Amber Archive Mar 2015 by author
653 messages
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Starting
Sun Mar 01 2015 - 07:00:02 PST,
Ending
Wed Apr 01 2015 - 00:00:03 PDT
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abdennour braka
[AMBER] PCA_representation_in_Cpptraj
(Mon Mar 09 2015 - 02:14:51 PDT)
Abhishek Tyagi
Re: [AMBER] MMPBSA error
(Fri Mar 27 2015 - 09:39:50 PDT)
[AMBER] MMGBSA error
(Wed Mar 25 2015 - 23:06:44 PDT)
achim.sandmann.chemie.stud.uni-erlangen.de
Re: [AMBER] acetyl lysine
(Mon Mar 09 2015 - 02:04:34 PDT)
Adrian Roitberg
[AMBER] HMR
(Mon Mar 16 2015 - 14:40:23 PDT)
Re: [AMBER] SMD average work
(Tue Mar 03 2015 - 09:04:06 PST)
Agnieszka Szarecka
Re: [AMBER] Amber on Red Hat?
(Tue Mar 17 2015 - 13:29:19 PDT)
Re: [AMBER] Amber on Red Hat?
(Tue Mar 17 2015 - 12:23:04 PDT)
Ahmet yıldırım
[AMBER] heat capacity
(Fri Mar 20 2015 - 13:07:34 PDT)
Akash Deep Biswas
Re: [AMBER] Error while creating force field
(Tue Mar 03 2015 - 03:50:12 PST)
amr hamed
[AMBER] Replica Exchange on a single Titan-X GPU
(Mon Mar 23 2015 - 08:19:09 PDT)
Anasuya Dighe
[AMBER] Starting antechamber for preparing ligand molecule
(Tue Mar 17 2015 - 10:23:51 PDT)
[AMBER] Sudden RMSD blow-up in trajectory analysis
(Tue Mar 10 2015 - 02:54:17 PDT)
anu chandra
[AMBER] Force field for Inositol triphosphate
(Fri Mar 13 2015 - 05:35:00 PDT)
Arjun Sharma
Re: [AMBER] AMBER Digest, Vol 1169, Issue 1
(Wed Mar 25 2015 - 14:54:31 PDT)
[AMBER] CpHMD-pHREX AMBER14
(Tue Mar 24 2015 - 10:37:29 PDT)
[AMBER] Bond distance and Box shape
(Fri Mar 20 2015 - 07:21:58 PDT)
[AMBER] set command and VMD
(Sat Mar 14 2015 - 15:44:23 PDT)
[AMBER] Truncated octahedron
(Wed Mar 11 2015 - 08:24:31 PDT)
Atila Petrosian
Re: [AMBER] General question about MM-PB(GB)SA
(Sun Mar 08 2015 - 05:22:16 PDT)
[AMBER] General question about MM-PB(GB)SA
(Fri Mar 06 2015 - 21:56:14 PST)
Re: [AMBER] Param PROC does not exist --- MM-PBSA problem
(Thu Mar 05 2015 - 08:39:33 PST)
[AMBER] Param PROC does not exist --- MM-PBSA problem
(Tue Mar 03 2015 - 23:49:18 PST)
[AMBER] Param PROC does not exist (MM-PBSA)
(Sun Mar 01 2015 - 06:49:33 PST)
Attilio Vittorio Vargiu
[AMBER] About generalized restraints in AMBER14 with GPU support
(Tue Mar 24 2015 - 07:29:28 PDT)
Beale, John
[AMBER] CUDA problems
(Mon Mar 23 2015 - 07:41:30 PDT)
Biao Ma
Re: [AMBER] How to calculate interaction energy between any two residues of one protein
(Tue Mar 03 2015 - 21:24:28 PST)
Bill Miller III
Re: [AMBER] error in MMPBSA.py
(Thu Mar 05 2015 - 07:04:45 PST)
Re: [AMBER] Decomposition of the MMGBSA based on multi trajectory input
(Thu Mar 05 2015 - 04:44:26 PST)
Re: [AMBER] Decomposition of the MMGBSA based on multi trajectory input
(Wed Mar 04 2015 - 07:38:10 PST)
Re: [AMBER] Decomposition of the MMGBSA based on multi trajectory input
(Tue Mar 03 2015 - 07:23:56 PST)
Bill Ross
Re: [AMBER] AMBER14 pmemd.cuda.MPI : *** in mdout files
(Tue Mar 31 2015 - 18:00:34 PDT)
Re: [AMBER] Leap warning
(Fri Mar 20 2015 - 11:07:47 PDT)
Re: [AMBER] Non-Standard Residue / Non-Integer Charge
(Fri Mar 20 2015 - 11:03:14 PDT)
Re: [AMBER] loading molecule in xleap and saving it in mol2 format
(Fri Mar 20 2015 - 08:31:38 PDT)
Re: [AMBER] loading molecule in xleap and saving it in mol2 format
(Fri Mar 20 2015 - 08:19:59 PDT)
Re: [AMBER] loading molecule in xleap and saving it in mol2 format
(Fri Mar 20 2015 - 07:45:23 PDT)
Re: [AMBER] RNA's sugar modification
(Sun Mar 15 2015 - 13:17:57 PDT)
Re: [AMBER] RNA's sugar modification
(Sun Mar 15 2015 - 13:13:20 PDT)
Re: [AMBER] RNA Simulation
(Thu Mar 12 2015 - 14:15:29 PDT)
Re: [AMBER] mmpbsa conflict with Ca2+ ?
(Wed Mar 11 2015 - 08:40:00 PDT)
Re: [AMBER] Truncated octahedron
(Wed Mar 11 2015 - 08:35:36 PDT)
Brent Krueger
Re: [AMBER] Multiple MEPs option in R.E.D tools
(Tue Mar 31 2015 - 04:40:40 PDT)
Brett
[AMBER] on the force field
(Sat Mar 07 2015 - 19:04:55 PST)
[AMBER] a question on molecular dynamics simulation
(Fri Mar 06 2015 - 05:14:35 PST)
Brian Radak
[AMBER] aMD boost parameters for CHARMM force field?
(Fri Mar 27 2015 - 08:39:13 PDT)
Re: [AMBER] trouble running pmemd.cuda
(Thu Mar 26 2015 - 11:08:24 PDT)
Re: [AMBER] trouble running pmemd.cuda
(Thu Mar 26 2015 - 10:08:54 PDT)
Re: [AMBER] trouble running pmemd.cuda
(Thu Mar 26 2015 - 07:41:38 PDT)
Re: [AMBER] trouble running pmemd.cuda
(Wed Mar 25 2015 - 11:46:24 PDT)
[AMBER] trouble running pmemd.cuda
(Wed Mar 25 2015 - 10:30:23 PDT)
Re: [AMBER] CHAMBER and CMAP difficulty
(Wed Mar 18 2015 - 09:59:33 PDT)
Re: [AMBER] CHAMBER and CMAP difficulty
(Wed Mar 18 2015 - 09:31:55 PDT)
Re: [AMBER] CHAMBER and CMAP difficulty
(Wed Mar 18 2015 - 09:13:28 PDT)
Re: [AMBER] CHAMBER and CMAP difficulty
(Wed Mar 18 2015 - 08:54:10 PDT)
Re: [AMBER] CHAMBER and CMAP difficulty
(Wed Mar 18 2015 - 08:27:29 PDT)
[AMBER] CHAMBER and CMAP difficulty
(Wed Mar 18 2015 - 08:03:53 PDT)
camm-kansai
Re: [AMBER] MMPBSA tutorial: MMPBSA.py
(Fri Mar 13 2015 - 06:18:22 PDT)
[AMBER] MMPBSA tutorial: MMPBSA.py
(Tue Mar 10 2015 - 04:32:06 PDT)
Carlos Simmerling
Re: [AMBER] Gromacs towards Amber conversion
(Sat Mar 28 2015 - 07:30:07 PDT)
Re: [AMBER] trajectory of minimization using generalized Born
(Fri Mar 20 2015 - 14:08:47 PDT)
Re: [AMBER] trajectory of minimization using generalized Born
(Fri Mar 20 2015 - 13:00:08 PDT)
Re: [AMBER] trajectory of minimization using generalized Born
(Fri Mar 20 2015 - 08:26:05 PDT)
Re: [AMBER] trajectory of minimization using generalized Born
(Fri Mar 20 2015 - 06:25:47 PDT)
Re: [AMBER] trajectory of minimization using generalized Born
(Thu Mar 19 2015 - 15:26:50 PDT)
Re: [AMBER] trajectory of minimization using generalized Born
(Thu Mar 19 2015 - 13:35:48 PDT)
Re: [AMBER] Nuclicacid forcefield in AMBER
(Wed Mar 18 2015 - 05:01:29 PDT)
Re: [AMBER] About TIP4-Ew water model usage
(Wed Mar 18 2015 - 03:16:36 PDT)
Re: [AMBER] PMF for dimer dissociation
(Tue Mar 17 2015 - 16:25:07 PDT)
Re: [AMBER] unfolding protein and solvent density
(Tue Mar 17 2015 - 03:30:29 PDT)
Re: [AMBER] [q4md-fft] Fwd: D- amino acids in ff10
(Fri Mar 13 2015 - 11:28:17 PDT)
Re: [AMBER] [q4md-fft] Fwd: D- amino acids in ff10
(Fri Mar 13 2015 - 10:01:04 PDT)
Re: [AMBER] D- amino acids in ff10
(Wed Mar 11 2015 - 06:55:01 PDT)
Re: [AMBER] Sudden RMSD blow-up in trajectory analysis
(Tue Mar 10 2015 - 03:25:03 PDT)
Re: [AMBER] Cofactor parametrization
(Thu Mar 05 2015 - 05:04:09 PST)
Re: [AMBER] Targeted MD shows blank output file!
(Wed Mar 04 2015 - 05:37:23 PST)
Re: [AMBER] Targeted MD shows blank output file!
(Wed Mar 04 2015 - 04:13:07 PST)
carmendigiovanni75.alice.it
[AMBER] R: Re: GTX980 PERFORMANCE
(Mon Mar 02 2015 - 01:22:28 PST)
Cassandra Churchill
[AMBER] MMGBSA pairwise decomposition - differences in Non-Polar Solv. & TOTAL for same residue pairs
(Tue Mar 17 2015 - 14:53:43 PDT)
Chinh Su Tran To
[AMBER] Fwd: CPPTRAJ trajout results "weird" pdb
(Wed Mar 18 2015 - 20:40:59 PDT)
Chris Gaughan
[AMBER] Problem with heating lipid bilayer in amber 12
(Thu Mar 19 2015 - 14:31:26 PDT)
christian.yongky.ui.ac.id
Re: [AMBER] "Error opening unit 30: File "inpcrd" is missing or unreadable" on Tutorial A15
(Mon Mar 23 2015 - 03:24:20 PDT)
[AMBER] "Error opening unit 30: File "inpcrd" is missing or unreadable" on Tutorial A15
(Sun Mar 22 2015 - 23:47:08 PDT)
Christina Bergonzo
Re: [AMBER] How to obtain potential energy using mdcrd trajectories in AMBER12
(Mon Mar 30 2015 - 07:08:17 PDT)
Re: [AMBER] Projection on distance covariance modes
(Mon Mar 30 2015 - 06:49:08 PDT)
Re: [AMBER] REMD jobs crashing repeatedly on GPUs
(Wed Mar 04 2015 - 10:19:35 PST)
Crowley, Michael
Re: [AMBER] Truncated octahedron
(Wed Mar 11 2015 - 08:39:03 PDT)
Daniel Roe
Re: [AMBER] Histogram analysis of the dihedral distributions using cpptraj
(Mon Mar 30 2015 - 07:04:50 PDT)
Re: [AMBER] Projection on modes calculated by distcovar matrix
(Sun Mar 29 2015 - 08:43:27 PDT)
Re: [AMBER] Histogram analysis of the dihedral distributions using cpptraj
(Fri Mar 27 2015 - 09:33:10 PDT)
Re: [AMBER] aMD boost parameters for CHARMM force field?
(Fri Mar 27 2015 - 08:43:13 PDT)
Re: [AMBER] Histogram analysis of the dihedral distributions using cpptraj
(Fri Mar 27 2015 - 08:39:26 PDT)
Re: [AMBER] help in hbond analysis
(Thu Mar 26 2015 - 10:33:46 PDT)
Re: [AMBER] vdw energy and electrostatic energy calculation for osmolyte
(Wed Mar 25 2015 - 12:18:47 PDT)
Re: [AMBER] iterative calculation in CPPTRAJ using "for... do... done"
(Wed Mar 25 2015 - 06:50:26 PDT)
Re: [AMBER] concave edge on torus has mismatched atoms
(Tue Mar 24 2015 - 13:02:16 PDT)
Re: [AMBER] error when doing lifetime calculation
(Mon Mar 23 2015 - 12:34:00 PDT)
Re: [AMBER] RMSF & changes of the secondary structure of protein
(Mon Mar 23 2015 - 11:50:55 PDT)
Re: [AMBER] error when doing lifetime calculation
(Mon Mar 23 2015 - 07:32:08 PDT)
Re: [AMBER] Evaluating hydrogen boding lifetime
(Sat Mar 21 2015 - 09:06:20 PDT)
Re: [AMBER] Backbone Rmsd
(Sat Mar 21 2015 - 08:44:56 PDT)
Re: [AMBER] Bond distance and Box shape
(Fri Mar 20 2015 - 07:34:53 PDT)
Re: [AMBER] Format of solventhb.dat file in hydrogen bonding calculation
(Fri Mar 20 2015 - 07:23:26 PDT)
Re: [AMBER] On the clustering of the ligand position within the cavity
(Fri Mar 20 2015 - 07:14:48 PDT)
Re: [AMBER] NetCDF AMBER file corrupted
(Thu Mar 19 2015 - 21:21:24 PDT)
Re: [AMBER] Fwd: CPPTRAJ trajout results "weird" pdb
(Thu Mar 19 2015 - 21:17:55 PDT)
Re: [AMBER] post processing temperature replica exchange trajectories
(Thu Mar 19 2015 - 19:57:03 PDT)
Re: [AMBER] trajectory of minimization using generalized Born
(Wed Mar 18 2015 - 19:50:25 PDT)
Re: [AMBER] finding angles
(Tue Mar 17 2015 - 07:12:39 PDT)
Re: [AMBER] finding angles
(Mon Mar 16 2015 - 06:58:33 PDT)
Re: [AMBER] finding angles
(Thu Mar 12 2015 - 20:15:39 PDT)
Re: [AMBER] Evaluating hydrogen boding lifetime
(Thu Mar 12 2015 - 08:33:36 PDT)
Re: [AMBER] finding angles
(Thu Mar 12 2015 - 08:20:19 PDT)
Re: [AMBER] : Dimer Imaging Problem
(Wed Mar 11 2015 - 09:31:23 PDT)
Re: [AMBER] Evaluating hydrogen boding lifetime
(Wed Mar 11 2015 - 08:11:50 PDT)
Re: [AMBER] calculating angle between to vectors
(Wed Mar 11 2015 - 07:39:54 PDT)
Re: [AMBER] help in getting 3D isodensity surface
(Wed Mar 11 2015 - 07:35:58 PDT)
Re: [AMBER] PCA_representation_in_Cpptraj
(Wed Mar 11 2015 - 07:25:57 PDT)
Re: [AMBER] Evaluating hydrogen boding lifetime
(Tue Mar 10 2015 - 20:50:13 PDT)
Re: [AMBER] PCA_representation_in_Cpptraj
(Tue Mar 10 2015 - 07:46:46 PDT)
Re: [AMBER] Sudden RMSD blow-up in trajectory analysis
(Tue Mar 10 2015 - 07:23:49 PDT)
Re: [AMBER] Evaluating hydrogen boding lifetime
(Tue Mar 10 2015 - 07:15:29 PDT)
Re: [AMBER] clustering in ptraj
(Tue Mar 10 2015 - 07:08:14 PDT)
Re: [AMBER] Solvent Box Issue When Running AMBER Dynamics
(Mon Mar 09 2015 - 07:58:42 PDT)
Re: [AMBER] cpptraj H-bond: clarification sought
(Mon Mar 09 2015 - 07:29:22 PDT)
Re: [AMBER] Reading two units from same .mol2 file
(Mon Mar 09 2015 - 07:17:36 PDT)
Re: [AMBER] clustering in ptraj
(Mon Mar 09 2015 - 07:12:25 PDT)
Re: [AMBER] PCA_representation_in_Cpptraj
(Mon Mar 09 2015 - 07:07:17 PDT)
Re: [AMBER] cpptraj H-bond: clarification sought
(Sat Mar 07 2015 - 14:38:03 PST)
danieldefoe
[AMBER] How to calculate interaction energy between any two residues of one protein
(Tue Mar 03 2015 - 21:04:40 PST)
David A Case
Re: [AMBER] Pressure units in 1D-RISM
(Tue Mar 31 2015 - 09:09:08 PDT)
Re: [AMBER] Restrained MD
(Tue Mar 31 2015 - 09:01:29 PDT)
Re: [AMBER] Restrained MD
(Tue Mar 31 2015 - 05:32:04 PDT)
Re: [AMBER] Restrained MD
(Mon Mar 30 2015 - 08:19:30 PDT)
Re: [AMBER] flag for fast water
(Mon Mar 30 2015 - 05:20:27 PDT)
Re: [AMBER] Restrained MD
(Sun Mar 29 2015 - 07:42:50 PDT)
Re: [AMBER] Error: Unable to run flex; this is required for NAB and antechamber Please check your PATH, or install the program
(Sat Mar 28 2015 - 15:10:25 PDT)
Re: [AMBER] Water sigma parameters
(Thu Mar 26 2015 - 14:38:43 PDT)
Re: [AMBER] Implicit solvent simulation with Andersen thermostat
(Thu Mar 26 2015 - 09:33:31 PDT)
Re: [AMBER] Error message from FEW in Amber14 tutorial A24
(Mon Mar 23 2015 - 11:50:59 PDT)
Re: [AMBER] heat capacity
(Sat Mar 21 2015 - 06:17:25 PDT)
[AMBER] Citation from the apostrophe police
(Fri Mar 20 2015 - 06:13:07 PDT)
Re: [AMBER] Reduce not working properly
(Fri Mar 20 2015 - 05:44:45 PDT)
Re: [AMBER] Error during Adding Fragment（about MCPB ）
(Thu Mar 19 2015 - 05:11:34 PDT)
Re: [AMBER] Fwd: CPPTRAJ trajout results "weird" pdb
(Thu Mar 19 2015 - 05:03:07 PDT)
Re: [AMBER] Amber 14 tests errors
(Wed Mar 18 2015 - 17:41:34 PDT)
Re: [AMBER] Non-Standard Residue / Non-Integer Charge
(Wed Mar 18 2015 - 17:32:35 PDT)
Re: [AMBER] trajectory of minimization using generalized Born
(Wed Mar 18 2015 - 15:03:54 PDT)
Re: [AMBER] **No Torsion terms
(Wed Mar 18 2015 - 10:39:51 PDT)
Re: [AMBER] Starting antechamber for preparing ligand molecule
(Wed Mar 18 2015 - 06:37:27 PDT)
Re: [AMBER] **No Torsion terms
(Wed Mar 18 2015 - 06:35:28 PDT)
Re: [AMBER] Backbone Rmsd
(Tue Mar 17 2015 - 04:52:50 PDT)
Re: [AMBER] Differences in AMBER force fields
(Tue Mar 17 2015 - 04:49:08 PDT)
Re: [AMBER] pmemd.MPI error
(Mon Mar 16 2015 - 14:48:39 PDT)
Re: [AMBER] facing problem to create a prmtop file for oxonium cation
(Mon Mar 16 2015 - 04:47:41 PDT)
Re: [AMBER] set command and VMD
(Sun Mar 15 2015 - 17:45:43 PDT)
Re: [AMBER] Nuclicacid forcefield in AMBER
(Sun Mar 15 2015 - 17:33:34 PDT)
Re: [AMBER] leap and centering
(Sat Mar 14 2015 - 06:31:56 PDT)
Re: [AMBER] leap and centering
(Fri Mar 13 2015 - 08:32:09 PDT)
Re: [AMBER] Error: Unable to run flex; this is required for NAB and antechamber Please check your PATH, or install the program
(Fri Mar 13 2015 - 04:06:53 PDT)
Re: [AMBER] Putting oxygen molecules around protein structure
(Thu Mar 12 2015 - 14:19:25 PDT)
Re: [AMBER] MMPBSA tutorial: MMPBSA.py
(Tue Mar 10 2015 - 04:51:45 PDT)
Re: [AMBER] Tutorial B0
(Mon Mar 09 2015 - 14:57:31 PDT)
Re: [AMBER] free energy plot
(Sun Mar 08 2015 - 10:50:18 PDT)
Re: [AMBER] on the force field
(Sun Mar 08 2015 - 06:18:30 PDT)
Re: [AMBER] Reading two units from same .mol2 file
(Sat Mar 07 2015 - 17:45:36 PST)
Re: [AMBER] acetyl lysine
(Sat Mar 07 2015 - 17:43:48 PST)
Re: [AMBER] Inability to use antechamber on Anion
(Fri Mar 06 2015 - 18:06:11 PST)
Re: [AMBER] a question on molecular dynamics simulation
(Fri Mar 06 2015 - 07:09:44 PST)
Re: [AMBER] Solvent Box Issue When Running AMBER Dynamics
(Thu Mar 05 2015 - 05:12:44 PST)
Re: [AMBER] Tutorial B0
(Wed Mar 04 2015 - 05:10:17 PST)
Re: [AMBER] matrix newtransform command
(Tue Mar 03 2015 - 14:35:19 PST)
Re: [AMBER] ATP and ADP-Pi simulations
(Tue Mar 03 2015 - 06:05:19 PST)
Re: [AMBER] ATP and ADP-Pi simulations
(Mon Mar 02 2015 - 17:38:22 PST)
Re: [AMBER] Replacing water with oxygen molecules
(Mon Mar 02 2015 - 17:29:57 PST)
David Case
Re: [AMBER] Solvent Box Issue When Running AMBER Dynamics
(Wed Mar 04 2015 - 17:02:12 PST)
David Poole
[AMBER] 10-12 Potentials, HBOND
(Fri Mar 13 2015 - 20:37:13 PDT)
DEBOSTUTI GHOSHDASTIDAR
[AMBER] Fitting velocity autocorrelation data
(Thu Mar 12 2015 - 03:27:00 PDT)
Dhiraj Srivastava
[AMBER] force field parameter for fructose 1 6 bisphosphate
(Sat Mar 07 2015 - 22:13:55 PST)
[AMBER] acetyl lysine
(Sat Mar 07 2015 - 14:15:29 PST)
Dr. M. Shahid
Re: [AMBER] Cofactor parametrization
(Tue Mar 03 2015 - 03:18:01 PST)
Edwin Helbert Aponte Angarita
[AMBER] Manual still ambiguous about igb=8 and pmemd
(Mon Mar 30 2015 - 09:32:44 PDT)
Re: [AMBER] trajectory of minimization using generalized Born
(Mon Mar 23 2015 - 04:47:37 PDT)
Re: [AMBER] trajectory of minimization using generalized Born
(Sat Mar 21 2015 - 04:48:56 PDT)
Re: [AMBER] trajectory of minimization using generalized Born
(Fri Mar 20 2015 - 13:47:16 PDT)
Re: [AMBER] trajectory of minimization using generalized Born
(Fri Mar 20 2015 - 12:03:27 PDT)
Re: [AMBER] trajectory of minimization using generalized Born
(Fri Mar 20 2015 - 06:13:25 PDT)
Re: [AMBER] trajectory of minimization using generalized Born
(Thu Mar 19 2015 - 16:00:42 PDT)
Re: [AMBER] trajectory of minimization using generalized Born
(Thu Mar 19 2015 - 15:05:25 PDT)
Re: [AMBER] trajectory of minimization using generalized Born
(Thu Mar 19 2015 - 13:21:55 PDT)
Re: [AMBER] trajectory of minimization using generalized Born
(Thu Mar 19 2015 - 12:30:23 PDT)
Re: [AMBER] trajectory of minimization using generalized Born
(Wed Mar 18 2015 - 13:27:44 PDT)
[AMBER] trajectory of minimization using generalized Born
(Wed Mar 18 2015 - 09:41:43 PDT)
Emilio Angelina
[AMBER] issue with LRT calculation in sander
(Mon Mar 30 2015 - 13:01:18 PDT)
Re: [AMBER] mm-pbsa & extra-point
(Thu Mar 05 2015 - 19:43:23 PST)
Re: [AMBER] mm-pbsa & extra-point
(Thu Mar 05 2015 - 16:21:21 PST)
[AMBER] mm-pbsa & extra-point
(Thu Mar 05 2015 - 13:42:19 PST)
[AMBER] error in MMPBSA.py
(Thu Mar 05 2015 - 03:26:43 PST)
Evans, Shalton
[AMBER] **No Torsion terms
(Tue Mar 17 2015 - 09:28:47 PDT)
[AMBER] ** No torsion terms
(Sun Mar 15 2015 - 17:57:30 PDT)
filip fratev
Re: [AMBER] Replica Exchange on a single Titan-X GPU
(Mon Mar 23 2015 - 12:19:56 PDT)
Re: [AMBER] Replica Exchange on a single Titan-X GPU
(Mon Mar 23 2015 - 08:35:13 PDT)
Re: [AMBER] GTX TITAN X was introduced
(Thu Mar 05 2015 - 00:16:34 PST)
[AMBER] GTX TITAN X was introduced
(Wed Mar 04 2015 - 13:38:54 PST)
Francesca Tessaro
Re: [AMBER] Cofactor parametrization
(Thu Mar 05 2015 - 04:55:06 PST)
Re: [AMBER] Cofactor parametrization
(Mon Mar 02 2015 - 03:08:08 PST)
Francesco Gentile
[AMBER] Reduce not working properly
(Thu Mar 19 2015 - 21:47:14 PDT)
FyD
Re: [AMBER] Multiple MEPs option in R.E.D tools
(Tue Mar 31 2015 - 12:07:43 PDT)
Re: [AMBER] Multiple MEPs option in R.E.D tools
(Tue Mar 31 2015 - 11:44:52 PDT)
[AMBER] flag for fast water
(Sun Mar 29 2015 - 07:54:06 PDT)
Re: [AMBER] Non-Standard Residue / Non-Integer Charge
(Mon Mar 23 2015 - 09:27:28 PDT)
Re: [AMBER] loading molecule in xleap and saving it in mol2 format
(Fri Mar 20 2015 - 03:14:19 PDT)
Re: [AMBER] Non-Standard Residue / Non-Integer Charge
(Thu Mar 19 2015 - 23:58:31 PDT)
Re: [AMBER] Starting antechamber for preparing ligand molecule
(Wed Mar 18 2015 - 06:09:04 PDT)
Re: [AMBER] Non-Standard Residue / Non-Integer Charge
(Wed Mar 18 2015 - 02:07:46 PDT)
Re: [AMBER] facing problem to create a prmtop file for oxonium cation
(Mon Mar 16 2015 - 05:31:01 PDT)
Re: [AMBER] [q4md-fft] Modify RNA's sugar and adding partial charges
(Mon Mar 16 2015 - 00:15:03 PDT)
Re: [AMBER] [q4md-fft] Fwd: D- amino acids in ff10
(Fri Mar 13 2015 - 10:51:42 PDT)
Re: [AMBER] [q4md-fft] Fwd: D- amino acids in ff10
(Fri Mar 13 2015 - 09:51:04 PDT)
Re: [AMBER] D- amino acids in ff10
(Fri Mar 13 2015 - 09:21:03 PDT)
Re: [AMBER] Problem with Creating Unit for Non-standard N-Cap Residue
(Sun Mar 08 2015 - 09:56:43 PDT)
Re: [AMBER] Problem with Creating Unit for Non-standard N-Cap Residue
(Fri Mar 06 2015 - 08:20:06 PST)
Re: [AMBER] Improper torsions in NMA
(Fri Mar 06 2015 - 00:02:49 PST)
Re: [AMBER] Cofactor parametrization
(Thu Mar 05 2015 - 07:43:44 PST)
Re: [AMBER] ATP and ADP-Pi simulations
(Wed Mar 04 2015 - 23:33:12 PST)
Re: [AMBER] ATP and ADP-Pi simulations
(Wed Mar 04 2015 - 00:56:52 PST)
Re: [AMBER] Cofactor parametrization
(Tue Mar 03 2015 - 04:47:26 PST)
Re: [AMBER] Problem with Creating Unit for Non-standard N-Cap Residue
(Tue Mar 03 2015 - 01:31:34 PST)
Re: [AMBER] ATP and ADP-Pi simulations
(Tue Mar 03 2015 - 01:28:50 PST)
Re: [AMBER] Cofactor parametrization
(Tue Mar 03 2015 - 01:18:13 PST)
Re: [AMBER] Error while creating force field
(Tue Mar 03 2015 - 01:15:25 PST)
Garisekurthi Satheesh
[AMBER] Fwd: Regarding the MCPB tutorial
(Mon Mar 23 2015 - 02:41:35 PDT)
George Tzotzos
Re: [AMBER] The unperturbed charge of the unit: -2.980000 is not integral
(Tue Mar 24 2015 - 19:48:08 PDT)
[AMBER] Leap warning
(Fri Mar 20 2015 - 10:55:18 PDT)
Re: [AMBER] sander.MPI error
(Thu Mar 19 2015 - 11:06:41 PDT)
[AMBER] sander.MPI error
(Thu Mar 19 2015 - 11:02:40 PDT)
[AMBER] pmemd.MPI error
(Mon Mar 16 2015 - 13:07:55 PDT)
Re: [AMBER] ante-mmpbsa.py: problem with the mask syntax
(Mon Mar 16 2015 - 12:59:49 PDT)
Re: [AMBER] ante-mmpbsa.py: problem with the mask syntax
(Mon Mar 16 2015 - 12:12:44 PDT)
[AMBER] ante-mmpbsa.py: problem with the mask syntax
(Mon Mar 16 2015 - 10:26:16 PDT)
Re: [AMBER] cpptraj H-bond: clarification sought
(Sat Mar 07 2015 - 15:12:12 PST)
[AMBER] cpptraj H-bond: clarification sought
(Fri Mar 06 2015 - 09:44:55 PST)
Gerald Monard
Re: [AMBER] Problems with Amber installation
(Tue Mar 31 2015 - 07:28:18 PDT)
Re: [AMBER] EGB and ESCF might not be converged if the net charge not equal to 0 in the QM/MM-GBSA
(Fri Mar 27 2015 - 01:27:39 PDT)
GG Smith
Re: [AMBER] Reg: Query on distance restrain and its effect on conformation
(Wed Mar 11 2015 - 22:20:30 PDT)
[AMBER] Reg: Query on distance restrain and its effect on conformation
(Tue Mar 10 2015 - 21:41:18 PDT)
Re: [AMBER] ideal range values for distance restraint b/w 2 non-bonded atoms.
(Sun Mar 08 2015 - 23:02:01 PDT)
Re: [AMBER] ideal range values for distance restraint b/w 2 non-bonded atoms.
(Sat Mar 07 2015 - 05:56:18 PST)
[AMBER] ideal range values for distance restraint b/w 2 non-bonded atoms.
(Sat Mar 07 2015 - 03:22:59 PST)
Glenn Carrington [bs10g3c]
Re: [AMBER] Implicit solvent simulation with Andersen thermostat
(Fri Mar 27 2015 - 04:31:17 PDT)
Re: [AMBER] Implicit solvent simulation with Andersen thermostat
(Thu Mar 26 2015 - 04:59:42 PDT)
[AMBER] Implicit solvent simulation with Andersen thermostat
(Wed Mar 25 2015 - 16:41:38 PDT)
Gustavo Avelar Molina
[AMBER] Amber 14 tests errors
(Wed Mar 18 2015 - 16:34:26 PDT)
Hai Nguyen
Re: [AMBER] Implicit solvent simulation with Andersen thermostat
(Wed Mar 25 2015 - 22:56:16 PDT)
Re: [AMBER] how to use cpptraj for pdb files generated from external software
(Wed Mar 18 2015 - 09:37:58 PDT)
Re: [AMBER] HMR
(Mon Mar 16 2015 - 17:27:31 PDT)
Hannes Loeffler
Re: [AMBER] Error message from FEW in Amber14 tutorial A24
(Mon Mar 23 2015 - 08:51:59 PDT)
Re: [AMBER] Error message from FEW in Amber14 tutorial A24
(Mon Mar 23 2015 - 07:52:14 PDT)
Re: [AMBER] loading molecule in xleap and saving it in mol2 format
(Fri Mar 20 2015 - 08:15:32 PDT)
Re: [AMBER] loading molecule in xleap and saving it in mol2 formatDear
(Fri Mar 20 2015 - 07:14:23 PDT)
Re: [AMBER] loading molecule in xleap and saving it in mol2 format
(Fri Mar 20 2015 - 03:37:29 PDT)
Re: [AMBER] Starting antechamber for preparing ligand molecule
(Wed Mar 18 2015 - 02:15:38 PDT)
Re: [AMBER] diisopropylethylene parameter
(Mon Mar 16 2015 - 03:37:41 PDT)
Re: [AMBER] facing problem to create a prmtop file for oxonium cation
(Mon Mar 16 2015 - 03:32:25 PDT)
Re: [AMBER] leap and centering
(Fri Mar 13 2015 - 09:04:45 PDT)
[AMBER] leap and centering
(Fri Mar 13 2015 - 08:20:35 PDT)
Re: [AMBER] error in antechamber: Bond types are assigned for valence state 1 with penalty of 1
(Fri Mar 13 2015 - 02:59:40 PDT)
Re: [AMBER] Cofactor parametrization
(Thu Mar 05 2015 - 05:34:00 PST)
Re: [AMBER] Error while creating force field
(Tue Mar 03 2015 - 03:59:39 PST)
Re: [AMBER] Error while creating force field
(Tue Mar 03 2015 - 03:55:24 PST)
Re: [AMBER] Cofactor parametrization
(Mon Mar 02 2015 - 03:29:31 PST)
Re: [AMBER] Error while creating force field
(Mon Mar 02 2015 - 02:28:57 PST)
hannes.loeffler.stfc.ac.uk
Re: [AMBER] REGARDING ATOM TYPE ERROR
(Sat Mar 28 2015 - 05:51:45 PDT)
Re: [AMBER] Free energy calculation: Thermodynamic integration with use of restraints
(Fri Mar 27 2015 - 09:30:57 PDT)
Re: [AMBER] Free energy calculation: Thermodynamic integration with use of restraints
(Thu Mar 26 2015 - 09:02:58 PDT)
Re: [AMBER] Antechamber - TURBOMOLE
(Thu Mar 26 2015 - 05:03:54 PDT)
Re: [AMBER] Free energy calculation: Thermodynamic integration with use of restraints
(Thu Mar 26 2015 - 02:20:25 PDT)
Re: [AMBER] Free energy calculation: Thermodynamic integration with use of restraints
(Thu Mar 26 2015 - 00:32:07 PDT)
Re: [AMBER] Free energy calculation: Thermodynamic integration with use of restraints
(Wed Mar 25 2015 - 12:12:34 PDT)
Re: [AMBER] Error message from FEW in Amber14 tutorial A24
(Mon Mar 23 2015 - 12:05:52 PDT)
Re: [AMBER] loading molecule in xleap and saving it in mol2 format
(Fri Mar 20 2015 - 01:01:48 PDT)
Re: [AMBER] leap and centering
(Sun Mar 15 2015 - 01:52:02 PDT)
Re: [AMBER] Inability to use antechamber on Anion
(Fri Mar 06 2015 - 23:50:52 PST)
Harshala Haldankar
[AMBER] Problem in protonating.
(Fri Mar 13 2015 - 04:16:02 PDT)
[AMBER] Problem in capping ACE and NME.
(Mon Mar 02 2015 - 22:13:19 PST)
Hector A. Baldoni
[AMBER] combinatorial library
(Thu Mar 26 2015 - 17:22:05 PDT)
Him Shweta
Re: [AMBER] Dielectric constant for dna-ligand in TIP3P system
(Wed Mar 18 2015 - 03:09:10 PDT)
[AMBER] Dielectric constant for dna-ligand in TIP3P system
(Tue Mar 17 2015 - 07:49:59 PDT)
[AMBER] Dielectric constant for dna-ligand in TIP3P system
(Tue Mar 17 2015 - 07:45:13 PDT)
Himanshu Joshi
[AMBER] AMBER14 pmemd.cuda.MPI : *** in mdout files
(Tue Mar 31 2015 - 10:58:51 PDT)
Re: [AMBER] Sudden RMSD blow-up in trajectory analysis
(Tue Mar 10 2015 - 03:27:56 PDT)
Huang Tao
Re: [AMBER] Problem with Creating Unit for Non-standard N-Cap Residue
(Sun Mar 08 2015 - 00:59:24 PST)
Re: [AMBER] Problem with Creating Unit for Non-standard N-Cap Residue
(Fri Mar 06 2015 - 00:26:24 PST)
[AMBER] Problem with Creating Unit for Non-standard N-Cap Residue
(Mon Mar 02 2015 - 17:33:51 PST)
Ibrahim Said
Re: [AMBER] unfolding protein and solvent density
(Tue Mar 17 2015 - 03:54:10 PDT)
[AMBER] unfolding protein and solvent density
(Tue Mar 17 2015 - 02:32:03 PDT)
jacob wick
Re: [AMBER] loading molecule in xleap and saving it in mol2 format
(Fri Mar 20 2015 - 08:09:50 PDT)
Re: [AMBER] loading molecule in xleap and saving it in mol2 formatDear
(Fri Mar 20 2015 - 07:27:21 PDT)
Re: [AMBER] loading molecule in xleap and saving it in mol2 format
(Fri Mar 20 2015 - 04:01:49 PDT)
Re: [AMBER] Backbone Rmsd
(Fri Mar 20 2015 - 03:03:43 PDT)
[AMBER] loading molecule in xleap and saving it in mol2 format
(Fri Mar 20 2015 - 00:17:05 PDT)
[AMBER] Backbone Rmsd
(Tue Mar 17 2015 - 03:17:46 PDT)
[AMBER] RNA's sugar modification
(Sun Mar 15 2015 - 11:05:20 PDT)
Re: [AMBER] Predefined number of water molecules in waterbox
(Fri Mar 13 2015 - 22:20:38 PDT)
[AMBER] Predefined number of water molecules in waterbox
(Thu Mar 12 2015 - 22:17:44 PDT)
Re: [AMBER] RNA Simulation
(Thu Mar 12 2015 - 22:17:12 PDT)
[AMBER] RNA Simulation
(Thu Mar 12 2015 - 11:28:59 PDT)
Jacopo Sgrignani
Re: [AMBER] NetCDF AMBER file corrupted
(Thu Mar 19 2015 - 08:46:36 PDT)
[AMBER] NetCDF AMBER file corrupted
(Thu Mar 19 2015 - 07:20:09 PDT)
James Starlight
Re: [AMBER] Restrained MD
(Tue Mar 31 2015 - 07:03:34 PDT)
Re: [AMBER] Restrained MD
(Tue Mar 31 2015 - 05:09:02 PDT)
Re: [AMBER] Restrained MD
(Tue Mar 31 2015 - 04:58:59 PDT)
Re: [AMBER] Histogram analysis of the dihedral distributions using cpptraj
(Mon Mar 30 2015 - 06:02:18 PDT)
Re: [AMBER] Restrained MD
(Mon Mar 30 2015 - 05:38:46 PDT)
Re: [AMBER] Histogram analysis of the dihedral distributions using cpptraj
(Mon Mar 30 2015 - 03:52:48 PDT)
[AMBER] Restrained MD
(Sun Mar 29 2015 - 03:50:31 PDT)
Re: [AMBER] Histogram analysis of the dihedral distributions using cpptraj
(Fri Mar 27 2015 - 09:28:07 PDT)
[AMBER] Histogram analysis of the dihedral distributions using cpptraj
(Fri Mar 27 2015 - 08:13:10 PDT)
Re: [AMBER] On the clustering of the ligand position within the cavity
(Thu Mar 19 2015 - 09:30:57 PDT)
[AMBER] On the clustering of the ligand position within the cavity
(Thu Mar 19 2015 - 08:50:12 PDT)
Re: [AMBER] Decomposition of the MMGBSA based on multi trajectory input
(Mon Mar 16 2015 - 06:42:16 PDT)
Re: [AMBER] Decomposition of the MMGBSA based on multi trajectory input
(Mon Mar 16 2015 - 06:00:19 PDT)
Re: [AMBER] Decomposition of the MMGBSA based on multi trajectory input
(Thu Mar 05 2015 - 03:39:16 PST)
Re: [AMBER] Decomposition of the MMGBSA based on multi trajectory input
(Thu Mar 05 2015 - 02:45:02 PST)
Re: [AMBER] Decomposition of the MMGBSA based on multi trajectory input
(Wed Mar 04 2015 - 06:48:34 PST)
Re: [AMBER] Decomposition of the MMGBSA based on multi trajectory input
(Wed Mar 04 2015 - 06:10:46 PST)
[AMBER] Decomposition of the MMGBSA based on multi trajectory input
(Tue Mar 03 2015 - 03:58:44 PST)
Jason Swails
Re: [AMBER] Multiple MEPs option in R.E.D tools
(Tue Mar 31 2015 - 13:53:52 PDT)
Re: [AMBER] Problems with Amber installation
(Tue Mar 31 2015 - 08:40:14 PDT)
Re: [AMBER] temp ramping in tutorial A5
(Tue Mar 31 2015 - 07:38:38 PDT)
Re: [AMBER] temp ramping in tutorial A5
(Tue Mar 31 2015 - 05:11:41 PDT)
Re: [AMBER] Multiple MEPs option in R.E.D tools
(Tue Mar 31 2015 - 05:07:41 PDT)
Re: [AMBER] Stability MMPBSA
(Tue Mar 31 2015 - 05:05:52 PDT)
Re: [AMBER] Manual still ambiguous about igb=8 and pmemd
(Mon Mar 30 2015 - 09:39:55 PDT)
Re: [AMBER] How to obtain potential energy using mdcrd trajectories in AMBER12
(Mon Mar 30 2015 - 08:34:08 PDT)
Re: [AMBER] Problem Regarding Different PMF Graph
(Mon Mar 30 2015 - 05:41:21 PDT)
Re: [AMBER] flag for fast water
(Mon Mar 30 2015 - 05:27:04 PDT)
Re: [AMBER] Error: Unable to run flex; this is required for NAB and antechamber Please check your PATH, or install the program
(Sat Mar 28 2015 - 11:51:53 PDT)
Re: [AMBER] MMPBSA error
(Fri Mar 27 2015 - 10:56:03 PDT)
Re: [AMBER] Implicit solvent simulation with Andersen thermostat
(Fri Mar 27 2015 - 04:43:16 PDT)
Re: [AMBER] trouble running pmemd.cuda
(Thu Mar 26 2015 - 11:14:57 PDT)
Re: [AMBER] trouble running pmemd.cuda
(Thu Mar 26 2015 - 10:17:07 PDT)
Re: [AMBER] trouble running pmemd.cuda
(Thu Mar 26 2015 - 09:46:51 PDT)
Re: [AMBER] trouble running pmemd.cuda
(Thu Mar 26 2015 - 08:07:05 PDT)
Re: [AMBER] vdw energy and electrostatic energy calculation for osmolyte
(Thu Mar 26 2015 - 07:29:28 PDT)
Re: [AMBER] Implicit solvent simulation with Andersen thermostat
(Thu Mar 26 2015 - 07:25:55 PDT)
Re: [AMBER] Implicit solvent simulation with Andersen thermostat
(Wed Mar 25 2015 - 19:06:18 PDT)
Re: [AMBER] trouble running pmemd.cuda
(Wed Mar 25 2015 - 11:49:52 PDT)
Re: [AMBER] vdw energy and electrostatic energy calculation for osmolyte
(Wed Mar 25 2015 - 11:47:02 PDT)
Re: [AMBER] iterative calculation in CPPTRAJ using "for... do... done"
(Wed Mar 25 2015 - 06:52:06 PDT)
Re: [AMBER] vdw energy and electrostatic energy calculation for osmolyte
(Wed Mar 25 2015 - 05:14:00 PDT)
Re: [AMBER] The unperturbed charge of the unit: -2.980000 is not integral
(Tue Mar 24 2015 - 19:06:34 PDT)
Re: [AMBER] CpHMD-pHREX AMBER14
(Tue Mar 24 2015 - 18:36:02 PDT)
Re: [AMBER] About generalized restraints in AMBER14 with GPU support
(Tue Mar 24 2015 - 07:48:46 PDT)
Re: [AMBER] vdw energy and electrostatic energy calculation for osmolyte
(Tue Mar 24 2015 - 06:55:54 PDT)
Re: [AMBER] Error message from FEW in Amber14 tutorial A24
(Mon Mar 23 2015 - 13:24:57 PDT)
Re: [AMBER] trajectory of minimization using generalized Born
(Mon Mar 23 2015 - 11:36:20 PDT)
Re: [AMBER] Error message from FEW in Amber14 tutorial A24
(Mon Mar 23 2015 - 08:17:31 PDT)
Re: [AMBER] Error message from FEW in Amber14 tutorial A24
(Mon Mar 23 2015 - 07:41:10 PDT)
Re: [AMBER] "Error opening unit 30: File "inpcrd" is missing or unreadable" on Tutorial A15
(Mon Mar 23 2015 - 02:33:58 PDT)
Re: [AMBER] Error message from FEW in Amber14 tutorial A24
(Sun Mar 22 2015 - 13:22:37 PDT)
Re: [AMBER] Backbone Rmsd
(Fri Mar 20 2015 - 18:26:32 PDT)
Re: [AMBER] trajectory of minimization using generalized Born
(Fri Mar 20 2015 - 12:49:50 PDT)
Re: [AMBER] error with mmpbsa.py
(Fri Mar 20 2015 - 09:23:29 PDT)
Re: [AMBER] Drifting molecules despite strong restraints
(Fri Mar 20 2015 - 08:23:15 PDT)
Re: [AMBER] trajectory of minimization using generalized Born
(Fri Mar 20 2015 - 06:23:50 PDT)
Re: [AMBER] trajectory of minimization using generalized Born
(Fri Mar 20 2015 - 05:29:03 PDT)
Re: [AMBER] post processing temperature replica exchange trajectories
(Fri Mar 20 2015 - 05:24:02 PDT)
Re: [AMBER] Drifting molecules despite strong restraints
(Fri Mar 20 2015 - 05:22:03 PDT)
Re: [AMBER] | ERROR: PMEMD does not support intermolecular PRFs!
(Fri Mar 20 2015 - 05:06:49 PDT)
Re: [AMBER] | ERROR: PMEMD does not support intermolecular PRFs!
(Thu Mar 19 2015 - 11:34:33 PDT)
Re: [AMBER] sander.MPI error
(Thu Mar 19 2015 - 11:13:52 PDT)
Re: [AMBER] NetCDF AMBER file corrupted
(Thu Mar 19 2015 - 08:26:55 PDT)
Re: [AMBER] trajectory of minimization using generalized Born
(Wed Mar 18 2015 - 14:03:42 PDT)
Re: [AMBER] CHAMBER and CMAP difficulty
(Wed Mar 18 2015 - 09:50:17 PDT)
Re: [AMBER] CHAMBER and CMAP difficulty
(Wed Mar 18 2015 - 09:03:47 PDT)
Re: [AMBER] CHAMBER and CMAP difficulty
(Wed Mar 18 2015 - 08:36:33 PDT)
Re: [AMBER] CHAMBER and CMAP difficulty
(Wed Mar 18 2015 - 08:14:29 PDT)
Re: [AMBER] Nuclicacid forcefield in AMBER
(Wed Mar 18 2015 - 04:54:59 PDT)
Re: [AMBER] PMF for dimer dissociation
(Tue Mar 17 2015 - 19:33:44 PDT)
Re: [AMBER] MMGBSA pairwise decomposition - differences in Non-Polar Solv. & TOTAL for same residue pairs
(Tue Mar 17 2015 - 19:25:47 PDT)
Re: [AMBER] topology file, segment id and the pathways plugin
(Tue Mar 17 2015 - 13:54:18 PDT)
Re: [AMBER] Amber on Red Hat?
(Tue Mar 17 2015 - 12:36:37 PDT)
Re: [AMBER] Dielectric constant for dna-ligand in TIP3P system
(Tue Mar 17 2015 - 08:15:01 PDT)
Re: [AMBER] finding angles
(Tue Mar 17 2015 - 07:23:33 PDT)
Re: [AMBER] unfolding protein and solvent density
(Tue Mar 17 2015 - 06:05:21 PDT)
Re: [AMBER] About TIP4-Ew water model usage
(Tue Mar 17 2015 - 05:53:54 PDT)
Re: [AMBER] Per-residue decomposition energy MMGBSA.py
(Tue Mar 17 2015 - 05:45:47 PDT)
Re: [AMBER] script to convert the Gromacs topology to Amber topology?
(Tue Mar 17 2015 - 05:39:36 PDT)
Re: [AMBER] Using WHAM to get 3D free energy surface in AMBER12
(Mon Mar 16 2015 - 18:44:53 PDT)
Re: [AMBER] finding angles
(Mon Mar 16 2015 - 17:23:18 PDT)
Re: [AMBER] ante-mmpbsa.py: problem with the mask syntax
(Mon Mar 16 2015 - 12:18:13 PDT)
Re: [AMBER] ante-mmpbsa.py: problem with the mask syntax
(Mon Mar 16 2015 - 11:37:47 PDT)
Re: [AMBER] finding angles
(Mon Mar 16 2015 - 10:53:12 PDT)
Re: [AMBER] Per-residue decomposition energy MMGBSA.py
(Mon Mar 16 2015 - 07:26:57 PDT)
Re: [AMBER] organic molecule
(Mon Mar 16 2015 - 07:15:59 PDT)
Re: [AMBER] Using WHAM to get 3D free energy surface in AMBER12
(Mon Mar 16 2015 - 05:19:18 PDT)
Re: [AMBER] set command and VMD
(Sat Mar 14 2015 - 18:16:02 PDT)
Re: [AMBER] 10-12 Potentials, HBOND
(Sat Mar 14 2015 - 16:12:10 PDT)
Re: [AMBER] Unable to load OLS OLT NLN in tleap (AmberTools14)
(Sat Mar 14 2015 - 08:56:22 PDT)
Re: [AMBER] Errors in AmberTools14
(Fri Mar 13 2015 - 13:32:13 PDT)
Re: [AMBER] Errors in AmberTools14
(Fri Mar 13 2015 - 12:27:36 PDT)
Re: [AMBER] Errors in AmberTools14
(Fri Mar 13 2015 - 12:21:24 PDT)
Re: [AMBER] Errors in AmberTools14
(Fri Mar 13 2015 - 11:14:58 PDT)
Re: [AMBER] Problem in protonating.
(Fri Mar 13 2015 - 05:14:42 PDT)
Re: [AMBER] mmpbsa conflict with Ca2+ ?
(Thu Mar 12 2015 - 05:32:59 PDT)
Re: [AMBER] mmpbsa conflict with Ca2+ ?
(Wed Mar 11 2015 - 09:21:45 PDT)
Re: [AMBER] Truncated octahedron
(Wed Mar 11 2015 - 09:19:03 PDT)
Re: [AMBER] Truncated octahedron
(Wed Mar 11 2015 - 09:06:19 PDT)
Re: [AMBER] Reg: Query on distance restrain and its effect on conformation
(Wed Mar 11 2015 - 08:41:12 PDT)
Re: [AMBER] PCA_representation_in_Cpptraj
(Wed Mar 11 2015 - 07:30:22 PDT)
Re: [AMBER] help in getting 3D isodensity surface
(Wed Mar 11 2015 - 07:15:52 PDT)
Re: [AMBER] Lipid14 POPE lipids
(Tue Mar 10 2015 - 11:06:49 PDT)
Re: [AMBER] PCA_representation_in_Cpptraj
(Tue Mar 10 2015 - 07:15:20 PDT)
Re: [AMBER] Tutorial B0
(Mon Mar 09 2015 - 19:10:12 PDT)
Re: [AMBER] PCA_representation_in_Cpptraj
(Mon Mar 09 2015 - 05:52:07 PDT)
Re: [AMBER] free energy plot
(Sun Mar 08 2015 - 18:44:13 PDT)
Re: [AMBER] General question about MM-PB(GB)SA
(Sun Mar 08 2015 - 18:40:24 PDT)
Re: [AMBER] ideal range values for distance restraint b/w 2 non-bonded atoms.
(Sat Mar 07 2015 - 04:30:39 PST)
Re: [AMBER] General question about MM-PB(GB)SA
(Sat Mar 07 2015 - 04:25:14 PST)
Re: [AMBER] ERROR: max pairlist cutoff must be less than unit cell max sphere radius!
(Fri Mar 06 2015 - 11:22:16 PST)
Re: [AMBER] Error: Unable to run flex; this is required for NAB and antechamber Please check your PATH, or install the program
(Fri Mar 06 2015 - 07:28:14 PST)
Re: [AMBER] a question on molecular dynamics simulation
(Fri Mar 06 2015 - 07:03:48 PST)
Re: [AMBER] mm-pbsa & extra-point
(Thu Mar 05 2015 - 17:36:04 PST)
Re: [AMBER] mm-pbsa & extra-point
(Thu Mar 05 2015 - 14:38:29 PST)
Re: [AMBER] Tutorial B0
(Wed Mar 04 2015 - 13:33:11 PST)
Re: [AMBER] Tutorial B0
(Wed Mar 04 2015 - 13:32:49 PST)
Re: [AMBER] Targeted MD shows blank output file!
(Wed Mar 04 2015 - 05:12:47 PST)
Re: [AMBER] Tutorial B0
(Wed Mar 04 2015 - 04:58:59 PST)
Re: [AMBER] Targeted MD shows blank output file!
(Wed Mar 04 2015 - 04:53:05 PST)
Re: [AMBER] How to calculate interaction energy between any two residues of one protein
(Wed Mar 04 2015 - 04:45:32 PST)
Re: [AMBER] Param PROC does not exist --- MM-PBSA problem
(Wed Mar 04 2015 - 04:43:11 PST)
Re: [AMBER] Problem in calculation per residue free energy decomposition
(Tue Mar 03 2015 - 05:53:42 PST)
Re: [AMBER] Problem in capping ACE and NME.
(Tue Mar 03 2015 - 05:27:54 PST)
Re: [AMBER] Chamber problem
(Mon Mar 02 2015 - 12:07:38 PST)
Re: [AMBER] using internal geometry
(Mon Mar 02 2015 - 10:35:10 PST)
Re: [AMBER] tleap box neutralization
(Mon Mar 02 2015 - 05:55:57 PST)
Re: [AMBER] COM restrain support in Amber14
(Mon Mar 02 2015 - 05:36:05 PST)
Re: [AMBER] Fwd: help in sdf
(Sun Mar 01 2015 - 07:47:50 PST)
Jennifer Vo
[AMBER] diisopropylethylene parameter
(Mon Mar 16 2015 - 03:06:47 PDT)
Jinfeng Huang
Re: [AMBER] mmpbsa conflict with Ca2+ ?
(Thu Mar 12 2015 - 01:31:01 PDT)
Re: [AMBER] mmpbsa conflict with Ca2+ ?
(Wed Mar 11 2015 - 19:35:09 PDT)
[AMBER] mmpbsa conflict with Ca2+ ?
(Wed Mar 11 2015 - 07:52:10 PDT)
Jiri Sponer
Re: [AMBER] Differences in AMBER force fields
(Fri Mar 20 2015 - 09:03:07 PDT)
Re: [AMBER] RNA Simulation
(Thu Mar 12 2015 - 12:28:48 PDT)
Re: [AMBER] RNA Simulation
(Thu Mar 12 2015 - 12:16:10 PDT)
Jonathan Gough
Re: [AMBER] Errors in AmberTools14
(Fri Mar 13 2015 - 12:28:53 PDT)
Re: [AMBER] Errors in AmberTools14
(Fri Mar 13 2015 - 12:27:23 PDT)
Re: [AMBER] Errors in AmberTools14
(Fri Mar 13 2015 - 11:31:49 PDT)
Re: [AMBER] Errors in AmberTools14
(Fri Mar 13 2015 - 10:54:38 PDT)
[AMBER] Errors in AmberTools14
(Fri Mar 13 2015 - 10:52:33 PDT)
Jordan Graziadei
Re: [AMBER] ERROR: max pairlist cutoff must be less than unit cell max sphere radius!
(Thu Mar 12 2015 - 09:33:19 PDT)
Re: [AMBER] ERROR: max pairlist cutoff must be less than unit cell max sphere radius!
(Fri Mar 06 2015 - 11:11:54 PST)
[AMBER] ERROR: max pairlist cutoff must be less than unit cell max sphere radius!
(Mon Mar 02 2015 - 14:01:41 PST)
Jorgen Simonsen
Re: [AMBER] | ERROR: PMEMD does not support intermolecular PRFs!
(Thu Mar 19 2015 - 15:12:50 PDT)
Re: [AMBER] | ERROR: PMEMD does not support intermolecular PRFs!
(Thu Mar 19 2015 - 12:51:16 PDT)
Re: [AMBER] | ERROR: PMEMD does not support intermolecular PRFs!
(Thu Mar 19 2015 - 12:31:19 PDT)
[AMBER] | ERROR: PMEMD does not support intermolecular PRFs!
(Thu Mar 19 2015 - 11:15:30 PDT)
Josep Maria Campanera Alsina
Re: [AMBER] script to convert the Gromacs topology to Amber topology?
(Tue Mar 17 2015 - 02:57:59 PDT)
Joseph Baker
Re: [AMBER] Lipid14 POPE lipids
(Tue Mar 10 2015 - 10:08:57 PDT)
Re: [AMBER] ATP and ADP-Pi simulations
(Wed Mar 04 2015 - 21:38:33 PST)
Re: [AMBER] ATP and ADP-Pi simulations
(Tue Mar 03 2015 - 21:36:07 PST)
Re: [AMBER] ATP and ADP-Pi simulations
(Mon Mar 02 2015 - 20:05:25 PST)
[AMBER] ATP and ADP-Pi simulations
(Mon Mar 02 2015 - 13:04:45 PST)
Juan Eiros Zamora
Re: [AMBER] PCA_representation_in_Cpptraj
(Wed Mar 11 2015 - 05:52:48 PDT)
Re: [AMBER] PCA_representation_in_Cpptraj
(Tue Mar 10 2015 - 04:37:50 PDT)
Karl Kirschner
Re: [AMBER] Gromacs towards Amber conversion
(Sun Mar 29 2015 - 03:12:51 PDT)
Kenneth Huang
Re: [AMBER] Stability MMPBSA
(Mon Mar 30 2015 - 19:47:59 PDT)
Re: [AMBER] MMPBSA error
(Fri Mar 27 2015 - 15:49:25 PDT)
[AMBER] MMGBSA error
(Thu Mar 26 2015 - 05:55:35 PDT)
Re: [AMBER] error with mmpbsa.py
(Fri Mar 20 2015 - 09:21:05 PDT)
Re: [AMBER] On the clustering of the ligand position within the cavity
(Thu Mar 19 2015 - 10:23:21 PDT)
Re: [AMBER] ante-mmpbsa.py: problem with the mask syntax
(Mon Mar 16 2015 - 11:21:13 PDT)
Kshatresh Dutta Dubey
[AMBER] Help regarding appropriate analysis for correlated motion using cpptraj
(Mon Mar 30 2015 - 12:44:39 PDT)
Lachele Foley
Re: [AMBER] Unable to load OLS OLT NLN in tleap (AmberTools14)
(Sat Mar 14 2015 - 12:36:06 PDT)
Re: [AMBER] Unable to load OLS OLT NLN in tleap (AmberTools14)
(Fri Mar 13 2015 - 17:40:33 PDT)
Re: [AMBER] force field parameter for fructose 1 6 bisphosphate
(Sat Mar 07 2015 - 22:23:35 PST)
Lara rajam
[AMBER] organic molecule
(Mon Mar 16 2015 - 06:45:47 PDT)
Mahendra B Thapa
Re: [AMBER] FW: how to use cpptraj for pdb files generated from external software
(Wed Mar 18 2015 - 09:57:18 PDT)
[AMBER] how to use cpptraj for pdb files generated from external software
(Wed Mar 18 2015 - 09:34:29 PDT)
Mahmood Jasim
[AMBER] SMD average work
(Tue Mar 03 2015 - 07:58:09 PST)
Maksim Mišin
Re: [AMBER] Pressure units in 1D-RISM
(Tue Mar 31 2015 - 10:25:28 PDT)
[AMBER] Pressure units in 1D-RISM
(Tue Mar 31 2015 - 07:27:00 PDT)
Maral Aminpour
Re: [AMBER] Non-Standard Residue / Non-Integer Charge
(Fri Mar 20 2015 - 19:27:15 PDT)
Re: [AMBER] Non-Standard Residue / Non-Integer Charge
(Fri Mar 20 2015 - 10:51:14 PDT)
Re: [AMBER] Non-Standard Residue / Non-Integer Charge
(Thu Mar 19 2015 - 12:35:39 PDT)
[AMBER] Non-Standard Residue / Non-Integer Charge
(Tue Mar 17 2015 - 14:09:50 PDT)
Marawan Hussien
[AMBER] Immediate Postdoctoral Position Opening In Dr. Khaled Barakat’s Lab, Faculty Of Pharmacy, University Of Alberta
(Sun Mar 22 2015 - 14:01:11 PDT)
Mary Varughese
Re: [AMBER] clustering in ptraj
(Tue Mar 10 2015 - 08:12:32 PDT)
Re: [AMBER] clustering in ptraj
(Mon Mar 09 2015 - 10:39:33 PDT)
[AMBER] clustering in ptraj
(Sun Mar 08 2015 - 23:48:43 PDT)
maryam azimzadehirani
Re: [AMBER] Per-residue decomposition energy MMGBSA.py
(Mon Mar 16 2015 - 20:52:58 PDT)
[AMBER] Per-residue decomposition energy MMGBSA.py
(Mon Mar 16 2015 - 06:49:12 PDT)
[AMBER] Problem in calculation per residue free energy decomposition
(Tue Mar 03 2015 - 02:04:42 PST)
Michael Shokhen
Re: [AMBER] Error message from FEW in Amber14 tutorial A24
(Mon Mar 23 2015 - 04:57:50 PDT)
[AMBER] Error message from FEW in Amber14 tutorial A24
(Sun Mar 22 2015 - 06:44:30 PDT)
Michele Bonus
Re: [AMBER] Error message from FEW in Amber14 tutorial A24
(Sun Mar 22 2015 - 11:19:28 PDT)
Re: [AMBER] Predefined number of water molecules in waterbox
(Thu Mar 12 2015 - 23:12:20 PDT)
mish
Re: [AMBER] Nuclicacid forcefield in AMBER
(Tue Mar 17 2015 - 09:27:54 PDT)
[AMBER] Nuclicacid forcefield in AMBER
(Sun Mar 15 2015 - 12:12:49 PDT)
MOHD HOMAIDUR RAHMAN
[AMBER] vdw energy and electrostatic energy calculation for osmolyte
(Wed Mar 25 2015 - 22:59:40 PDT)
N.R. Jena
[AMBER] Fwd: [Fwd: Purchase of Amber-14]
(Sat Mar 14 2015 - 12:14:23 PDT)
Neha Gandhi
[AMBER] D- amino acids in ff10
(Wed Mar 11 2015 - 06:45:07 PDT)
newamber list
Re: [AMBER] using internal geometry
(Mon Mar 02 2015 - 11:34:11 PST)
[AMBER] using internal geometry
(Mon Mar 02 2015 - 10:07:47 PST)
Nhai
Re: [AMBER] Nuclicacid forcefield in AMBER
(Wed Mar 18 2015 - 08:20:35 PDT)
Re: [AMBER] on the force field
(Sat Mar 07 2015 - 20:57:52 PST)
Norbert GARNIER
Re: [AMBER] error with mmpbsa.py
(Fri Mar 20 2015 - 10:08:52 PDT)
[AMBER] error with mmpbsa.py
(Fri Mar 20 2015 - 08:32:24 PDT)
Novosielski, Ryan
Re: [AMBER] Intel Compiler and MKL
(Fri Mar 27 2015 - 13:39:16 PDT)
[AMBER] Intel Compiler and MKL
(Fri Mar 27 2015 - 11:03:32 PDT)
Pallavi Mohanty
Re: [AMBER] Targeted MD shows blank output file!
(Wed Mar 04 2015 - 22:10:50 PST)
Re: [AMBER] Targeted MD shows blank output file!
(Wed Mar 04 2015 - 05:05:07 PST)
Re: [AMBER] Targeted MD shows blank output file!
(Wed Mar 04 2015 - 04:21:32 PST)
[AMBER] Targeted MD shows blank output file!
(Wed Mar 04 2015 - 02:44:22 PST)
Paolo Tosco
[AMBER] Water sigma parameters
(Thu Mar 26 2015 - 13:16:44 PDT)
Parker de Waal
Re: [AMBER] Stability MMPBSA
(Mon Mar 30 2015 - 19:47:00 PDT)
[AMBER] Stability MMPBSA
(Mon Mar 30 2015 - 18:44:20 PDT)
Re: [AMBER] HMR
(Mon Mar 16 2015 - 15:28:05 PDT)
Pedro Swagger
Re: [AMBER] Unable to load OLS OLT NLN in tleap (AmberTools14)
(Sat Mar 14 2015 - 08:04:09 PDT)
[AMBER] Unable to load OLS OLT NLN in tleap (AmberTools14)
(Fri Mar 13 2015 - 17:28:43 PDT)
Petr Jurecka
Re: [AMBER] Differences in AMBER force fields
(Tue Mar 17 2015 - 10:47:57 PDT)
Pinchas Aped
Re: [AMBER] Problems with Amber installation
(Tue Mar 31 2015 - 08:07:09 PDT)
[AMBER] Problems with Amber installation
(Tue Mar 31 2015 - 06:45:53 PDT)
Pragya Priyadarshini
[AMBER] ERROR no map function for FE2 FE2 :data= 91 CYS SG 170 FE2 FE2 2.4
(Mon Mar 02 2015 - 03:37:48 PST)
psu4.uic.edu
[AMBER] EGB and ESCF might not be converged if the net charge not equal to 0 in the QM/MM-GBSA
(Tue Mar 24 2015 - 10:06:49 PDT)
Rebeca García Fandiño
[AMBER] error in antechamber: Bond types are assigned for valence state 1 with penalty of 1
(Fri Mar 13 2015 - 02:24:20 PDT)
Robert Molt
[AMBER] Syntax Confusion on Radial Command
(Sun Mar 08 2015 - 14:55:59 PDT)
Re: [AMBER] Inability to use antechamber on Anion
(Fri Mar 06 2015 - 17:43:23 PST)
Robert Wohlhueter
Re: [AMBER] temp ramping in tutorial A5
(Tue Mar 31 2015 - 13:22:30 PDT)
Re: [AMBER] temp ramping in tutorial A5
(Tue Mar 31 2015 - 06:52:12 PDT)
[AMBER] temp ramping in tutorial A5
(Mon Mar 30 2015 - 15:33:31 PDT)
Robin Jain
[AMBER] help in hbond analysis
(Tue Mar 17 2015 - 23:26:35 PDT)
[AMBER] help in getting 3D isodensity surface
(Wed Mar 11 2015 - 01:09:48 PDT)
[AMBER] Fwd: help in sdf
(Sun Mar 01 2015 - 06:40:44 PST)
Ross Walker
Re: [AMBER] AMBER14 pmemd.cuda.MPI : *** in mdout files
(Tue Mar 31 2015 - 23:33:34 PDT)
Re: [AMBER] AMBER14 pmemd.cuda.MPI : *** in mdout files
(Tue Mar 31 2015 - 20:39:06 PDT)
Re: [AMBER] AMBER14 pmemd.cuda.MPI : *** in mdout files
(Tue Mar 31 2015 - 11:06:19 PDT)
Re: [AMBER] trouble running pmemd.cuda
(Thu Mar 26 2015 - 10:17:54 PDT)
Re: [AMBER] Implicit solvent simulation with Andersen thermostat
(Thu Mar 26 2015 - 08:57:17 PDT)
Re: [AMBER] Implicit solvent simulation with Andersen thermostat
(Thu Mar 26 2015 - 08:54:14 PDT)
Re: [AMBER] trouble running pmemd.cuda
(Thu Mar 26 2015 - 08:49:53 PDT)
Re: [AMBER] trouble running pmemd.cuda
(Wed Mar 25 2015 - 10:41:27 PDT)
Re: [AMBER] Replica Exchange on a single Titan-X GPU
(Mon Mar 23 2015 - 11:28:30 PDT)
Re: [AMBER] Replica Exchange on a single Titan-X GPU
(Mon Mar 23 2015 - 10:01:04 PDT)
Re: [AMBER] CUDA problems
(Mon Mar 23 2015 - 09:52:29 PDT)
Re: [AMBER] Problem with heating lipid bilayer in amber 12
(Thu Mar 19 2015 - 14:49:30 PDT)
[AMBER] Invitation to Computational Chemical Biology Conference (Aug 6th to 9th 2015), Cairns, Australia (http://tinyurl.com/nyblv7o)
(Sun Mar 08 2015 - 18:14:45 PDT)
Re: [AMBER] GTX TITAN X was introduced
(Wed Mar 04 2015 - 18:19:18 PST)
Saikat Dutta chowdhury
Re: [AMBER] About TIP4-Ew water model usage
(Thu Mar 19 2015 - 01:25:35 PDT)
Re: [AMBER] About TIP4-Ew water model usage
(Tue Mar 17 2015 - 23:47:16 PDT)
[AMBER] About TIP4-Ew water model usage
(Tue Mar 17 2015 - 03:31:56 PDT)
Sandeep Somani
Re: [AMBER] post processing temperature replica exchange trajectories
(Fri Mar 20 2015 - 04:42:42 PDT)
[AMBER] post processing temperature replica exchange trajectories
(Thu Mar 19 2015 - 13:00:49 PDT)
Sanja Zivanovic
[AMBER] Antechamber - TURBOMOLE
(Thu Mar 26 2015 - 04:48:26 PDT)
Sanmeet Chahal
Re: [AMBER] Drifting molecules despite strong restraints
(Fri Mar 20 2015 - 07:18:19 PDT)
[AMBER] Drifting molecules despite strong restraints
(Thu Mar 19 2015 - 15:32:42 PDT)
Re: [AMBER] PMF for dimer dissociation
(Tue Mar 17 2015 - 19:04:53 PDT)
[AMBER] PMF for dimer dissociation
(Tue Mar 17 2015 - 14:18:33 PDT)
Re: [AMBER] Tutorial B0
(Mon Mar 09 2015 - 14:11:17 PDT)
Re: [AMBER] Reading two units from same .mol2 file
(Mon Mar 09 2015 - 07:44:36 PDT)
[AMBER] Reading two units from same .mol2 file
(Fri Mar 06 2015 - 17:16:10 PST)
Re: [AMBER] Tutorial B0
(Fri Mar 06 2015 - 16:06:18 PST)
Re: [AMBER] Tutorial B0
(Fri Mar 06 2015 - 13:25:27 PST)
Re: [AMBER] Tutorial B0
(Wed Mar 04 2015 - 13:32:28 PST)
Re: [AMBER] Tutorial B0
(Wed Mar 04 2015 - 13:29:24 PST)
Re: [AMBER] Tutorial B0
(Wed Mar 04 2015 - 08:49:48 PST)
Re: [AMBER] Tutorial B0
(Wed Mar 04 2015 - 08:47:02 PST)
Re: [AMBER] Tutorial B0
(Wed Mar 04 2015 - 08:44:43 PST)
Re: [AMBER] Tutorial B0
(Wed Mar 04 2015 - 08:34:51 PST)
[AMBER] Tutorial B0
(Tue Mar 03 2015 - 15:05:57 PST)
Scott Brozell
Re: [AMBER] Intel Compiler and MKL
(Fri Mar 27 2015 - 14:14:22 PDT)
Re: [AMBER] Intel Compiler and MKL
(Fri Mar 27 2015 - 13:04:44 PDT)
Sergio Decherchi
Re: [AMBER] tleap box neutralization
(Mon Mar 02 2015 - 06:01:28 PST)
[AMBER] tleap box neutralization
(Mon Mar 02 2015 - 01:13:58 PST)
shahab shariati
[AMBER] RMSF & changes of the secondary structure of protein
(Mon Mar 23 2015 - 11:45:41 PDT)
Shoresh Shafei
[AMBER] topology file, segment id and the pathways plugin
(Tue Mar 17 2015 - 13:33:32 PDT)
Shubhadip Das
[AMBER] Problem Regarding Different PMF Graphs
(Sun Mar 29 2015 - 22:04:22 PDT)
[AMBER] Problem Regarding Different PMF Graph
(Sun Mar 29 2015 - 22:02:34 PDT)
[AMBER] problem regarding different pmf graph
(Thu Mar 26 2015 - 21:21:52 PDT)
Shukla, Saurabh
[AMBER] Putting oxygen molecules around protein structure
(Wed Mar 11 2015 - 20:38:24 PDT)
Re: [AMBER] Chamber problem
(Mon Mar 02 2015 - 11:50:29 PST)
[AMBER] Replacing water with oxygen molecules
(Mon Mar 02 2015 - 10:19:51 PST)
Simone Fulle
[AMBER] Gromacs towards Amber conversion
(Sat Mar 28 2015 - 07:25:27 PDT)
Sohag Biswas
Re: [AMBER] AMBER Digest, Vol 1160, Issue 1
(Tue Mar 17 2015 - 01:39:53 PDT)
[AMBER] facing problem to create a prmtop file for oxonium cation
(Mon Mar 16 2015 - 02:59:06 PDT)
Srinivasaraghavan Kannan
[AMBER] COM restrain support in Amber14
(Mon Mar 02 2015 - 02:29:42 PST)
Subrata Paul
Re: [AMBER] vdw energy and electrostatic energy calculation for osmolyte
(Wed Mar 25 2015 - 11:40:58 PDT)
Re: [AMBER] vdw energy and electrostatic energy calculation for osmolyte
(Tue Mar 24 2015 - 22:30:26 PDT)
[AMBER] vdw energy and electrostatic energy calculation for osmolyte
(Tue Mar 24 2015 - 00:31:49 PDT)
Swithin Hanosh
[AMBER] REGARDING ATOM TYPE ERROR
(Sat Mar 28 2015 - 05:01:43 PDT)
[AMBER] Error while creating force field
(Tue Mar 03 2015 - 03:35:37 PST)
[AMBER] Error while creating force field
(Mon Mar 02 2015 - 02:21:07 PST)
Sylvester Tumusiime
Re: [AMBER] concave edge on torus has mismatched atoms
(Tue Mar 24 2015 - 13:06:15 PDT)
[AMBER] concave edge on torus has mismatched atoms
(Tue Mar 24 2015 - 12:28:12 PDT)
Re: [AMBER] matrix newtransform command
(Wed Mar 04 2015 - 14:51:46 PST)
[AMBER] matrix newtransform command
(Tue Mar 03 2015 - 12:03:24 PST)
Thomas Cheatham
Re: [AMBER] Dielectric constant for dna-ligand in TIP3P system
(Tue Mar 17 2015 - 08:40:36 PDT)
Re: [AMBER] Syntax Confusion on Radial Command
(Sun Mar 08 2015 - 15:29:37 PDT)
Thomas Exner
[AMBER] Differences in AMBER force fields
(Tue Mar 17 2015 - 02:46:24 PDT)
Tyler Luchko
Re: [AMBER] Pressure units in 1D-RISM
(Tue Mar 31 2015 - 22:00:08 PDT)
Vijay Achari
Re: [AMBER] iterative calculation in CPPTRAJ using "for... do... done"
(Wed Mar 25 2015 - 09:53:56 PDT)
Re: [AMBER] iterative calculation in CPPTRAJ using "for... do... done"
(Wed Mar 25 2015 - 09:51:56 PDT)
[AMBER] iterative calculation in CPPTRAJ using "for... do... done"
(Wed Mar 25 2015 - 04:42:16 PDT)
Re: [AMBER] Format of solventhb.dat file in hydrogen bonding calculation
(Tue Mar 24 2015 - 01:14:54 PDT)
Re: [AMBER] Evaluating hydrogen boding lifetime
(Mon Mar 23 2015 - 20:42:32 PDT)
Re: [AMBER] error when doing lifetime calculation
(Mon Mar 23 2015 - 09:06:44 PDT)
[AMBER] error when doing lifetime calculation
(Sun Mar 22 2015 - 23:32:36 PDT)
Re: [AMBER] Evaluating hydrogen boding lifetime
(Sat Mar 21 2015 - 22:23:50 PDT)
Re: [AMBER] finding angles
(Mon Mar 16 2015 - 19:22:09 PDT)
[AMBER] Format of solventhb.dat file in hydrogen bonding calculation
(Mon Mar 16 2015 - 19:10:40 PDT)
Re: [AMBER] finding angles
(Mon Mar 16 2015 - 15:36:03 PDT)
Re: [AMBER] finding angles
(Mon Mar 16 2015 - 10:49:31 PDT)
Re: [AMBER] Evaluating hydrogen boding lifetime
(Mon Mar 16 2015 - 09:50:20 PDT)
Re: [AMBER] finding angles
(Mon Mar 16 2015 - 03:18:03 PDT)
Re: [AMBER] finding angles
(Thu Mar 12 2015 - 20:40:49 PDT)
Re: [AMBER] finding angles
(Thu Mar 12 2015 - 18:24:05 PDT)
[AMBER] finding angles
(Thu Mar 12 2015 - 07:00:31 PDT)
Re: [AMBER] calculating angle between to vectors
(Thu Mar 12 2015 - 03:14:19 PDT)
Re: [AMBER] Evaluating hydrogen boding lifetime
(Thu Mar 12 2015 - 01:53:20 PDT)
Re: [AMBER] calculating angle between to vectors
(Wed Mar 11 2015 - 22:22:45 PDT)
[AMBER] calculating angle between to vectors
(Wed Mar 11 2015 - 01:01:28 PDT)
Re: [AMBER] Evaluating hydrogen boding lifetime
(Tue Mar 10 2015 - 23:57:17 PDT)
Re: [AMBER] Evaluating hydrogen boding lifetime
(Tue Mar 10 2015 - 20:24:34 PDT)
[AMBER] Evaluating hydrogen boding lifetime
(Tue Mar 10 2015 - 01:53:39 PDT)
Re: [AMBER] calculating HB lifetime
(Mon Mar 09 2015 - 23:52:03 PDT)
vijay kumar narsapuram
Re: [AMBER] Error: Unable to run flex; this is required for NAB and antechamber Please check your PATH, or install the program
(Sat Mar 28 2015 - 04:47:48 PDT)
Re: [AMBER] Error: Unable to run flex; this is required for NAB and antechamber Please check your PATH, or install the program
(Fri Mar 13 2015 - 02:12:01 PDT)
Re: [AMBER] Error: Unable to run flex; this is required for NAB and antechamber Please check your PATH, or install the program
(Fri Mar 06 2015 - 08:56:46 PST)
Re: [AMBER] Error: Unable to run flex; this is required for NAB and antechamber Please check your PATH, or install the program
(Fri Mar 06 2015 - 07:22:58 PST)
Vishal Kumar Jaiswal
[AMBER] Projection on distance covariance modes
(Mon Mar 30 2015 - 06:11:55 PDT)
[AMBER] Projection on modes calculated by distcovar matrix
(Sun Mar 29 2015 - 02:53:00 PDT)
vladimir.palivec.marge.uochb.cas.cz
Re: [AMBER] Free energy calculation: Thermodynamic integration with use of restraints
(Fri Mar 27 2015 - 08:46:47 PDT)
Re: [AMBER] Free energy calculation: Thermodynamic integration with use of restraints
(Thu Mar 26 2015 - 08:22:03 PDT)
Re: [AMBER] Free energy calculation: Thermodynamic integration with use of restraints
(Thu Mar 26 2015 - 01:34:47 PDT)
[AMBER] Free energy calculation: Thermodynamic integration with use of restraints
(Wed Mar 25 2015 - 10:55:45 PDT)
[AMBER] [Fwd: ]
(Sat Mar 21 2015 - 04:46:19 PDT)
Waldner, Birgit
Re: [AMBER] : Dimer Imaging Problem
(Wed Mar 11 2015 - 09:41:00 PDT)
[AMBER] : Dimer Imaging Problem
(Wed Mar 11 2015 - 09:28:35 PDT)
Wang Moye
[AMBER] How to obtain potential energy using mdcrd trajectories in AMBER12
(Mon Mar 30 2015 - 05:39:03 PDT)
Re: [AMBER] Using WHAM to get 3D free energy surface in AMBER12
(Wed Mar 18 2015 - 18:21:21 PDT)
Re: [AMBER] Using WHAM to get 3D free energy surface in AMBER12
(Mon Mar 16 2015 - 18:06:56 PDT)
[AMBER] Using WHAM to get 3D free energy surface in AMBER12
(Mon Mar 16 2015 - 00:30:40 PDT)
wjli
[AMBER] Amber standard residue name
(Thu Mar 19 2015 - 03:45:34 PDT)
[AMBER] Error during Adding Fragment（about MCPB ）
(Thu Mar 19 2015 - 03:33:23 PDT)
Yip Yew Mun
[AMBER] Multiple MEPs option in R.E.D tools
(Mon Mar 30 2015 - 19:26:05 PDT)
zahra khatti
[AMBER] free energy plot
(Sun Mar 08 2015 - 08:18:25 PDT)
[AMBER] free energy plot
(Sat Mar 07 2015 - 22:12:53 PST)
[AMBER] free energy plot
(Sat Mar 07 2015 - 22:09:59 PST)
Zhang, Sixue
Re: [AMBER] Solvent Box Issue When Running AMBER Dynamics
(Mon Mar 09 2015 - 13:58:53 PDT)
Re: [AMBER] Solvent Box Issue When Running AMBER Dynamics
(Wed Mar 04 2015 - 18:44:51 PST)
[AMBER] Solvent Box Issue When Running AMBER Dynamics
(Wed Mar 04 2015 - 14:46:37 PST)
王华
[AMBER] The unperturbed charge of the unit: -2.980000 is not integral
(Tue Mar 24 2015 - 18:40:20 PDT)
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Wed Apr 01 2015 - 00:00:03 PDT
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: Sun Nov 24 2024 - 05:55:21 PST
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