PST)
francesco oteri
[AMBER] spectrum simulation
(Sun Feb 24 2013 - 12:56:18 PST)
FyD
Re: [AMBER] Building a new structure!
(Wed Feb 27 2013 - 01:35:01 PST)
Re: [AMBER] adding rings using sequence command
(Wed Feb 27 2013 - 01:06:21 PST)
Re: [AMBER] pseudoatom
(Mon Feb 25 2013 - 12:48:08 PST)
Re: [AMBER] Building a new structure!
(Thu Feb 21 2013 - 23:17:26 PST)
Re: [AMBER] Building a new structure!
(Sun Feb 17 2013 - 04:38:42 PST)
Re: [AMBER] Building a new structure!
(Fri Feb 15 2013 - 08:09:56 PST)
Re: [AMBER] Building a new structure!
(Fri Feb 15 2013 - 01:57:06 PST)
Re: [AMBER] simulation of a nucleic acid linked on a gold surface
(Wed Feb 13 2013 - 23:06:47 PST)
Re: [AMBER] Building a new structure!
(Wed Feb 13 2013 - 23:00:33 PST)
Re: [AMBER] NMA(n-methylacetamide)
(Tue Feb 12 2013 - 01:16:45 PST)
Re: [AMBER] NMA(n-methylacetamide)
(Sun Feb 10 2013 - 08:40:31 PST)
gabrielg.uvic.ca
[AMBER] Defining parameters for and undefined element. Solid Surface
(Mon Feb 18 2013 - 14:10:14 PST)
gargi borgohai
[AMBER] Analysis in ptraj
(Tue Feb 19 2013 - 01:38:29 PST)
[AMBER] Query about checking of convergence in REMD
(Wed Feb 06 2013 - 04:21:24 PST)
George A. Khoury
[AMBER] Small bug in MMPBSA.py tutorial
(Sat Feb 16 2013 - 09:47:03 PST)
George Tzotzos
[AMBER] iAPBS
(Tue Feb 05 2013 - 05:57:31 PST)
Giulia
[AMBER] heme parameters
(Mon Feb 25 2013 - 05:58:15 PST)
Gonzalo Jimenez
Re: [AMBER] GTX 680 vs GTX Titan
(Thu Feb 28 2013 - 00:41:21 PST)
[AMBER] GTX 680 vs GTX Titan
(Wed Feb 27 2013 - 23:22:33 PST)
Gould, Ian R
Re: [AMBER] GTX 680 vs GTX Titan
(Thu Feb 28 2013 - 05:52:06 PST)
Re: [AMBER] GTX 680 vs GTX Titan
(Thu Feb 28 2013 - 05:40:59 PST)
Re: [AMBER] GTX 680 vs GTX Titan
(Thu Feb 28 2013 - 02:49:38 PST)
Hai Nguyen
Re: [AMBER] igb=7 & 8 CalcError: "pathway" failed with prmtop "protein".prmtop
(Mon Feb 04 2013 - 14:55:29 PST)
HIMANSHU JOSHI
Re: [AMBER] espgen cannot deal with Gaussian 09 log file
(Mon Feb 04 2013 - 21:42:28 PST)
[AMBER] espgen cannot deal with Gaussian 09 log file
(Mon Feb 04 2013 - 03:51:52 PST)
Hirdesh Kumar
Re: [AMBER] Analysis in ptraj
(Tue Feb 19 2013 - 03:06:06 PST)
HM
Re: [AMBER] generate MDCRD file for two points
(Thu Feb 28 2013 - 06:29:04 PST)
[AMBER] generate MDCRD file for two points
(Thu Feb 28 2013 - 04:00:32 PST)
Re: [AMBER] Dumping of center of mass coordinates of protein domain
(Thu Feb 28 2013 - 03:54:15 PST)
[AMBER] Dumping of center of mass coordinates of protein domain
(Tue Feb 19 2013 - 04:11:18 PST)
Re: [AMBER] active site rmsd (residue 5A around bound ligand) ???
(Tue Feb 05 2013 - 11:28:16 PST)
Re: [AMBER] active site rmsd (residue 5A around bound ligand) ???
(Tue Feb 05 2013 - 11:07:30 PST)
[AMBER] active site rmsd (residue 5A around bound ligand) ???
(Tue Feb 05 2013 - 05:40:45 PST)
[AMBER] Query regarding cpptraj multiple input in a single file
(Fri Feb 01 2013 - 07:11:59 PST)
Re: [AMBER] How to save secondary structure gnuplot as image
(Fri Feb 01 2013 - 07:06:58 PST)
Holger Gohlke
Re: [AMBER] MM PBSA and entropy decomposition
(Sun Feb 17 2013 - 04:01:48 PST)
Ibrahim Moustafa
[AMBER] Problem with xleap/tleap
(Wed Feb 20 2013 - 10:14:07 PST)
Ibrahim Said
Re: [AMBER] Building a new structure!
(Tue Feb 26 2013 - 10:45:20 PST)
Re: [AMBER] Building a new structure!
(Thu Feb 21 2013 - 08:56:46 PST)
Re: [AMBER] Building a new structure!
(Sun Feb 17 2013 - 01:08:48 PST)
Re: [AMBER] Building a new structure!
(Thu Feb 14 2013 - 10:20:06 PST)
Re: [AMBER] Building a new structure!
(Wed Feb 13 2013 - 00:37:50 PST)
Ilyas Yildirim
[AMBER] Amber MD using NAMD
(Thu Feb 28 2013 - 15:32:32 PST)
Re: [AMBER] periodic image of octahedron box in VMD
(Tue Feb 26 2013 - 19:04:56 PST)
Re: [AMBER] GTX Titan was finally released
(Tue Feb 19 2013 - 10:37:41 PST)
Re: [AMBER] simulation of a nucleic acid linked on a gold surface
(Wed Feb 13 2013 - 17:17:58 PST)
Indrajit Deb
Re: [AMBER] Adding buffer and salt
(Thu Feb 07 2013 - 09:23:04 PST)
Re: [AMBER] Adding buffer and salt
(Thu Feb 07 2013 - 09:18:36 PST)
Re: [AMBER] Adding buffer and salt
(Thu Feb 07 2013 - 02:46:00 PST)
[AMBER] Adding buffer and salt
(Thu Feb 07 2013 - 00:23:55 PST)
Ismail, Mohd F.
Re: [AMBER] charged molecule with antechamber
(Wed Feb 13 2013 - 10:56:48 PST)
Re: [AMBER] Problem using solvatebox for large, linear peptide
(Fri Feb 01 2013 - 15:34:54 PST)
Re: [AMBER] error while running mmpbsa.py in amber12
(Fri Feb 01 2013 - 14:39:03 PST)
Re: [AMBER] error while running mmpbsa.py in amber12
(Fri Feb 01 2013 - 14:22:19 PST)
Jason Swails
Re: [AMBER] MMGBSA/MMPBSA Decomposition Analysis
(Thu Feb 28 2013 - 10:21:10 PST)
Re: [AMBER] Problem to run sander with more than 60 atom types
(Thu Feb 28 2013 - 09:02:01 PST)
Re: [AMBER] generate MDCRD file for two points
(Thu Feb 28 2013 - 07:17:21 PST)
Re: [AMBER] Problem to run sander with more than 60 atom types
(Thu Feb 28 2013 - 07:14:17 PST)
Re: [AMBER] generate MDCRD file for two points
(Thu Feb 28 2013 - 05:33:28 PST)
Re: [AMBER] GTX 680 vs GTX Titan
(Thu Feb 28 2013 - 05:29:30 PST)
Re: [AMBER] Error analysing an RNA trajectory with anal
(Thu Feb 28 2013 - 05:23:43 PST)
Re: [AMBER] MMGBSA/MMPBSA Decomposition Analysis
(Wed Feb 27 2013 - 18:02:36 PST)
Re: [AMBER] MMGBSA/MMPBSA Decomposition Analysis
(Wed Feb 27 2013 - 17:53:50 PST)
Re: [AMBER] NPT with pmemd.amoeba.MPI Density alway decreasing
(Wed Feb 27 2013 - 11:23:56 PST)
Re: [AMBER] possibility to increase max . num. of bonded atoms ?
(Wed Feb 27 2013 - 11:12:43 PST)
Re: [AMBER] error in nmode
(Wed Feb 27 2013 - 07:07:13 PST)
Re: [AMBER] error in nmode
(Wed Feb 27 2013 - 07:05:02 PST)
Re: [AMBER] NPT with pmemd.amoeba.MPI Density alway decreasing
(Wed Feb 27 2013 - 03:58:38 PST)
Re: [AMBER] periodic image of octahedron box in VMD
(Tue Feb 26 2013 - 18:37:06 PST)
Re: [AMBER] Install amber in Mac Lion
(Tue Feb 26 2013 - 17:51:58 PST)
Re: [AMBER] TI without ifsc = 1 crashes
(Tue Feb 26 2013 - 15:31:55 PST)
Re: [AMBER] adding rings using sequence command
(Tue Feb 26 2013 - 12:25:43 PST)
Re: [AMBER] bond angle fitting
(Tue Feb 26 2013 - 11:29:50 PST)
Re: [AMBER] error in nmode
(Tue Feb 26 2013 - 09:01:42 PST)
Re: [AMBER] adding rings using sequence command
(Tue Feb 26 2013 - 07:53:57 PST)
Re: [AMBER] question on input for MMPBSA.py
(Tue Feb 26 2013 - 07:27:35 PST)
Re: [AMBER] MMPBSA problem
(Tue Feb 26 2013 - 05:40:17 PST)
Re: [AMBER] MMPBSA free energy
(Tue Feb 26 2013 - 04:50:35 PST)
Re: [AMBER] question on input for MMPBSA.py
(Mon Feb 25 2013 - 17:20:37 PST)
Re: [AMBER] possibility to increase max . num. of bonded atoms ?
(Mon Feb 25 2013 - 17:19:17 PST)
Re: [AMBER] converting AMBER minimized file to PDB/MOL2
(Mon Feb 25 2013 - 12:27:54 PST)
Re: [AMBER] problem in running MMPBSA
(Mon Feb 25 2013 - 11:29:16 PST)
Re: [AMBER] dihedral distribution plot
(Mon Feb 25 2013 - 05:41:03 PST)
Re: [AMBER] Error in RNA simulation
(Mon Feb 25 2013 - 05:00:51 PST)
Re: [AMBER] pseudoatom
(Mon Feb 25 2013 - 04:55:57 PST)
Re: [AMBER] PBSA vs MMPBSA.py
(Mon Feb 25 2013 - 04:44:14 PST)
Re: [AMBER] Fwd: Installing Amber in parallel whit Lion
(Mon Feb 25 2013 - 03:01:25 PST)
Re: [AMBER] problem in running MMPBSA
(Sun Feb 24 2013 - 06:43:13 PST)
Re: [AMBER] Linear peptide using non standard amino acids
(Thu Feb 21 2013 - 14:01:38 PST)
Re: [AMBER] leap insert missing atoms in aminoacids according to ...
(Thu Feb 21 2013 - 08:55:50 PST)
Re: [AMBER] constant pH for transmemrane proteins
(Thu Feb 21 2013 - 07:31:43 PST)
Re: [AMBER] Using OPLS force field parameters in Amber MD run
(Thu Feb 21 2013 - 05:22:24 PST)
Re: [AMBER] problem reading CHARMM lipid parameters into chamber
(Thu Feb 21 2013 - 04:25:47 PST)
Re: [AMBER] About EPTOT
(Wed Feb 20 2013 - 16:47:08 PST)
Re: [AMBER] Problem with xleap/tleap
(Wed Feb 20 2013 - 10:20:02 PST)
Re: [AMBER] problem in nmode
(Wed Feb 20 2013 - 06:50:25 PST)
Re: [AMBER] problem reading CHARMM lipid parameters into chamber
(Wed Feb 20 2013 - 05:06:43 PST)
Re: [AMBER] PROBLEMS IN SETTING UP PHOSPHORYLATED SIMULATION MODELS
(Wed Feb 20 2013 - 04:31:03 PST)
Re: [AMBER] Missing comma in input file
(Tue Feb 19 2013 - 08:29:01 PST)
Re: [AMBER] xleap problem using savemol2
(Tue Feb 19 2013 - 07:07:41 PST)
Re: [AMBER] Dumping of center of mass coordinates of protein domain
(Tue Feb 19 2013 - 07:06:22 PST)
Re: [AMBER] problem in running MMPBSA
(Tue Feb 19 2013 - 06:43:34 PST)
Re: [AMBER] problem in running MMPBSA
(Tue Feb 19 2013 - 06:00:37 PST)
Re: [AMBER] Error with MMPBSA calculation
(Tue Feb 19 2013 - 04:50:47 PST)
Re: [AMBER] xleap problem using savemol2
(Mon Feb 18 2013 - 10:51:50 PST)
Re: [AMBER] Fwd: PSF file, atom radii and chamber
(Mon Feb 18 2013 - 05:25:16 PST)
Re: [AMBER] Error with MMPBSA calculation
(Mon Feb 18 2013 - 04:31:49 PST)
Re: [AMBER] Small bug in MMPBSA.py tutorial
(Sun Feb 17 2013 - 06:58:18 PST)
Re: [AMBER] Small bug in MMPBSA.py tutorial
(Sat Feb 16 2013 - 12:24:51 PST)
Re: [AMBER] MM PBSA and entropy decomposition
(Sat Feb 16 2013 - 12:24:14 PST)
Re: [AMBER] problems with NAB
(Sat Feb 16 2013 - 05:47:30 PST)
Re: [AMBER] idecomp output frequency
(Wed Feb 13 2013 - 18:30:16 PST)
Re: [AMBER] Compilation problems for parallel build after applying patches
(Tue Feb 12 2013 - 09:20:14 PST)
Re: [AMBER] Compilation problems for parallel build after applying patches
(Tue Feb 12 2013 - 08:29:11 PST)
Re: [AMBER] Compilation problems for parallel build after applying patches
(Tue Feb 12 2013 - 07:43:09 PST)
Re: [AMBER] igb=7 & 8 CalcError: "pathway" failed with prmtop "protein".prmtop
(Tue Feb 12 2013 - 05:01:51 PST)
Re: [AMBER] Issues with idecomp
(Mon Feb 11 2013 - 14:32:46 PST)
Re: [AMBER] Problems with MMPBSA.py for running pbsa calculations
(Mon Feb 11 2013 - 14:06:56 PST)
Re: [AMBER] Problems with MMPBSA.py for running pbsa calculations
(Mon Feb 11 2013 - 03:18:20 PST)
Re: [AMBER] Warnings when saving prmtop and inpcrd files.
(Mon Feb 11 2013 - 03:06:05 PST)
Re: [AMBER] NMA(n-methylacetamide)
(Mon Feb 11 2013 - 03:01:19 PST)
Re: [AMBER] Using cpptraj to trim a range of water residues while maintaining a periodic box
(Sun Feb 10 2013 - 18:32:30 PST)
Re: [AMBER] problem using autoimage from cpptraj
(Sun Feb 10 2013 - 14:33:56 PST)
Re: [AMBER] Problem in running TREMD in AMBER10
(Sat Feb 09 2013 - 09:27:16 PST)
Re: [AMBER] Problem in running TREMD in AMBER10
(Sat Feb 09 2013 - 08:45:53 PST)
Re: [AMBER] PMEMD amd mmpbsa.py mpi
(Fri Feb 08 2013 - 16:41:43 PST)
Re: [AMBER] Problem in running TREMD in AMBER10
(Fri Feb 08 2013 - 12:53:49 PST)
Re: [AMBER] igb=7 & 8 CalcError: "pathway" failed with prmtop "protein".prmtop
(Thu Feb 07 2013 - 19:24:55 PST)
Re: [AMBER] parmed.py error IndexError: list index out of range
(Thu Feb 07 2013 - 12:40:51 PST)
Re: [AMBER] parmed.py error IndexError: list index out of range
(Thu Feb 07 2013 - 08:13:30 PST)
Re: [AMBER] Adding buffer and salt
(Thu Feb 07 2013 - 06:30:47 PST)
Re: [AMBER] topology file issue with entropy calculation
(Wed Feb 06 2013 - 18:24:23 PST)
Re: [AMBER] AMBER-Tools cpptraj residue numbering incorrect
(Tue Feb 05 2013 - 17:43:57 PST)
Re: [AMBER] about iwrap=1 and ntxo=2
(Tue Feb 05 2013 - 12:27:48 PST)
Re: [AMBER] 3D-RISM input file error
(Tue Feb 05 2013 - 11:16:01 PST)
Re: [AMBER] Could you please remove me from AMBER mailing list
(Tue Feb 05 2013 - 09:43:44 PST)
Re: [AMBER] Fwd:
(Tue Feb 05 2013 - 07:23:08 PST)
Re: [AMBER] (no subject)
(Tue Feb 05 2013 - 07:16:45 PST)
Re: [AMBER] igb=7 & 8 CalcError: "pathway" failed with prmtop "protein".prmtop
(Mon Feb 04 2013 - 14:16:26 PST)
Re: [AMBER] Setting up a Periodic Box Size
(Sat Feb 02 2013 - 12:36:04 PST)
Re: [AMBER] Problem using solvatebox for large, linear peptide
(Fri Feb 01 2013 - 19:22:54 PST)
Re: [AMBER] Fwd: Sampling of a point by a molecule while keeping the relative position of the molecule unchanged in TMD
(Fri Feb 01 2013 - 19:11:20 PST)
Re: [AMBER] error while running mmpbsa.py in amber12
(Fri Feb 01 2013 - 14:28:25 PST)
Re: [AMBER] average structure
(Fri Feb 01 2013 - 05:15:28 PST)
Re: [AMBER] Problem using solvatebox for large, linear peptide
(Fri Feb 01 2013 - 05:00:01 PST)
javier alejandro rendon carrillo
[AMBER] Install amber in Mac Lion
(Tue Feb 26 2013 - 16:57:16 PST)
[AMBER] Fwd: Installing Amber in parallel whit Lion
(Sun Feb 24 2013 - 22:17:12 PST)
Jerome.GOLEBIOWSKI.unice.fr
Re: [AMBER] issues with PDB file and tleap
(Thu Feb 07 2013 - 05:00:40 PST)
Jian Yin
Re: [AMBER] Amber 11 Installment problem
(Thu Feb 21 2013 - 18:34:48 PST)
Re: [AMBER] Amber 11 Installment problem
(Thu Feb 21 2013 - 17:44:34 PST)
Re: [AMBER] Problem related to different version of amber
(Wed Feb 20 2013 - 11:39:33 PST)
Re: [AMBER] simulation MD - basic questions
(Fri Feb 08 2013 - 13:29:11 PST)
Jio M
Re: [AMBER] adding rings using sequence command
(Wed Feb 27 2013 - 01:52:49 PST)
Re: [AMBER] adding rings using sequence command
(Tue Feb 26 2013 - 12:58:53 PST)
Re: [AMBER] adding rings using sequence command
(Tue Feb 26 2013 - 12:37:29 PST)
Re: [AMBER] adding rings using sequence command
(Tue Feb 26 2013 - 12:19:49 PST)
Re: [AMBER] adding rings using sequence command
(Tue Feb 26 2013 - 11:49:59 PST)
[AMBER] adding rings using sequence command
(Tue Feb 26 2013 - 06:55:50 PST)
[AMBER] parmed.py error IndexError: list index out of range
(Thu Feb 07 2013 - 07:52:49 PST)
Jiri Sponer
Re: [AMBER] use of parmbsc0 for protein-DNA complex along with ff99SB
(Mon Feb 04 2013 - 07:37:12 PST)
Re: [AMBER] use of parmbsc0 for protein-DNA complex along with ff99SB
(Mon Feb 04 2013 - 05:01:24 PST)
Joe Passman
Re: [AMBER] Using cpptraj to trim a range of water residues while maintaining a periodic box
(Mon Feb 11 2013 - 20:51:44 PST)
[AMBER] Using cpptraj to trim a range of water residues while maintaining a periodic box
(Sun Feb 10 2013 - 17:15:21 PST)
Re: [AMBER] Problem using solvatebox for large, linear peptide
(Tue Feb 05 2013 - 12:47:00 PST)
Re: [AMBER] Problem using solvatebox for large, linear peptide
(Fri Feb 01 2013 - 15:32:49 PST)
[AMBER] Problem using solvatebox for large, linear peptide
(Thu Jan 31 2013 - 18:16:09 PST)
Joel Tyndall
Re: [AMBER] AMBER 10 install issue
(Mon Feb 04 2013 - 12:28:21 PST)
[AMBER] AMBER 10 install issue
(Thu Jan 31 2013 - 17:27:50 PST)
Jonathan Gough
[AMBER] PCI-E 2.0 vs 3.0 (AMD vs INTEL?)
(Thu Feb 28 2013 - 18:53:41 PST)
Jonathan Saboury
Re: [AMBER] problem using autoimage from cpptraj
(Sun Feb 10 2013 - 13:19:45 PST)
Re: [AMBER] problem using autoimage from cpptraj
(Sat Feb 09 2013 - 17:13:26 PST)
[AMBER] problem using autoimage from cpptraj
(Fri Feb 08 2013 - 20:35:23 PST)
[AMBER] setting certain atoms as static
(Tue Feb 05 2013 - 23:14:11 PST)
Re: [AMBER] ERROR: the best APS is not zero, bonds involved by this atom are frozen
(Mon Feb 04 2013 - 21:32:46 PST)
[AMBER] ERROR: the best APS is not zero, bonds involved by this atom are frozen
(Sun Feb 03 2013 - 20:44:08 PST)
[AMBER] Setting up a Periodic Box Size
(Sat Feb 02 2013 - 11:36:15 PST)
Joseph Maxwell
Re: [AMBER] Calculating Hydrogen bond energy
(Sun Feb 24 2013 - 06:39:20 PST)
Kasam, Vinod
Re: [AMBER] converting AMBER minimized file to PDB/MOL2
(Mon Feb 25 2013 - 12:21:38 PST)
Kepa K. Burusco
Re: [AMBER] Hydrogens AMBER 1H6 and 2H6 vs. Glycam H61 and H62 for Glucose
(Mon Feb 11 2013 - 12:49:19 PST)
[AMBER] Hydrogens AMBER 1H6 and 2H6 vs. Glycam H61 and H62 for Glucose
(Mon Feb 11 2013 - 05:48:07 PST)
Kim Hyunsik
[AMBER] remd exchange acceptance
(Wed Feb 27 2013 - 22:08:24 PST)
kurisaki
Re: [AMBER] What algorithm does ptraj use for solvation of eigen-value problem.
(Sat Feb 16 2013 - 22:35:30 PST)
Re: [AMBER] What algorithm does ptraj use for solvation of eigen-value problem.
(Sat Feb 16 2013 - 00:14:35 PST)
Re: [AMBER] What algorithm does ptraj use for solvation of eigen-value problem.
(Fri Feb 15 2013 - 21:40:50 PST)
Re: [AMBER] Anomalous Termination of PMEMD.CUDA jobs
(Fri Feb 15 2013 - 21:09:40 PST)
Re: [AMBER] Anomalous Termination of PMEMD.CUDA jobs
(Fri Feb 15 2013 - 01:27:38 PST)
[AMBER] What algorithm does ptraj use for solvation of eigen-value problem.
(Fri Feb 15 2013 - 01:08:46 PST)
Re: [AMBER] Anomalous Termination of PMEMD.CUDA jobs
(Wed Feb 13 2013 - 17:39:29 PST)
Re: [AMBER] Anomalous Termination of PMEMD.CUDA jobs
(Wed Feb 13 2013 - 02:17:05 PST)
[AMBER] Anomalous Termination of PMEMD.CUDA jobs
(Wed Feb 13 2013 - 02:02:23 PST)
Re: [AMBER] Wrong Annotation of PREPIN generated by RESIDUEGEN
(Sun Feb 10 2013 - 19:47:06 PST)
[AMBER] Wrong Annotation of PREPIN generated by RESIDUEGEN
(Sun Feb 10 2013 - 01:20:26 PST)
Lachele Foley
Re: [AMBER] adding rings using sequence command
(Wed Feb 27 2013 - 12:29:19 PST)
Re: [AMBER] adding rings using sequence command
(Tue Feb 26 2013 - 12:49:47 PST)
Re: [AMBER] adding rings using sequence command
(Tue Feb 26 2013 - 12:02:11 PST)
Re: [AMBER] Building a new structure!
(Fri Feb 15 2013 - 07:11:41 PST)
Lachele Foley (Lists)
Re: [AMBER] Hydrogens AMBER 1H6 and 2H6 vs. Glycam H61 and H62 for Glucose
(Mon Feb 11 2013 - 12:01:42 PST)
Re: [AMBER] Hydrogens AMBER 1H6 and 2H6 vs. Glycam H61 and H62 for Glucose
(Mon Feb 11 2013 - 06:47:45 PST)
Leandro Bortot
Re: [AMBER] problem with 3-ring system in antechamber
(Fri Feb 08 2013 - 12:55:28 PST)
Re: [AMBER] problem with 3-ring system in antechamber
(Fri Feb 08 2013 - 11:14:48 PST)
Re: [AMBER] problem with 3-ring system in antechamber
(Fri Feb 08 2013 - 10:18:27 PST)
[AMBER] problem with 3-ring system in antechamber
(Fri Feb 08 2013 - 07:59:49 PST)
m.wisniewska.aol.pl
[AMBER] ODP: Re: glucose
(Wed Feb 20 2013 - 09:11:09 PST)
manikanthan bhavaraju
Re: [AMBER] Problems with MMPBSA.py for running pbsa calculations
(Mon Feb 11 2013 - 14:58:17 PST)
Re: [AMBER] Problems with MMPBSA.py for running pbsa calculations
(Mon Feb 11 2013 - 12:48:28 PST)
[AMBER] Problems with MMPBSA.py for running pbsa calculations
(Sat Feb 09 2013 - 12:36:19 PST)
Mannan
[AMBER] Steered Molecular Dynamics
(Sat Feb 09 2013 - 17:28:56 PST)
[AMBER] Steered Molecular Dynamics
(Sat Feb 09 2013 - 17:29:11 PST)
[AMBER] Steered Molecular Dynamics
(Fri Feb 08 2013 - 06:05:32 PST)
Marek Maly
Re: [AMBER] possibility to increase max . num. of bonded atoms ?
(Wed Feb 27 2013 - 12:27:07 PST)
Re: [AMBER] possibility to increase max . num. of bonded atoms ?
(Wed Feb 27 2013 - 11:40:32 PST)
Re: [AMBER] GTX Titan was finally released
(Wed Feb 27 2013 - 10:23:20 PST)
Re: [AMBER] possibility to increase max . num. of bonded atoms ?
(Wed Feb 27 2013 - 10:03:52 PST)
Re: [AMBER] possibility to increase max . num. of bonded atoms ?
(Mon Feb 25 2013 - 16:31:22 PST)
[AMBER] possibility to increase max . num. of bonded atoms ?
(Sat Feb 23 2013 - 19:43:18 PST)
Re: [AMBER] GTX Titan was finally released
(Wed Feb 20 2013 - 05:22:55 PST)
Re: [AMBER] GTX Titan was finally released
(Tue Feb 19 2013 - 10:14:01 PST)
Re: [AMBER] GTX Titan was finally released
(Tue Feb 19 2013 - 08:55:24 PST)
Re: [AMBER] scaling problem in RADIAL of CPPTRAJ
(Fri Feb 01 2013 - 12:54:50 PST)
Re: [AMBER] scaling problem in RADIAL of CPPTRAJ
(Fri Feb 01 2013 - 12:40:07 PST)
Re: [AMBER] scaling problem in RADIAL of CPPTRAJ
(Fri Feb 01 2013 - 10:00:24 PST)
Re: [AMBER] scaling problem in RADIAL of CPPTRAJ
(Fri Feb 01 2013 - 08:51:35 PST)
Re: [AMBER] scaling problem in RADIAL of CPPTRAJ
(Thu Jan 31 2013 - 21:27:54 PST)
[AMBER] scaling problem in RADIAL of CPPTRAJ
(Thu Jan 31 2013 - 15:47:13 PST)
Marko Wehle
Re: [AMBER] AMBER pmemd and pmemd.cuda, not restart files after minimization - fort.16 file instead
(Wed Feb 06 2013 - 03:47:40 PST)
Re: [AMBER] AMBER-Tools cpptraj residue numbering incorrect
(Tue Feb 05 2013 - 13:27:53 PST)
Re: [AMBER] AMBER pmemd and pmemd.cuda, not restart files after minimization - fort.16 file instead
(Tue Feb 05 2013 - 03:07:47 PST)
Re: [AMBER] AMBER-Tools cpptraj residue numbering incorrect
(Mon Feb 04 2013 - 11:03:22 PST)
[AMBER] AMBER-Tools cpptraj residue numbering incorrect
(Mon Feb 04 2013 - 07:52:55 PST)
Re: [AMBER] AMBER pmemd and pmemd.cuda, not restart files after minimization - fort.16 file instead
(Mon Feb 04 2013 - 04:31:21 PST)
Marta Perez
[AMBER] leap insert missing atoms in aminoacids according to ...
(Thu Feb 21 2013 - 07:59:20 PST)
marta wisniewska.
[AMBER] glucose
(Wed Feb 20 2013 - 07:58:25 PST)
Mary Varughese
[AMBER] amber 11 installation on server
(Mon Feb 25 2013 - 10:24:31 PST)
Re: [AMBER] amber11 installation test files
(Wed Feb 06 2013 - 20:05:19 PST)
Re: [AMBER] amber11 installation test files
(Mon Feb 04 2013 - 19:56:55 PST)
[AMBER] amber11 installation test files
(Sun Feb 03 2013 - 21:11:30 PST)
Massimiliano Porrini
[AMBER] Fwd: radial distribution function between atoms of the two masks
(Mon Feb 25 2013 - 12:54:20 PST)
[AMBER] radial distribution function between atoms of the two masks
(Thu Feb 21 2013 - 06:12:24 PST)
[AMBER] Fwd: PSF file, atom radii and chamber
(Mon Feb 18 2013 - 01:04:46 PST)
[AMBER] PSF file, atom radii and chamber
(Mon Feb 11 2013 - 10:05:48 PST)
Re: [AMBER] issues with PDB file and tleap
(Thu Feb 07 2013 - 06:56:44 PST)
[AMBER] issues with PDB file and tleap
(Thu Feb 07 2013 - 03:45:58 PST)
Matthias Leeder
Re: [AMBER] Cannot open the input file: XYZ.pdb in rpdb(), exit
(Thu Feb 14 2013 - 01:43:20 PST)
[AMBER] Cannot open the input file: XYZ.pdb in rpdb(), exit
(Wed Feb 13 2013 - 10:42:02 PST)
meandme_meandme2003.yahoo.com
Re: [AMBER] 0
(Wed Feb 27 2013 - 19:54:29 PST)
Miguel Ortiz Lombardia
Re: [AMBER] Compilation problems for parallel build after applying patches
(Tue Feb 12 2013 - 11:50:28 PST)
Miguel Ortiz Lombardía
Re: [AMBER] MMPBSA.py: about sasopt value with inp=1
(Wed Feb 13 2013 - 06:15:22 PST)
[AMBER] MMPBSA.py: about sasopt value with inp=1
(Wed Feb 13 2013 - 05:55:45 PST)
Re: [AMBER] Compilation problems for parallel build after applying patches
(Tue Feb 12 2013 - 08:38:46 PST)
Re: [AMBER] Compilation problems for parallel build after applying patches
(Tue Feb 12 2013 - 08:04:37 PST)
[AMBER] Compilation problems for parallel build after applying patches
(Tue Feb 12 2013 - 06:55:18 PST)
Mo Chen
[AMBER] About EPTOT
(Wed Feb 20 2013 - 15:50:01 PST)
moitrayee.mbu.iisc.ernet.in
Re: [AMBER] Modified amino acid parameter generation
(Thu Feb 28 2013 - 09:59:28 PST)
[AMBER] Linear peptide using non standard amino acids
(Thu Feb 21 2013 - 13:12:03 PST)
Moth, Chris
Re: [AMBER] aMD
(Thu Feb 28 2013 - 08:16:39 PST)
Neha Gandhi
[AMBER] amber phosphorylated parameters
(Mon Feb 25 2013 - 04:01:07 PST)
Prabal Maiti
Re: [AMBER] OPLS to AMBER vdw parameters conversion
(Tue Feb 05 2013 - 13:34:55 PST)
[AMBER] OPLS to AMBER vdw parameters conversion
(Tue Feb 05 2013 - 12:07:01 PST)
Prajwal Nandekar
Re: [AMBER] amber error about protein containing heme
(Fri Feb 22 2013 - 08:33:30 PST)
Re: [AMBER] regarding frcmod preparation
(Fri Feb 22 2013 - 03:11:57 PST)
Re: [AMBER] amber error about protein containing heme
(Fri Feb 22 2013 - 01:42:17 PST)
psu4.uic.edu
Re: [AMBER] igb=7 & 8 CalcError: "pathway" failed with prmtop "protein".prmtop
(Wed Feb 20 2013 - 11:03:57 PST)
Re: [AMBER] igb=7 & 8 CalcError: "pathway" failed with prmtop "protein".prmtop
(Mon Feb 11 2013 - 22:23:42 PST)
Re: [AMBER] igb=7 & 8 CalcError: "pathway" failed with prmtop "protein".prmtop
(Thu Feb 07 2013 - 17:23:39 PST)
Re: [AMBER] igb=7 & 8 CalcError: "pathway" failed with prmtop "protein".prmtop
(Mon Feb 04 2013 - 13:47:52 PST)
Re: [AMBER] igb=7 & 8 CalcError: "pathway" failed with prmtop "protein".prmtop
(Sun Feb 03 2013 - 13:55:38 PST)
[AMBER] igb=7 & 8 CalcError: "pathway" failed with prmtop "protein".prmtop
(Sat Feb 02 2013 - 15:48:00 PST)
rajith bhaskar
[AMBER] Inquiry from beginner
(Sun Feb 10 2013 - 20:55:15 PST)
Rasha Alqus
[AMBER] error in nmode
(Wed Feb 27 2013 - 07:03:03 PST)
[AMBER] error in nmode
(Tue Feb 26 2013 - 08:46:16 PST)
Re: [AMBER] problem in nmode
(Wed Feb 20 2013 - 09:11:37 PST)
[AMBER] mmpbsa_py_nabnmode for single macromolecule
(Wed Feb 20 2013 - 07:27:16 PST)
[AMBER] problem in nmode
(Wed Feb 20 2013 - 06:39:39 PST)
[AMBER] How to calculate the vibrational frequancy
(Tue Feb 19 2013 - 08:47:11 PST)
[AMBER] VIBRATIONAL FREQUANCY USING NMODE
(Wed Feb 13 2013 - 05:32:43 PST)
Ray Luo, Ph.D.
Re: [AMBER] Problems with MMPBSA.py for running pbsa calculations
(Tue Feb 12 2013 - 16:06:35 PST)
Re: [AMBER] Problems with MMPBSA.py for running pbsa calculations
(Mon Feb 11 2013 - 15:24:02 PST)
Re: [AMBER] Problems with MMPBSA.py for running pbsa calculations
(Mon Feb 11 2013 - 13:08:01 PST)
Re: [AMBER] Problems with MMPBSA.py for running pbsa calculations
(Sat Feb 09 2013 - 13:17:00 PST)
Rebeca García Fandiño
Re: [AMBER] charged molecule with antechamber
(Wed Feb 13 2013 - 11:19:56 PST)
[AMBER] charged molecule with antechamber
(Wed Feb 13 2013 - 10:45:47 PST)
Rejwan
Re: [AMBER] topology file issue with entropy calculation
(Thu Feb 07 2013 - 11:48:22 PST)
Re: [AMBER] topology file issue with entropy calculation
(Wed Feb 06 2013 - 17:14:29 PST)
[AMBER] topology file issue with entropy calculation
(Mon Feb 04 2013 - 22:58:01 PST)
Robert Konecny
Re: [AMBER] iAPBS
(Tue Feb 05 2013 - 10:42:48 PST)
Romelia Salomon
Re: [AMBER] aMD
(Thu Feb 28 2013 - 08:22:09 PST)
Re: [AMBER] aMD
(Thu Feb 28 2013 - 07:59:18 PST)
Ross Walker
Re: [AMBER] GTX 680 vs GTX Titan
(Thu Feb 28 2013 - 00:10:43 PST)
Re: [AMBER] bond angle fitting
(Tue Feb 26 2013 - 11:38:18 PST)
Re: [AMBER] GTX Titan was finally released
(Mon Feb 25 2013 - 17:46:23 PST)
Re: [AMBER] GTX Titan was finally released
(Fri Feb 22 2013 - 20:45:06 PST)
Re: [AMBER] unspecified launch failure launching kernel kRecalculateVelocities
(Fri Feb 22 2013 - 15:04:41 PST)
Re: [AMBER] GTX Titan was finally released
(Wed Feb 20 2013 - 13:03:28 PST)
Re: [AMBER] Kepler GTX680 MD Workstation
(Tue Feb 19 2013 - 19:29:07 PST)
Re: [AMBER] GTX Titan was finally released
(Tue Feb 19 2013 - 14:18:01 PST)
Re: [AMBER] GTX Titan was finally released
(Tue Feb 19 2013 - 11:24:54 PST)
Re: [AMBER] GTX Titan was finally released
(Tue Feb 19 2013 - 10:43:28 PST)
Re: [AMBER] GTX Titan was finally released
(Tue Feb 19 2013 - 09:58:54 PST)
Re: [AMBER] GTX Titan was finally released
(Tue Feb 19 2013 - 09:46:42 PST)
Re: [AMBER] Anomalous Termination of PMEMD.CUDA jobs
(Fri Feb 15 2013 - 10:36:14 PST)
Re: [AMBER] Anomalous Termination of PMEMD.CUDA jobs
(Wed Feb 13 2013 - 09:16:41 PST)
Re: [AMBER] Problem in running TREMD in AMBER10
(Fri Feb 08 2013 - 13:17:28 PST)
Re: [AMBER] Amber 12 and CUDA 5.0 K20 vs GTX 680: GTX 680 is two time faster than K20
(Fri Feb 08 2013 - 13:15:37 PST)
Re: [AMBER] Problem in running TREMD in AMBER10
(Fri Feb 08 2013 - 13:12:12 PST)
Re: [AMBER] Problem in running TREMD in AMBER10
(Fri Feb 08 2013 - 12:46:09 PST)
Re: [AMBER] AMBER pmemd and pmemd.cuda, not restart files after minimization - fort.16 file instead
(Mon Feb 04 2013 - 08:55:01 PST)
Sajeewa Pemasinghe
Re: [AMBER] A general question about umbrella sampling
(Tue Feb 12 2013 - 14:48:10 PST)
[AMBER] A general question about umbrella sampling
(Tue Feb 12 2013 - 12:51:47 PST)
Re: [AMBER] Problem in running TREMD in AMBER10
(Sat Feb 09 2013 - 09:44:21 PST)
Re: [AMBER] Problem in running TREMD in AMBER10
(Sat Feb 09 2013 - 09:06:18 PST)
Re: [AMBER] Problem in running TREMD in AMBER10
(Fri Feb 08 2013 - 21:30:42 PST)
Re: [AMBER] Problem in running TREMD in AMBER10
(Fri Feb 08 2013 - 13:37:19 PST)
Re: [AMBER] Problem in running TREMD in AMBER10
(Fri Feb 08 2013 - 13:11:06 PST)
Re: [AMBER] Problem in running TREMD in AMBER10
(Fri Feb 08 2013 - 13:04:01 PST)
[AMBER] Problem in running TREMD in AMBER10
(Fri Feb 08 2013 - 12:37:45 PST)
Re: [AMBER] Fwd: Sampling of a point by a molecule while keeping the relative position of the molecule unchanged in TMD
(Fri Feb 01 2013 - 21:18:47 PST)
[AMBER] Fwd: Sampling of a point by a molecule while keeping the relative position of the molecule unchanged in TMD
(Fri Feb 01 2013 - 14:59:54 PST)
Sally Pias
Re: [AMBER] problem reading CHARMM lipid parameters into chamber
(Thu Feb 21 2013 - 08:32:30 PST)
[AMBER] problem reading CHARMM lipid parameters into chamber
(Tue Feb 19 2013 - 13:07:56 PST)
Sangita Kachhap
Re: [AMBER] use of parmbsc0 for protein-DNA complex along with ff99SB
(Mon Feb 04 2013 - 08:21:03 PST)
Re: [AMBER] use of parmbsc0 for protein-DNA complex along with ff99SB
(Mon Feb 04 2013 - 07:21:58 PST)
[AMBER] use of parmbsc0 for protein-DNA complex along with ff99SB
(Mon Feb 04 2013 - 04:39:14 PST)
Sanjib Paul
[AMBER] Warnings when saving prmtop and inpcrd files.
(Sun Feb 10 2013 - 23:39:51 PST)
Re: [AMBER] xleap could not find the type Cl-
(Sat Feb 09 2013 - 09:54:03 PST)
[AMBER] xleap could not find the type Cl-
(Sat Feb 09 2013 - 04:26:32 PST)
Sasha Perkins
[AMBER] Missing comma in input file
(Tue Feb 19 2013 - 08:18:03 PST)
Saugata Hazra
Re: [AMBER] problem in running MMPBSA
(Mon Feb 25 2013 - 15:20:51 PST)
Re: [AMBER] problem in running MMPBSA
(Mon Feb 25 2013 - 10:33:33 PST)
Re: [AMBER] problem in running MMPBSA
(Sat Feb 23 2013 - 16:51:20 PST)
Re: [AMBER] problem in running MMPBSA
(Wed Feb 20 2013 - 00:08:04 PST)
[AMBER] problem in running MMPBSA
(Tue Feb 19 2013 - 06:31:43 PST)
[AMBER] problem in running MMPBSA
(Tue Feb 19 2013 - 05:02:45 PST)
Scott Le Grand
Re: [AMBER] GTX Titan was finally released
(Tue Feb 26 2013 - 08:14:01 PST)
Re: [AMBER] GTX Titan was finally released
(Tue Feb 19 2013 - 13:27:38 PST)
Re: [AMBER] GTX Titan was finally released
(Tue Feb 19 2013 - 11:08:36 PST)
Re: [AMBER] distance restraints between the primary molecule and its periodic image
(Sat Feb 09 2013 - 10:17:30 PST)
Shashidhar Rao
Re: [AMBER] question on input for MMPBSA.py
(Tue Feb 26 2013 - 08:03:53 PST)
Re: [AMBER] question on input for MMPBSA.py
(Tue Feb 26 2013 - 06:56:15 PST)
[AMBER] question on input for MMPBSA.py
(Mon Feb 25 2013 - 13:08:32 PST)
Re: [AMBER] converting AMBER minimized file to PDB/MOL2
(Mon Feb 25 2013 - 12:43:37 PST)
[AMBER] converting AMBER minimized file to PDB/MOL2
(Mon Feb 25 2013 - 12:17:26 PST)
Shobana, G .
[AMBER] NaN error in restart file
(Fri Feb 08 2013 - 02:26:46 PST)
Sindrila Dutta banik
Re: [AMBER] Problem related to the bfactor calculation
(Mon Feb 25 2013 - 23:24:20 PST)
[AMBER] Problem related to the bfactor calculation
(Mon Feb 25 2013 - 21:03:39 PST)
Re: [AMBER] Problem related to the umbrella sampling
(Fri Feb 08 2013 - 21:34:13 PST)
Re: [AMBER] Problem related to the umbrella sampling
(Fri Feb 08 2013 - 11:44:02 PST)
[AMBER] problem with umbrella sampling
(Fri Feb 08 2013 - 09:33:13 PST)
[AMBER] Problem related to the umbrella sampling
(Fri Feb 08 2013 - 09:30:03 PST)
[AMBER] Problem related with umbrella sampling
(Fri Feb 08 2013 - 03:20:13 PST)
Soumya Lipsa Rath
Re: [AMBER] MMPBSA free energy
(Tue Feb 26 2013 - 06:04:07 PST)
[AMBER] MMPBSA free energy
(Tue Feb 26 2013 - 03:50:13 PST)
Souvik Sur
[AMBER] Query regarding PNA-DNA duplex parameterization in AMBER
(Fri Feb 08 2013 - 23:26:19 PST)
steinbrt.rci.rutgers.edu
Re: [AMBER] TI without ifsc = 1 crashes
(Wed Feb 27 2013 - 00:36:31 PST)
Subrata Paul
Re: [AMBER] NMA(n-methylacetamide)
(Mon Feb 11 2013 - 07:35:17 PST)
Re: [AMBER] NMA(n-methylacetamide)
(Mon Feb 11 2013 - 02:31:33 PST)
[AMBER] NMA(n-methylacetamide)
(Fri Feb 08 2013 - 02:12:31 PST)
[AMBER] Fwd: charge for NMA molecule
(Wed Feb 06 2013 - 22:05:52 PST)
[AMBER] charge for NMA molecule
(Wed Feb 06 2013 - 04:58:57 PST)
Sun
[AMBER] the position of counterion
(Sun Feb 17 2013 - 10:54:00 PST)
Symon Gathiaka
[AMBER] unspecified launch failure launching kernel kRecalculateVelocities
(Fri Feb 22 2013 - 10:58:04 PST)
[AMBER] Sander error - Segmentation fault (core dumped)
(Fri Feb 15 2013 - 11:28:51 PST)
Sören Wacker
Re: [AMBER] espgen cannot deal with Gaussian 09 log file
(Wed Feb 06 2013 - 05:22:59 PST)
Re: [AMBER] espgen cannot deal with Gaussian 09 log file
(Wed Feb 06 2013 - 02:32:16 PST)
Re: [AMBER] espgen cannot deal with Gaussian 09 log file
(Mon Feb 04 2013 - 04:04:41 PST)
Tamer Ibrahim
[AMBER] silhouette.pl
(Mon Feb 04 2013 - 07:35:45 PST)
Theodosia Teo
Re: [AMBER] PROBLEMS IN SETTING UP PHOSPHORYLATED SIMULATION MODELS
(Tue Feb 19 2013 - 22:11:07 PST)
Re: [AMBER] PROBLEMS IN SETTING UP PHOSPHORYLATED SIMULATION MODELS
(Tue Feb 19 2013 - 13:35:48 PST)
[AMBER] PROBLEMS IN SETTING UP PHOSPHORYLATED SIMULATION MODELS
(Mon Feb 18 2013 - 19:46:53 PST)
Thomas Cheatham
Re: [AMBER] scaling problem in RADIAL of CPPTRAJ
(Fri Feb 01 2013 - 10:30:48 PST)
Thomas Evangelidis
[AMBER] constant pH for transmemrane proteins
(Thu Feb 21 2013 - 07:19:13 PST)
Re: [AMBER] change starting time of simulation
(Fri Feb 08 2013 - 07:07:32 PST)
[AMBER] change starting time of simulation
(Fri Feb 08 2013 - 01:38:19 PST)
Re: [AMBER] about iwrap=1 and ntxo=2
(Tue Feb 05 2013 - 11:20:43 PST)
Re: [AMBER] about iwrap=1 and ntxo=2
(Sat Feb 02 2013 - 12:08:40 PST)
tianchuan1015
Re: [AMBER] amber error about protein containing heme
(Fri Feb 22 2013 - 06:31:08 PST)
[AMBER] amber error about protein containing heme
(Thu Feb 21 2013 - 23:58:31 PST)
Tomasz Borowski
Re: [AMBER] espgen cannot deal with Gaussian 09 log file
(Mon Feb 04 2013 - 03:59:35 PST)
Tommy Yap
[AMBER] MMPBSA problem
(Mon Feb 25 2013 - 18:15:05 PST)
Tyler Luchko
Re: [AMBER] 3D-RISM input file error
(Tue Feb 05 2013 - 11:36:58 PST)
uday spike
Re: [AMBER] problems with NAB
(Tue Feb 19 2013 - 00:25:55 PST)
Re: [AMBER] problems with NAB
(Sat Feb 16 2013 - 01:34:51 PST)
[AMBER] problems with NAB
(Wed Feb 06 2013 - 23:49:37 PST)
Urszula Uciechowska
[AMBER] average structure
(Fri Feb 01 2013 - 02:31:55 PST)
Vaibhav Dixit
Re: [AMBER] short bonds in average pdb
(Wed Feb 20 2013 - 01:17:57 PST)
Re: [AMBER] short bonds in average pdb
(Wed Feb 20 2013 - 01:04:37 PST)
[AMBER] PCA analysis query
(Sun Feb 17 2013 - 23:34:23 PST)
Re: [AMBER] Small bug in MMPBSA.py tutorial
(Sat Feb 16 2013 - 21:21:37 PST)
Re: [AMBER] protein-protein binding free energy
(Sat Feb 02 2013 - 21:03:09 PST)
Vivek Shankar Bharadwaj
Re: [AMBER] MMGBSA/MMPBSA Decomposition Analysis
(Thu Feb 28 2013 - 10:00:00 PST)
[AMBER] MMGBSA/MMPBSA Decomposition Analysis
(Wed Feb 27 2013 - 16:28:38 PST)
WenJuan Huang
Re: [AMBER] Problems with MMPBSA.py for running pbsa calculations
(Sun Feb 10 2013 - 21:04:05 PST)
[AMBER] 3D-RISM input file error
(Tue Feb 05 2013 - 11:05:43 PST)
Yulin Huang
[AMBER] Could you please remove me from AMBER mailing list
(Tue Feb 05 2013 - 09:32:48 PST)
Yun Shi
Re: [AMBER] Adding buffer and salt
(Thu Feb 07 2013 - 10:32:33 PST)
吴云剑
[AMBER] periodic image of octahedron box in VMD
(Tue Feb 26 2013 - 18:10:08 PST)
徐立平
[AMBER] force field file
(Mon Feb 25 2013 - 23:53:29 PST)
纪晓峰
[AMBER] missing parameter of B in .frcmod
(Thu Feb 07 2013 - 19:19:54 PST)
Last message date
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Thu Feb 28 2013 - 19:00:03 PST
Archived on
: Fri Apr 19 2024 - 05:54:29 PDT
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