Amber Archive Jun 2011 by author
789 messages
:
Starting
Tue May 31 2011 - 21:30:02 PDT,
Ending
Fri Jul 01 2011 - 02:00:03 PDT
sort by
: [
thread
] [ author ] [
date
] [
subject
] [
attachment
]
475649770
[AMBER] how to assess the convergence of the clustering
(Sun Jun 26 2011 - 20:19:12 PDT)
abc def
Re: [AMBER] Restraint Minimization
(Wed Jun 15 2011 - 07:41:37 PDT)
Re: [AMBER] Restraint Minimization
(Wed Jun 15 2011 - 07:37:29 PDT)
Re: [AMBER] Restraint Minimization
(Wed Jun 15 2011 - 07:26:04 PDT)
Re: [AMBER] Restraint Minimization
(Wed Jun 15 2011 - 07:11:38 PDT)
abhay.strubi.ox.ac.uk
[AMBER] restraint simulation
(Wed Jun 15 2011 - 03:51:29 PDT)
[AMBER] concerted effect of the backbone movement
(Fri Jun 03 2011 - 08:11:03 PDT)
Ada Sedova
Re: [AMBER] algorithm for rms
(Fri Jun 17 2011 - 08:11:24 PDT)
Re: [AMBER] algorithm for rms
(Fri Jun 17 2011 - 08:08:22 PDT)
Re: [AMBER] algorithm for rms
(Fri Jun 17 2011 - 07:41:01 PDT)
[AMBER] algorithm for rms
(Fri Jun 17 2011 - 07:36:27 PDT)
Adrian Roitberg
Re: [AMBER] VMD-Chamber interface
(Wed Jun 29 2011 - 13:31:04 PDT)
Re: [AMBER] Steered Molecular Dynamics
(Mon Jun 27 2011 - 13:58:31 PDT)
Re: [AMBER] System temperature
(Fri Jun 24 2011 - 03:25:44 PDT)
Re: [AMBER] System temperature
(Wed Jun 22 2011 - 12:35:43 PDT)
Re: [AMBER] System temperature
(Wed Jun 22 2011 - 11:53:31 PDT)
Re: [AMBER] secstruct analysis
(Tue Jun 14 2011 - 00:54:29 PDT)
Re: [AMBER] secstruct analysis
(Tue Jun 14 2011 - 00:16:40 PDT)
Re: [AMBER] running a MD with a innert gas
(Fri Jun 10 2011 - 10:09:26 PDT)
Re: [AMBER] non-bonded cutoff in the case of REMD in explicit solvent
(Wed Jun 08 2011 - 03:21:17 PDT)
Re: [AMBER] non-bonded cutoff in the case of REMD in explicit solvent
(Wed Jun 08 2011 - 03:21:04 PDT)
Re: [AMBER] non-bonded cutoff in the case of REMD in explicit solvent
(Wed Jun 08 2011 - 01:28:06 PDT)
Re: [AMBER] MMPBSA: general question
(Tue Jun 07 2011 - 10:01:15 PDT)
Re: [AMBER] Ligand Minimization with Simulated Annealing
(Mon Jun 06 2011 - 07:45:29 PDT)
Re: [AMBER] pH-dependent folding simulation
(Wed Jun 01 2011 - 12:49:52 PDT)
Re: [AMBER] pH-dependent folding simulation
(Wed Jun 01 2011 - 09:36:35 PDT)
Aiello, Daniel
Re: [AMBER] Residue numbering
(Thu Jun 16 2011 - 12:50:15 PDT)
Aimin Guo
[AMBER] About the coordinates of input or output files
(Fri Jun 24 2011 - 10:21:37 PDT)
Ake Sandgren
Re: [AMBER] Where to send patches?
(Wed Jun 01 2011 - 01:45:29 PDT)
Alan
Re: [AMBER] sleap never worked anymore since AT 1.2
(Wed Jun 22 2011 - 01:50:43 PDT)
[AMBER] sleap never worked anymore since AT 1.2
(Fri Jun 17 2011 - 01:45:01 PDT)
Alessio Atzori
[AMBER] R: R: forrtl: severe (64): input conversion error, unit 9
(Wed Jun 22 2011 - 16:51:09 PDT)
[AMBER] R: forrtl: severe (64): input conversion error, unit 9
(Wed Jun 22 2011 - 04:21:45 PDT)
[AMBER] forrtl: severe (64): input conversion error, unit 9
(Wed Jun 22 2011 - 04:10:56 PDT)
Alexander Drozdetski
[AMBER] Nucleic residues with methylphosphonates
(Thu Jun 16 2011 - 13:49:33 PDT)
[AMBER] RDF
(Thu Jun 16 2011 - 11:56:39 PDT)
Ali Faruqi
[AMBER] NETCDF Installation Error
(Wed Jun 29 2011 - 04:10:02 PDT)
[AMBER] Sander Compilation Problem
(Tue Jun 28 2011 - 23:51:14 PDT)
Re: [AMBER] Architecture/compiler is not supported Error!
(Mon Jun 27 2011 - 01:21:21 PDT)
Re: [AMBER] Sander Error
(Mon Jun 27 2011 - 01:20:21 PDT)
[AMBER] Architecture/compiler is not supported Error!
(Sat Jun 25 2011 - 03:36:53 PDT)
Re: [AMBER] Sander Error
(Sat Jun 25 2011 - 01:59:22 PDT)
Re: [AMBER] Sander Error
(Fri Jun 24 2011 - 07:33:17 PDT)
[AMBER] Sander Error
(Fri Jun 24 2011 - 01:07:12 PDT)
Alison Lynton
Re: [AMBER] Problems Compiling Amber11 Parallel GPU
(Mon Jun 27 2011 - 19:47:44 PDT)
[AMBER] Problems Compiling Amber11 Parallel GPU
(Sun Jun 26 2011 - 20:33:40 PDT)
Re: [AMBER] noesy and dip Program error when testing Amber11 Parallel
(Tue Jun 14 2011 - 19:24:29 PDT)
[AMBER] noesy and dip Program error when testing Amber11 Parallel
(Mon Jun 13 2011 - 00:53:16 PDT)
Andreas Goetz
[AMBER] AMBER Workshop in Shanghai, China, August 22-26, 2011
(Thu Jun 30 2011 - 00:50:28 PDT)
André C. Stiel
Re: [AMBER] single amino acid energies
(Sat Jun 25 2011 - 03:22:00 PDT)
[AMBER] single amino acid energies
(Fri Jun 24 2011 - 00:14:04 PDT)
[AMBER] energy of a single amino acid during minimization
(Wed Jun 22 2011 - 03:10:47 PDT)
aneesh cna
Re: [AMBER] simulation of small molecule with organic solvent and water
(Thu Jun 02 2011 - 21:56:56 PDT)
Anna Reymer
[AMBER] Force fields for DNA, what to choose?
(Thu Jun 02 2011 - 07:26:31 PDT)
Anselm Horn
Re: [AMBER] amber10 output
(Thu Jun 16 2011 - 14:17:49 PDT)
Re: [AMBER] prep files ATP-MG++ and for phosphorylated threonine
(Mon Jun 06 2011 - 16:14:26 PDT)
Re: [AMBER] prep files ATP-MG++ and for phosphorylated threonine
(Sun Jun 05 2011 - 14:15:04 PDT)
Antonija Tomić
Re: [AMBER] loadPdbUsingSeq command
(Thu Jun 16 2011 - 04:53:06 PDT)
Re: [AMBER] loadPdbUsingSeq command
(Wed Jun 15 2011 - 01:02:48 PDT)
Re: [AMBER] loadPdbUsingSeq command
(Tue Jun 14 2011 - 05:47:26 PDT)
[AMBER] loadPdbUsingSeq command
(Tue Jun 14 2011 - 02:26:00 PDT)
Antonio Peón López
[AMBER] AMBER: error in reading namelist cntrl
(Sat Jun 25 2011 - 14:14:50 PDT)
Aust, Susanne
Re: [AMBER] MM-GBSA with QM/MM
(Tue Jun 28 2011 - 04:18:38 PDT)
[AMBER] MM-GBSA with QM/MM
(Tue Jun 28 2011 - 02:27:34 PDT)
Azat Mukhametov
Re: [AMBER] How to prepare ATP with Antechamber?
(Tue Jun 21 2011 - 02:24:42 PDT)
[AMBER] How to prepare ATP with Antechamber?
(Tue Jun 21 2011 - 01:57:08 PDT)
Re: [AMBER] Using PQR files produced by PDB2PQR as input for tleap/xleap
(Thu Jun 09 2011 - 03:03:20 PDT)
Re: [AMBER] Using PQR files produced by PDB2PQR as input for tleap/xleap
(Thu Jun 09 2011 - 00:21:20 PDT)
Re: [AMBER] Using PQR files produced by PDB2PQR as input for tleap/xleap
(Wed Jun 08 2011 - 23:57:53 PDT)
Re: [AMBER] Using PQR files produced by PDB2PQR as input for tleap/xleap
(Wed Jun 08 2011 - 23:56:53 PDT)
Re: [AMBER] Using PQR files produced by PDB2PQR as input for tleap/xleap
(Wed Jun 08 2011 - 19:57:15 PDT)
[AMBER] Using PQR files produced by PDB2PQR as input for tleap/xleap
(Wed Jun 08 2011 - 19:35:42 PDT)
balaji nagarajan
[AMBER] give_diff_runs
(Thu Jun 23 2011 - 12:29:47 PDT)
Balazs Jojart
Re: [AMBER] Entropy Decomposition
(Fri Jun 24 2011 - 14:47:03 PDT)
Re: [AMBER] Entropy Decomposition
(Fri Jun 24 2011 - 13:56:02 PDT)
baljinder
Re: [AMBER] MMPBSA-binding energy calculation
(Tue Jun 21 2011 - 10:17:58 PDT)
[AMBER] MMPBSA-binding energy calculation
(Tue Jun 21 2011 - 07:25:51 PDT)
Bashford, Donald
Re: [AMBER] loadPdbUsingSeq command
(Tue Jun 14 2011 - 08:23:00 PDT)
Re: [AMBER] Using PQR files produced by PDB2PQR as input fortleap/x leap. .
(Thu Jun 09 2011 - 10:42:15 PDT)
Ben Roberts
Re: [AMBER] Non-Standard Residues Problems
(Wed Jun 29 2011 - 10:50:25 PDT)
Re: [AMBER] AmberTools 1.5 gnu compilation fails under FC15
(Mon Jun 20 2011 - 13:12:14 PDT)
Re: [AMBER] amber10 output
(Thu Jun 16 2011 - 14:48:08 PDT)
Re: [AMBER] production run duration
(Fri Jun 03 2011 - 08:45:07 PDT)
Re: [AMBER] production run duration
(Thu Jun 02 2011 - 22:02:36 PDT)
Bernhard Poll
[AMBER] MM-PBSA/GBSA of charged molecules
(Tue Jun 07 2011 - 04:29:48 PDT)
Bill Miller III
Re: [AMBER] regarding per residue wise free energy decomposition
(Wed Jun 29 2011 - 03:49:53 PDT)
Re: [AMBER] MM-GBSA with QM/MM
(Tue Jun 28 2011 - 03:47:06 PDT)
Re: [AMBER] Error mmpbsa
(Mon Jun 27 2011 - 20:01:41 PDT)
Re: [AMBER] mmpbsa.py
(Mon Jun 27 2011 - 13:08:56 PDT)
Re: [AMBER] Error mmpbsa
(Mon Jun 27 2011 - 03:41:58 PDT)
Re: [AMBER] regarding per residue wise free energy decomposition
(Fri Jun 24 2011 - 05:30:09 PDT)
Re: [AMBER] single amino acid energies
(Fri Jun 24 2011 - 05:24:53 PDT)
Re: [AMBER] regarding per residue wise free energy decomposition
(Thu Jun 23 2011 - 13:49:24 PDT)
Re: [AMBER] MMPBSA.py decomp
(Wed Jun 22 2011 - 03:47:29 PDT)
Re: [AMBER] Energy decomposition
(Sat Jun 18 2011 - 05:17:40 PDT)
Re: [AMBER] format error from mmpbsa.py
(Mon Jun 13 2011 - 03:44:24 PDT)
Re: [AMBER] Alanine scanning
(Fri Jun 10 2011 - 07:01:53 PDT)
Re: [AMBER] energy decomposition with mmpbsa.py
(Mon Jun 06 2011 - 20:44:36 PDT)
Re: [AMBER] energy decomposition with mmpbsa.py
(Mon Jun 06 2011 - 10:14:58 PDT)
Re: [AMBER] energy decomposition with mmpbsa.py
(Mon Jun 06 2011 - 10:10:33 PDT)
Re: [AMBER] Energy Decomposition Error using Perl Script (#RECMAP + #LIGMAP != #COMPRI)
(Thu Jun 02 2011 - 03:41:06 PDT)
Re: [AMBER] Alanine scanning with CYS
(Wed Jun 01 2011 - 04:51:54 PDT)
Re: [AMBER] Alanine scanning with CYS
(Wed Jun 01 2011 - 03:48:13 PDT)
Bill Ross
Re: [AMBER] Natural Language Angle Restraint
(Mon Jun 27 2011 - 14:16:52 PDT)
Re: [AMBER] Problem related to teh residue template and add ion
(Thu Jun 09 2011 - 16:34:08 PDT)
Re: [AMBER] Delete Solvatebox
(Wed Jun 01 2011 - 12:19:39 PDT)
Bill Snapko
Re: [AMBER] CUDA 4.0 RC
(Thu Jun 23 2011 - 09:12:55 PDT)
Bin Wu
Re: [AMBER] About difference between Sander and Pmemd
(Fri Jun 17 2011 - 07:07:22 PDT)
Re: [AMBER] About difference between Sander and Pmemd
(Thu Jun 16 2011 - 18:24:54 PDT)
[AMBER] About difference between Sander and Pmemd
(Wed Jun 15 2011 - 19:54:38 PDT)
[AMBER] About "Must have more residues than processors"
(Sun Jun 12 2011 - 13:35:04 PDT)
Bongkeun Kim
Re: [AMBER] ptraj error with *** glibc detected *** ptraj: free(): invalid next size (normal)
(Fri Jun 10 2011 - 13:53:54 PDT)
Re: [AMBER] ptraj error with *** glibc detected *** ptraj: free(): invalid next size (normal)
(Thu Jun 09 2011 - 11:00:56 PDT)
Re: [AMBER] ptraj error with *** glibc detected *** ptraj: free(): invalid next size (normal)
(Thu Jun 09 2011 - 10:14:33 PDT)
Re: [AMBER] ptraj error with *** glibc detected *** ptraj: free(): invalid next size (normal)
(Thu Jun 09 2011 - 00:49:10 PDT)
Re: [AMBER] ptraj error with *** glibc detected *** ptraj: free(): invalid next size (normal)
(Tue Jun 07 2011 - 14:29:46 PDT)
[AMBER] ptraj error with *** glibc detected *** ptraj: free(): invalid next size (normal)
(Mon Jun 06 2011 - 13:30:03 PDT)
Brendan Duggan
Re: [AMBER] secondary structure plotting
(Fri Jun 24 2011 - 07:51:13 PDT)
Re: [AMBER] residual dipolar coupling restraints
(Tue Jun 07 2011 - 07:03:29 PDT)
[AMBER] residual dipolar coupling restraints
(Wed Jun 01 2011 - 13:14:15 PDT)
Re: [AMBER] NMR restraints file format
(Wed Jun 01 2011 - 05:53:52 PDT)
Brian Radak
Re: [AMBER] unexpected behavior of ambpdb
(Fri Jun 03 2011 - 10:15:40 PDT)
[AMBER] unexpected behavior of ambpdb
(Fri Jun 03 2011 - 08:16:19 PDT)
Bruno Rodrigues
Re: [AMBER] re-image
(Thu Jun 09 2011 - 07:34:26 PDT)
Re: [AMBER] re-image
(Thu Jun 09 2011 - 06:47:30 PDT)
[AMBER] re-image
(Thu Jun 09 2011 - 06:28:19 PDT)
caobb0214
[AMBER] alanine mutagenisis in amber
(Tue Jun 21 2011 - 17:44:25 PDT)
[AMBER] problem about entropy calculation
(Wed Jun 08 2011 - 17:21:36 PDT)
Carlos Simmerling
Re: [AMBER] Adding NH2 at the end of peptide
(Thu Jun 30 2011 - 07:59:11 PDT)
Re: [AMBER] Non-Standard Residues Problems
(Wed Jun 29 2011 - 10:48:58 PDT)
Re: [AMBER] Kinetic energy in mdout file is not identical to that calculated from mdvel file.
(Tue Jun 28 2011 - 11:50:14 PDT)
Re: [AMBER] Kinetic energy in mdout file is not identical to that calculated from mdvel file.
(Tue Jun 28 2011 - 03:47:41 PDT)
Re: [AMBER] R: forrtl: severe (64): input conversion error, unit 9
(Wed Jun 22 2011 - 12:01:55 PDT)
Re: [AMBER] System temperature
(Wed Jun 22 2011 - 11:51:03 PDT)
Re: [AMBER] System temperature
(Wed Jun 22 2011 - 10:57:32 PDT)
Re: [AMBER] forrtl: severe (64): input conversion error, unit 9
(Wed Jun 22 2011 - 04:14:50 PDT)
Re: [AMBER] Suggestion for minor user manual clarification
(Tue Jun 21 2011 - 11:22:47 PDT)
Re: [AMBER] Non-periodic behavior of NMR restraints upon restart in a periodic system
(Tue Jun 21 2011 - 10:59:02 PDT)
Re: [AMBER] Can I directly compare the PMF for two compounds with different size and chemical structures?
(Sun Jun 19 2011 - 03:10:46 PDT)
Re: [AMBER] algorithm for rms
(Fri Jun 17 2011 - 07:38:26 PDT)
Re: [AMBER] ptraj, alignment, and rmsd
(Wed Jun 15 2011 - 13:17:06 PDT)
Re: [AMBER] Estimation of free energy of solvation ?
(Wed Jun 15 2011 - 08:35:02 PDT)
Re: [AMBER] Restraint Minimization
(Wed Jun 15 2011 - 07:32:42 PDT)
Re: [AMBER] Restraint Minimization
(Wed Jun 15 2011 - 07:16:33 PDT)
Re: [AMBER] ptraj: Could not find target 300.000000 in any of the replica trajectories
(Wed Jun 15 2011 - 07:01:39 PDT)
Re: [AMBER] ptraj: Could not find target 300.000000 in any of the replica trajectories
(Wed Jun 15 2011 - 06:53:33 PDT)
Re: [AMBER] Restraint Minimization
(Wed Jun 15 2011 - 03:32:18 PDT)
Re: [AMBER] About "Must have more residues than processors"
(Mon Jun 13 2011 - 07:41:07 PDT)
Re: [AMBER] High-temperature output in REMD
(Mon Jun 13 2011 - 06:19:29 PDT)
Re: [AMBER] Ligand Minimization with Simulated Annealing
(Mon Jun 06 2011 - 07:44:12 PDT)
Re: [AMBER] Ligand Minimization with Simulated Annealing
(Mon Jun 06 2011 - 07:28:11 PDT)
Re: [AMBER] Problem related with the Ptraj
(Sat Jun 04 2011 - 04:17:38 PDT)
Re: [AMBER] Choosing the number of replicas in NEB
(Fri Jun 03 2011 - 09:27:02 PDT)
Re: [AMBER] sander terminates abruptly
(Thu Jun 02 2011 - 04:15:18 PDT)
case
Re: [AMBER] Non-Standard Residues Problems
(Thu Jun 30 2011 - 18:25:52 PDT)
Re: [AMBER] System temperature
(Sun Jun 19 2011 - 07:30:43 PDT)
Re: [AMBER] Resp charge
(Sun Jun 19 2011 - 07:22:15 PDT)
Re: [AMBER] Antechamber: Failure to calculate Mulliken partial charges using a Tripos MOL2 input file
(Sun Jun 19 2011 - 07:00:51 PDT)
Re: [AMBER] Amoeba with water and ion
(Sat Jun 18 2011 - 05:56:49 PDT)
Re: [AMBER] Antechamber Error
(Mon Jun 13 2011 - 19:17:51 PDT)
Re: [AMBER] running a MD with a innert gas
(Sat Jun 11 2011 - 10:58:37 PDT)
Re: [AMBER] Simulating a periodic System about Molecular Crystal
(Sun Jun 05 2011 - 07:26:22 PDT)
Re: [AMBER] AMBER11 Installation on FEDORA 15
(Wed Jun 01 2011 - 19:21:52 PDT)
Re: [AMBER] residual dipolar coupling restraints
(Wed Jun 01 2011 - 19:09:21 PDT)
Catein Catherine
[AMBER] Can I directly compare the PMF for two compounds with different size and chemical structures?
(Sat Jun 18 2011 - 21:55:37 PDT)
Caterina Bianchi
[AMBER] ANTECHAMBER/RESP
(Fri Jun 10 2011 - 03:02:24 PDT)
[AMBER] Antechamber
(Thu Jun 09 2011 - 07:09:57 PDT)
CHAMI F.
Re: [AMBER] Sirius software
(Wed Jun 22 2011 - 17:17:40 PDT)
Re: [AMBER] Sirius software
(Wed Jun 22 2011 - 05:31:33 PDT)
Re: [AMBER] Sirius software
(Wed Jun 22 2011 - 03:11:58 PDT)
Re: [AMBER] Sirius software
(Tue Jun 21 2011 - 09:28:01 PDT)
[AMBER] Sirius software
(Tue Jun 21 2011 - 03:03:35 PDT)
Charles Johnson
[AMBER] RNA duplex
(Tue Jun 28 2011 - 17:33:45 PDT)
chicago.ecnu
[AMBER] Prevent tleap to rearrange my ions?
(Sun Jun 26 2011 - 03:18:13 PDT)
Chirag Vora
[AMBER] Leap adds atoms to pdb (tutorial B1)
(Wed Jun 29 2011 - 22:48:48 PDT)
Chris Bryant
[AMBER] Choosing the number of replicas in NEB
(Fri Jun 03 2011 - 07:58:18 PDT)
Chris Chris
Re: [AMBER] mmpbsa.py
(Mon Jun 27 2011 - 14:33:58 PDT)
Christoph Klein
Re: [AMBER] Suggestion for minor user manual clarification
(Tue Jun 21 2011 - 12:38:35 PDT)
[AMBER] Suggestion for minor user manual clarification
(Tue Jun 21 2011 - 11:13:53 PDT)
[AMBER] Methane with no surface area?
(Wed Jun 15 2011 - 12:45:39 PDT)
clwg
[AMBER] interaction energies of DNA
(Wed Jun 22 2011 - 08:24:54 PDT)
[AMBER] intra- and interstrand interaction energies of DNA
(Tue Jun 21 2011 - 07:23:42 PDT)
Crowley, Michael
Re: [AMBER] VMD-Chamber interface
(Wed Jun 29 2011 - 13:43:47 PDT)
Daniel Aiello
Re: [AMBER] Entropy Decomposition
(Fri Jun 24 2011 - 10:43:33 PDT)
[AMBER] Entropy Decomposition
(Fri Jun 24 2011 - 08:08:39 PDT)
[AMBER] Residue numbering
(Thu Jun 16 2011 - 10:42:43 PDT)
Daniel Roe
Re: [AMBER] Uracil is not recognised as a nucleotide in Xleap - in FF99
(Wed Jun 29 2011 - 08:53:18 PDT)
Re: [AMBER] Problem in the energetics of the system Shake cannot be accomplished.
(Wed Jun 29 2011 - 08:45:13 PDT)
Re: [AMBER] ptraj cluster
(Mon Jun 27 2011 - 22:09:38 PDT)
Re: [AMBER] Question on the construction of a topology file
(Mon Jun 27 2011 - 21:57:37 PDT)
Re: [AMBER] saving the first solvent shell molecules by Ptraj
(Mon Jun 27 2011 - 21:41:55 PDT)
Re: [AMBER] netcdf
(Mon Jun 27 2011 - 21:23:37 PDT)
Re: [AMBER] Bfactor calculation in cpptraj
(Thu Jun 16 2011 - 07:44:40 PDT)
Re: [AMBER] how to interprete x.ss file
(Wed Jun 15 2011 - 09:52:22 PDT)
Re: [AMBER] keyword ref
(Tue Jun 14 2011 - 20:58:50 PDT)
Re: [AMBER] secstruct analysis
(Tue Jun 14 2011 - 04:36:58 PDT)
Re: [AMBER] keyword ref
(Mon Jun 13 2011 - 07:55:33 PDT)
Re: [AMBER] CPPTRAJ- segmentation fault
(Fri Jun 10 2011 - 08:03:01 PDT)
Re: [AMBER] ptraj error with *** glibc detected *** ptraj: free(): invalid next size (normal)
(Thu Jun 09 2011 - 10:06:17 PDT)
Re: [AMBER] ptraj error with *** glibc detected *** ptraj: free(): invalid next size (normal)
(Wed Jun 08 2011 - 07:28:36 PDT)
Re: [AMBER] Detection of residues within a sphere
(Wed Jun 08 2011 - 06:07:39 PDT)
Re: [AMBER] rmsd calculation
(Wed Jun 08 2011 - 05:57:29 PDT)
Re: [AMBER] ptraj error with *** glibc detected *** ptraj: free(): invalid next size (normal)
(Tue Jun 07 2011 - 04:12:54 PDT)
Re: [AMBER] rmsd calculation
(Tue Jun 07 2011 - 04:08:16 PDT)
Re: [AMBER] rmsd calculation
(Tue Jun 07 2011 - 04:07:19 PDT)
Re: [AMBER] Negative value of SASA calculated by surf command in cpptraj
(Sun Jun 05 2011 - 20:59:05 PDT)
Re: [AMBER] AmberTools 1.5 installation problem
(Thu Jun 02 2011 - 04:45:59 PDT)
Re: [AMBER] sander terminates abruptly
(Thu Jun 02 2011 - 04:17:00 PDT)
Re: [AMBER] Sorry again..this is right
(Wed Jun 01 2011 - 07:02:11 PDT)
Re: [AMBER] Error message for cpptraj
(Wed Jun 01 2011 - 04:20:01 PDT)
Re: [AMBER] AMBER11 Installation on FEDORA 15
(Tue May 31 2011 - 21:14:07 PDT)
Daniel Schaal
[AMBER] Calculating energies
(Mon Jun 06 2011 - 04:11:19 PDT)
Daniel Sindhikara
Re: [AMBER] Error compiling ambertools 1.5
(Mon Jun 20 2011 - 19:57:38 PDT)
[AMBER] Error compiling ambertools 1.5
(Mon Jun 20 2011 - 03:23:56 PDT)
Re: [AMBER] Using PQR files produced by PDB2PQR as input for tleap/xleap
(Thu Jun 09 2011 - 00:10:13 PDT)
Re: [AMBER] Using PQR files produced by PDB2PQR as input for tleap/xleap
(Wed Jun 08 2011 - 19:50:00 PDT)
David A Case
Re: [AMBER] AMBER9- error in LEaP while learning MMPBSA tutorial
(Thu Jun 30 2011 - 05:29:31 PDT)
Re: [AMBER] Leap adds atoms to pdb (tutorial B1)
(Thu Jun 30 2011 - 05:22:06 PDT)
Re: [AMBER] dist restraint
(Thu Jun 30 2011 - 05:10:04 PDT)
Re: [AMBER] NETCDF Installation Error
(Thu Jun 30 2011 - 05:05:46 PDT)
Re: [AMBER] Suggestion for minor user manual clarification
(Thu Jun 23 2011 - 13:36:43 PDT)
Re: [AMBER] give_diff_runs
(Thu Jun 23 2011 - 13:07:03 PDT)
Re: [AMBER] NMR chemical shift restraints for an intrinsically disordered peptide
(Thu Jun 23 2011 - 11:02:39 PDT)
Re: [AMBER] DIELC constant for normal mode analyses in vacuum ?
(Thu Jun 23 2011 - 09:13:51 PDT)
Re: [AMBER] NMR chemical shift restraints for an intrinsically disordered peptide
(Thu Jun 23 2011 - 05:22:40 PDT)
Re: [AMBER] Antechamber Error
(Thu Jun 23 2011 - 05:11:15 PDT)
Re: [AMBER] AMBER 11 and Ambertools 1.5 Installs failing tests for mmpbsa_py
(Thu Jun 23 2011 - 05:07:15 PDT)
Re: [AMBER] Antechamber Error
(Wed Jun 22 2011 - 10:17:51 PDT)
Re: [AMBER] Vibrational entropy with NAB
(Wed Jun 22 2011 - 08:56:58 PDT)
Re: [AMBER] trouble installing Amber 10
(Wed Jun 22 2011 - 08:47:54 PDT)
Re: [AMBER] trouble installing Amber 10
(Wed Jun 22 2011 - 06:41:54 PDT)
Re: [AMBER] sleap never worked anymore since AT 1.2
(Wed Jun 22 2011 - 05:10:42 PDT)
Re: [AMBER] Antechamber Error
(Wed Jun 22 2011 - 05:08:04 PDT)
Re: [AMBER] Vibrational entropy with NAB
(Wed Jun 22 2011 - 05:05:14 PDT)
Re: [AMBER] Non-periodic behavior of NMR restraints upon restart in a periodic system
(Tue Jun 21 2011 - 10:54:25 PDT)
Re: [AMBER] problems ahout simulating a molecular crystal
(Tue Jun 21 2011 - 08:06:11 PDT)
Re: [AMBER] small inconsistencies in parm99.dat and parm94.dat
(Tue Jun 21 2011 - 06:31:00 PDT)
Re: [AMBER] sleap never worked anymore since AT 1.2
(Tue Jun 21 2011 - 06:26:13 PDT)
Re: [AMBER] Amoeba with water and ions (2)
(Tue Jun 21 2011 - 06:20:20 PDT)
Re: [AMBER] Error compiling ambertools 1.5
(Mon Jun 20 2011 - 08:44:10 PDT)
Re: [AMBER] ambertools 1.2 compilation error on Debian Linux
(Mon Jun 20 2011 - 08:39:13 PDT)
Re: [AMBER] ambertools.1.5 installation errors on Linux
(Mon Jun 20 2011 - 04:57:55 PDT)
Re: [AMBER] RDF
(Fri Jun 17 2011 - 04:46:50 PDT)
Re: [AMBER] Methane with no surface area?
(Thu Jun 16 2011 - 12:00:02 PDT)
Re: [AMBER] PMEMD does not support intermolecular PRFs
(Thu Jun 16 2011 - 07:13:32 PDT)
Re: [AMBER] Installation Problem : Amber 9
(Thu Jun 16 2011 - 05:13:09 PDT)
Re: [AMBER] Parallel compilation of AmberTools1.5 failed (2)
(Thu Jun 16 2011 - 05:03:34 PDT)
Re: [AMBER] About difference between Sander and Pmemd
(Thu Jun 16 2011 - 04:48:01 PDT)
Re: [AMBER] MPI_ABORT errorcode 1 sander
(Wed Jun 15 2011 - 13:40:01 PDT)
Re: [AMBER] MPI_ABORT errorcode 1 for sander.MPI
(Wed Jun 15 2011 - 12:46:36 PDT)
Re: [AMBER] MPI_ABORT errorcode 1 for sander.MPI
(Wed Jun 15 2011 - 12:15:38 PDT)
Re: [AMBER] Installation Problem : Amber 9
(Wed Jun 15 2011 - 06:10:46 PDT)
Re: [AMBER] Problem related to Missing amino acids in pdb
(Wed Jun 15 2011 - 05:27:37 PDT)
Re: [AMBER] Parallel compilation of AmberTools1.5 failed
(Wed Jun 15 2011 - 05:07:43 PDT)
Re: [AMBER] loadPdbUsingSeq command
(Wed Jun 15 2011 - 04:40:51 PDT)
Re: [AMBER] loadPdbUsingSeq command
(Tue Jun 14 2011 - 06:39:48 PDT)
Re: [AMBER] loadPdbUsingSeq command
(Tue Jun 14 2011 - 06:27:41 PDT)
Re: [AMBER] loadPdbUsingSeq command
(Tue Jun 14 2011 - 05:00:14 PDT)
Re: [AMBER] problems ahout simulating a molecular crystal
(Mon Jun 13 2011 - 06:46:22 PDT)
Re: [AMBER] Structured water molecules with leap
(Mon Jun 13 2011 - 06:08:09 PDT)
Re: [AMBER] Leap question/suggestion for leap developers
(Mon Jun 13 2011 - 05:37:40 PDT)
Re: [AMBER] noesy and dip Program error when testing Amber11 Parallel
(Mon Jun 13 2011 - 05:14:35 PDT)
Re: [AMBER] Can Amoeba force field be used with divalent ions?
(Mon Jun 13 2011 - 04:58:54 PDT)
Re: [AMBER] Simulating a periodic System about Molecular Crystal
(Mon Jun 06 2011 - 04:45:45 PDT)
Re: [AMBER] unexpected behavior of ambpdb
(Fri Jun 03 2011 - 09:54:40 PDT)
Re: [AMBER] AmberTools 1.5 installation problem
(Thu Jun 02 2011 - 08:42:41 PDT)
Re: [AMBER] Force fields for DNA, what to choose?
(Thu Jun 02 2011 - 08:40:36 PDT)
Re: [AMBER] AmberTools 1.5 installation problem
(Thu Jun 02 2011 - 08:01:51 PDT)
Re: [AMBER] AmberTools 1.5 installation problem
(Thu Jun 02 2011 - 05:16:36 PDT)
Re: [AMBER] Bug - AMBER Atom type - iodine
(Wed Jun 01 2011 - 11:52:41 PDT)
Re: [AMBER] RAM requirements
(Wed Jun 01 2011 - 10:29:51 PDT)
Re: [AMBER] Question about the influence of trajectory format (ioutfm) on results - part 2
(Wed Jun 01 2011 - 09:30:07 PDT)
Re: [AMBER] AMBER
(Wed Jun 01 2011 - 05:49:23 PDT)
Re: [AMBER] NMR restraints file format
(Wed Jun 01 2011 - 04:53:32 PDT)
Re: [AMBER] Sorry again..this is right
(Wed Jun 01 2011 - 04:49:38 PDT)
Re: [AMBER] Question about the influence of trajectory format (ioutfm) on results
(Wed Jun 01 2011 - 04:45:05 PDT)
David A. Case
Re: [AMBER] ff03 force field
(Tue Jun 28 2011 - 13:24:48 PDT)
Re: [AMBER] Sander Error
(Sat Jun 25 2011 - 07:52:10 PDT)
Re: [AMBER] Architecture/compiler is not supported Error!
(Sat Jun 25 2011 - 07:49:17 PDT)
Re: [AMBER] installing ambertools
(Fri Jun 24 2011 - 14:15:04 PDT)
Re: [AMBER] Entropy Decomposition
(Fri Jun 24 2011 - 14:12:20 PDT)
Re: [AMBER] Entropy Decomposition
(Fri Jun 24 2011 - 08:57:27 PDT)
Re: [AMBER] Sander Error
(Fri Jun 24 2011 - 08:01:59 PDT)
Re: [AMBER] DIELC constant for normal mode analyses in vacuum ?
(Thu Jun 23 2011 - 19:35:40 PDT)
Re: [AMBER] ptraj error with *** glibc detected *** ptraj: free(): invalid next size (normal)
(Sat Jun 11 2011 - 08:12:41 PDT)
Re: [AMBER] Issues with Generating Prep File from Gaussian output using Antechamber
(Sat Jun 11 2011 - 07:27:17 PDT)
Re: [AMBER] problems ahout simulating a molecular crystal
(Sat Jun 11 2011 - 07:03:23 PDT)
Re: [AMBER] Amber 10: Compilation error
(Sat Jun 11 2011 - 06:56:59 PDT)
Re: [AMBER] Using PQR files produced by PDB2PQR as input fortleap/x leap. .
(Fri Jun 10 2011 - 03:12:38 PDT)
Re: [AMBER] ptraj error with *** glibc detected *** ptraj: free(): invalid next size (normal)
(Fri Jun 10 2011 - 03:12:01 PDT)
Re: [AMBER] problems ahout simulating a molecular crystal
(Fri Jun 10 2011 - 03:11:49 PDT)
Re: [AMBER] Loadin AMBER9 in linux
(Fri Jun 10 2011 - 03:08:45 PDT)
Re: [AMBER] problems ahout simulating a molecular crystal
(Thu Jun 09 2011 - 09:59:26 PDT)
Re: [AMBER] Problem related to teh residue template and add ion
(Thu Jun 09 2011 - 09:55:38 PDT)
Re: [AMBER] Using PQR files produced by PDB2PQR as input for tleap/xleap
(Thu Jun 09 2011 - 03:32:34 PDT)
Re: [AMBER] Installation problem
(Thu Jun 09 2011 - 01:57:42 PDT)
Re: [AMBER] problem about entropy calculation
(Thu Jun 09 2011 - 01:45:40 PDT)
Re: [AMBER] Using PQR files produced by PDB2PQR as input for tleap/xleap
(Thu Jun 09 2011 - 01:36:55 PDT)
Re: [AMBER] sander.mpi with amoeba?
(Wed Jun 08 2011 - 14:15:09 PDT)
Re: [AMBER] Normal Mode Analysis
(Wed Jun 08 2011 - 09:48:22 PDT)
Re: [AMBER] rmsd calculation
(Tue Jun 07 2011 - 04:32:26 PDT)
David Cantu
Re: [AMBER] Non-Standard Residues Problems
(Thu Jun 30 2011 - 19:33:30 PDT)
Re: [AMBER] Non-Standard Residues Problems
(Thu Jun 30 2011 - 16:10:12 PDT)
Re: [AMBER] Non-Standard Residues Problems
(Thu Jun 30 2011 - 10:47:05 PDT)
Re: [AMBER] Non-Standard Residues Problems
(Wed Jun 29 2011 - 15:14:40 PDT)
Re: [AMBER] Non-Standard Residues Problems
(Wed Jun 29 2011 - 12:36:49 PDT)
[AMBER] Non-Standard Residues Problems
(Wed Jun 29 2011 - 10:38:36 PDT)
Re: [AMBER] Antechamber Error
(Thu Jun 23 2011 - 08:53:43 PDT)
Re: [AMBER] Antechamber Error
(Wed Jun 22 2011 - 15:11:31 PDT)
Re: [AMBER] Antechamber Error
(Wed Jun 22 2011 - 08:48:54 PDT)
Re: [AMBER] Antechamber Error
(Tue Jun 21 2011 - 18:16:43 PDT)
Re: [AMBER] Normal Mode Analysis
(Mon Jun 13 2011 - 14:11:18 PDT)
[AMBER] Antechamber Error
(Mon Jun 13 2011 - 14:09:42 PDT)
Re: [AMBER] Normal Mode Analysis
(Wed Jun 08 2011 - 08:10:10 PDT)
[AMBER] Normal Mode Analysis
(Tue Jun 07 2011 - 16:08:48 PDT)
David Case
Re: [AMBER] Recompiling amber 8 on IBM
(Wed Jun 29 2011 - 10:16:42 PDT)
Re: [AMBER] trouble installing Amber 10
(Tue Jun 21 2011 - 19:39:59 PDT)
Re: [AMBER] Nucleic residues with methylphosphonates
(Thu Jun 16 2011 - 18:40:41 PDT)
Dean Cuebas
[AMBER] Frequency analysis of small molecule, constructing heterocyclic ring systems
(Tue Jun 21 2011 - 21:07:28 PDT)
Re: [AMBER] Restraint Minimization
(Wed Jun 15 2011 - 18:34:41 PDT)
DEBOSTUTI GHOSHDASTIDAR
Re: [AMBER] NMR chemical shift restraints for an intrinsically disordered peptide
(Thu Jun 23 2011 - 05:58:38 PDT)
[AMBER] Velocity autocorrelation function
(Wed Jun 22 2011 - 02:10:28 PDT)
Dian Jiao
Re: [AMBER] Can Amoeba force field be used with divalent ions?
(Mon Jun 13 2011 - 08:37:08 PDT)
Dmitry Nilov
Re: [AMBER] Steered Molecular Dynamics
(Tue Jun 28 2011 - 02:07:08 PDT)
Re: [AMBER] Steered Molecular Dynamics
(Tue Jun 28 2011 - 00:34:42 PDT)
Re: [AMBER] Steered Molecular Dynamics
(Mon Jun 27 2011 - 13:06:01 PDT)
Re: [AMBER] Units of SMD Simulation Output
(Mon Jun 06 2011 - 20:57:42 PDT)
Dmitry Osolodkin
Re: [AMBER] RAM requirements
(Wed Jun 01 2011 - 09:36:07 PDT)
Dwight McGee
Re: [AMBER] Steered Molecular Dynamics
(Mon Jun 27 2011 - 14:38:30 PDT)
Re: [AMBER] Normal Mode Analysis
(Tue Jun 07 2011 - 18:07:45 PDT)
e p
[AMBER] dist restraint
(Wed Jun 29 2011 - 06:08:00 PDT)
Eliac Brown
[AMBER] PDB survey
(Mon Jun 13 2011 - 20:56:48 PDT)
Elisa Frezza
[AMBER] Installation Problem
(Tue Jun 28 2011 - 10:19:54 PDT)
Emmanuel Baribefe Naziga
Re: [AMBER] Vibrational entropy with NAB
(Wed Jun 22 2011 - 09:51:11 PDT)
Re: [AMBER] Vibrational entropy with NAB
(Wed Jun 22 2011 - 08:24:22 PDT)
[AMBER] Vibrational entropy with NAB
(Tue Jun 21 2011 - 17:17:42 PDT)
Erin Kelly
[AMBER] MPI_ABORT errorcode 1 sander
(Wed Jun 15 2011 - 12:58:40 PDT)
Re: [AMBER] MPI_ABORT errorcode 1 for sander.MPI
(Wed Jun 15 2011 - 12:25:39 PDT)
Re: [AMBER] MPI_ABORT errorcode 1 for sander.MPI
(Wed Jun 15 2011 - 12:24:58 PDT)
[AMBER] MPI_ABORT errorcode 1 for sander.MPI
(Wed Jun 15 2011 - 11:44:37 PDT)
Esam Tolba
[AMBER] Adding NH2 at the end of peptide
(Thu Jun 30 2011 - 03:51:55 PDT)
[AMBER] I want to add amide group at the end of my peptide ?
(Tue Jun 28 2011 - 03:12:04 PDT)
Fabrício Bracht
[AMBER] ptraj in parallel
(Tue Jun 28 2011 - 11:06:06 PDT)
[AMBER] Restart problems with pmemd.cuda
(Mon Jun 13 2011 - 08:42:04 PDT)
fatahiya
[AMBER] how to interprete x.ss file
(Wed Jun 15 2011 - 01:27:38 PDT)
Re: [AMBER] secstruct analysis
(Tue Jun 14 2011 - 01:14:36 PDT)
Re: [AMBER] secstruct analysis
(Tue Jun 14 2011 - 00:52:24 PDT)
[AMBER] secstruct analysis
(Tue Jun 14 2011 - 00:12:52 PDT)
Fernando Martín García
Re: [AMBER] System temperature
(Fri Jun 24 2011 - 03:47:01 PDT)
Re: [AMBER] System temperature
(Fri Jun 24 2011 - 00:10:07 PDT)
Re: [AMBER] System temperature
(Wed Jun 22 2011 - 05:09:53 PDT)
Re: [AMBER] System temperature
(Thu Jun 16 2011 - 02:00:29 PDT)
[AMBER] System temperature
(Wed Jun 15 2011 - 07:31:12 PDT)
Francesco Oteri
Re: [AMBER] algorithm for rms
(Fri Jun 17 2011 - 08:03:11 PDT)
Francesco Pietra
[AMBER] Suggestions for additions to AmberTools
(Tue Jun 28 2011 - 14:21:25 PDT)
Re: [AMBER] AmberTools 1.5 gnu compilation fails under FC15
(Mon Jun 20 2011 - 13:38:08 PDT)
Re: [AMBER] ambertools 1.2 compilation error on Debian Linux
(Mon Jun 20 2011 - 13:33:37 PDT)
[AMBER] ambertools 1.2 compilation error on Debian Linux
(Mon Jun 20 2011 - 07:36:58 PDT)
[AMBER] ambertools.1.5 installation errors on Linux
(Mon Jun 20 2011 - 01:15:48 PDT)
Fredrick Devadoss
Re: [AMBER] rmsd calculation
(Tue Jun 07 2011 - 04:32:26 PDT)
FyD
Re: [AMBER] Non-Standard Residues Problems
(Thu Jun 30 2011 - 12:38:21 PDT)
Re: [AMBER] Non-Standard Residues Problems
(Thu Jun 30 2011 - 07:07:00 PDT)
Re: [AMBER] Glycam Parameters for O-SIALIC ACID
(Fri Jun 24 2011 - 22:46:08 PDT)
Re: [AMBER] Nucleic residues with methylphosphonates
(Thu Jun 16 2011 - 22:37:40 PDT)
Re: [AMBER] Error While running RED III.4
(Tue Jun 14 2011 - 12:29:56 PDT)
Re: [AMBER] ANTECHAMBER/RESP
(Sat Jun 11 2011 - 00:22:38 PDT)
Re: [AMBER] RED
(Fri Jun 03 2011 - 15:58:07 PDT)
George Tzotzos
Re: [AMBER] Steered Molecular Dynamics
(Tue Jun 28 2011 - 01:40:30 PDT)
Re: [AMBER] Steered Molecular Dynamics
(Mon Jun 27 2011 - 15:18:23 PDT)
Re: [AMBER] Steered Molecular Dynamics
(Mon Jun 27 2011 - 14:56:26 PDT)
Re: [AMBER] Steered Molecular Dynamics
(Mon Jun 27 2011 - 14:14:39 PDT)
Re: [AMBER] Steered Molecular Dynamics
(Mon Jun 27 2011 - 13:40:14 PDT)
Re: [AMBER] Steered Molecular Dynamics
(Mon Jun 27 2011 - 13:33:46 PDT)
[AMBER] Steered Molecular Dynamics
(Mon Jun 27 2011 - 10:49:57 PDT)
Re: [AMBER] Sirius software
(Wed Jun 22 2011 - 01:55:54 PDT)
Re: [AMBER] MMPBSA: general question
(Tue Jun 07 2011 - 10:07:54 PDT)
[AMBER] MMPBSA: general question
(Tue Jun 07 2011 - 09:51:12 PDT)
[AMBER] ptaj: contacts
(Fri Jun 03 2011 - 08:31:53 PDT)
Re: [AMBER] ptraj: cluster
(Thu Jun 02 2011 - 07:50:05 PDT)
Re: [AMBER] ptraj: cluster
(Thu Jun 02 2011 - 06:51:10 PDT)
Re: [AMBER] ptraj: cluster
(Thu Jun 02 2011 - 06:11:41 PDT)
[AMBER] ptraj: cluster
(Thu Jun 02 2011 - 05:45:27 PDT)
Re: [AMBER] pH-dependent folding simulation
(Wed Jun 01 2011 - 13:25:24 PDT)
Re: [AMBER] pH-dependent folding simulation
(Wed Jun 01 2011 - 10:25:29 PDT)
[AMBER] pH-dependent folding simulation
(Wed Jun 01 2011 - 09:32:50 PDT)
german.erlenkamp.pharmazie.uni-halle.de
[AMBER] Zotac GTX 580 3 GB
(Wed Jun 01 2011 - 01:24:09 PDT)
gloriarg
[AMBER] problems with relaxing a phosphonamide parametrizated with Antechamber
(Mon Jun 20 2011 - 10:36:59 PDT)
Gordon Freeman
[AMBER] Problems Compiling Amber10
(Fri Jun 10 2011 - 10:02:52 PDT)
Gould, Ian R
Re: [AMBER] Zotac GTX 580 3 GB
(Wed Jun 01 2011 - 08:09:47 PDT)
Re: [AMBER] Zotac GTX 580 3 GB
(Wed Jun 01 2011 - 01:54:25 PDT)
Re: [AMBER] Zotac GTX 580 3 GB
(Wed Jun 01 2011 - 01:53:12 PDT)
Guenegou, Guillaume [ORDFR]
[AMBER] sleap/tleap mol2 features
(Tue Jun 28 2011 - 02:03:46 PDT)
[AMBER] mmpbsa.py
(Mon Jun 27 2011 - 08:38:38 PDT)
[AMBER] MMPBSA.py decomp
(Wed Jun 22 2011 - 02:07:03 PDT)
[AMBER] Energy decomposition
(Fri Jun 17 2011 - 06:25:56 PDT)
[AMBER] Alanine scanning
(Fri Jun 10 2011 - 06:51:02 PDT)
[AMBER] Structured water molecules with leap
(Fri Jun 10 2011 - 06:39:48 PDT)
[AMBER] Detection of residues within a sphere
(Wed Jun 08 2011 - 05:40:53 PDT)
Re: [AMBER] Alanine scanning with CYS
(Wed Jun 01 2011 - 04:42:05 PDT)
[AMBER] Alanine scanning with CYS
(Wed Jun 01 2011 - 01:53:57 PDT)
Gustavo Seabra
Re: [AMBER] Antechamber Error
(Wed Jun 22 2011 - 06:24:45 PDT)
Hai Long
[AMBER] Dihedral parameters for sp carbon in GAFF
(Wed Jun 29 2011 - 16:38:08 PDT)
hanlu0366
Re: [AMBER] problems ahout simulating a molecular crystal
(Tue Jun 21 2011 - 07:25:02 PDT)
Re: [AMBER] problems ahout simulating a molecular crystal
(Mon Jun 13 2011 - 06:20:19 PDT)
Re: [AMBER] problems ahout simulating a molecular crystal
(Fri Jun 10 2011 - 05:55:30 PDT)
Re: [AMBER] problems ahout simulating a molecular crystal
(Fri Jun 10 2011 - 00:11:13 PDT)
[AMBER] problems ahout simulating a molecular crystal
(Thu Jun 09 2011 - 04:51:45 PDT)
Re: [AMBER] Simulating a periodic System about Molecular Crystal
(Sun Jun 05 2011 - 20:34:12 PDT)
Re: [AMBER] Simulating a periodic System about Molecular Crystal
(Sun Jun 05 2011 - 19:09:14 PDT)
[AMBER] Simulating a periodic System about Molecular Crystal
(Sun Jun 05 2011 - 06:27:07 PDT)
Hannes Loeffler
Re: [AMBER] velocity auto correlation function; resident time;
(Thu Jun 16 2011 - 23:58:40 PDT)
hari krishna
Re: [AMBER] Problem in the energetics of the system Shake cannot be accomplished.
(Wed Jun 29 2011 - 09:44:34 PDT)
[AMBER] Problem in the energetics of the system Shake cannot be accomplished.
(Wed Jun 29 2011 - 08:06:24 PDT)
[AMBER] Uracil is not recognised as a nucleotide in Xleap - in FF99
(Tue Jun 28 2011 - 23:50:40 PDT)
[AMBER] Error While running RED III.4
(Tue Jun 14 2011 - 03:02:41 PDT)
[AMBER] Solution for frozen atom type
(Sat Jun 11 2011 - 02:07:39 PDT)
Hirdesh Kumar
Re: [AMBER] regarding per residue wise free energy decomposition
(Sun Jun 26 2011 - 22:49:03 PDT)
Re: [AMBER] regarding per residue wise free energy decomposition
(Fri Jun 24 2011 - 00:59:30 PDT)
[AMBER] query regarding void volume calculation in protein-ligand complex
(Wed Jun 22 2011 - 12:09:05 PDT)
[AMBER] regarding per residue wise free energy decomposition
(Tue Jun 21 2011 - 21:57:05 PDT)
[AMBER] regarding per residue decomposition of binding free energy using perl script
(Tue Jun 21 2011 - 09:45:09 PDT)
Re: [AMBER] MMPBSA-binding energy calculation
(Tue Jun 21 2011 - 09:09:46 PDT)
[AMBER] regarding pi-pi interaction
(Tue Jun 07 2011 - 03:19:32 PDT)
Re: [AMBER] energy decomposition with mmpbsa.py
(Mon Jun 06 2011 - 20:28:00 PDT)
Re: [AMBER] Energy Decomposition Error using Perl Script (#RECMAP + #LIGMAP != #COMPRI)
(Thu Jun 02 2011 - 03:51:54 PDT)
[AMBER] Energy Decomposition Error using Perl Script (#RECMAP + #LIGMAP != #COMPRI)
(Thu Jun 02 2011 - 02:58:46 PDT)
Re: [AMBER] sander terminates abruptly
(Thu Jun 02 2011 - 01:42:42 PDT)
Hiromichi Tsurui
Re: [AMBER] Does anyone know a screening program of hardware validity for GeForce GTX board?
(Wed Jun 08 2011 - 18:11:44 PDT)
[AMBER] Does anyone know a screening program of hardware validity for GeForce GTX board?
(Wed Jun 08 2011 - 03:48:01 PDT)
Hugh Heldenbrand
Re: [AMBER] Hairpin
(Tue Jun 14 2011 - 04:41:07 PDT)
Ignacio J. General
Re: [AMBER] Estimation of free energy of solvation ?
(Wed Jun 15 2011 - 07:45:30 PDT)
Re: [AMBER] Detection of residues within a sphere
(Wed Jun 08 2011 - 06:39:48 PDT)
Irene Newhouse
Re: [AMBER] using Mg with ff99SB
(Fri Jul 01 2011 - 01:43:25 PDT)
[AMBER] using Mg with ff99SB
(Thu Jun 30 2011 - 14:24:20 PDT)
Jacopo Sgrignani
Re: [AMBER] NMR chemical shift restraints for an intrinsically disordered peptide
(Thu Jun 23 2011 - 04:50:53 PDT)
Jagur Lambix
Re: [AMBER] secondary structure plotting
(Fri Jun 24 2011 - 13:50:21 PDT)
[AMBER] secondary structure plotting
(Thu Jun 23 2011 - 13:45:44 PDT)
Jason Swails
Re: [AMBER] software assistance
(Tue Jun 28 2011 - 10:54:18 PDT)
Re: [AMBER] Steered Molecular Dynamics
(Mon Jun 27 2011 - 16:46:07 PDT)
Re: [AMBER] mmpbsa.py
(Mon Jun 27 2011 - 16:41:32 PDT)
Re: [AMBER] AMBER: error in reading namelist cntrl
(Sat Jun 25 2011 - 17:34:22 PDT)
Re: [AMBER] single amino acid energies
(Sat Jun 25 2011 - 13:27:52 PDT)
Re: [AMBER] Entropy Decomposition
(Fri Jun 24 2011 - 14:14:23 PDT)
Re: [AMBER] AmberTools 1.5 + Amber 11 installation - bugfixes conflicts?
(Thu Jun 23 2011 - 13:02:53 PDT)
Re: [AMBER] AMBER 11 and Ambertools 1.5 Installs failing tests for mmpbsa_py
(Wed Jun 22 2011 - 20:25:29 PDT)
Re: [AMBER] Nmode calculations using Amber 8
(Wed Jun 22 2011 - 00:50:57 PDT)
Re: [AMBER] Vibrational entropy with NAB
(Wed Jun 22 2011 - 00:48:28 PDT)
Re: [AMBER] System temperature
(Fri Jun 17 2011 - 18:55:46 PDT)
Re: [AMBER] Problem related to the load PDB
(Fri Jun 17 2011 - 09:14:49 PDT)
Re: [AMBER] Installation of Amber 9 : Problem
(Fri Jun 17 2011 - 09:12:57 PDT)
Re: [AMBER] [q4md-fft] Re: Error While running RED III.4
(Fri Jun 17 2011 - 09:09:36 PDT)
Re: [AMBER] About difference between Sander and Pmemd
(Thu Jun 16 2011 - 23:48:20 PDT)
Re: [AMBER] PMEMD does not support intermolecular PRFs
(Thu Jun 16 2011 - 23:37:56 PDT)
Re: [AMBER] PMEMD does not support intermolecular PRFs
(Thu Jun 16 2011 - 18:29:53 PDT)
Re: [AMBER] Residue numbering
(Thu Jun 16 2011 - 12:15:23 PDT)
Re: [AMBER] PMEMD does not support intermolecular PRFs
(Thu Jun 16 2011 - 07:44:24 PDT)
Re: [AMBER] PMEMD does not support intermolecular PRFs
(Thu Jun 16 2011 - 07:34:17 PDT)
Re: [AMBER] PMEMD does not support intermolecular PRFs
(Wed Jun 15 2011 - 14:28:16 PDT)
Re: [AMBER] Parallel compilation of AmberTools1.5 failed
(Tue Jun 14 2011 - 22:26:14 PDT)
Re: [AMBER] Compile Python error
(Tue Jun 14 2011 - 07:04:18 PDT)
Re: [AMBER] Compile Python error
(Mon Jun 13 2011 - 23:53:27 PDT)
Re: [AMBER] Compile Python error
(Mon Jun 13 2011 - 21:01:39 PDT)
Re: [AMBER] Normal Mode Analysis
(Mon Jun 13 2011 - 14:59:15 PDT)
Re: [AMBER] High-temperature output in REMD
(Sun Jun 12 2011 - 21:25:03 PDT)
Re: [AMBER] About "Must have more residues than processors"
(Sun Jun 12 2011 - 16:14:30 PDT)
Re: [AMBER] Amber 11 and AmberTools 1.5 on Debian 6
(Sun Jun 12 2011 - 09:48:46 PDT)
Re: [AMBER] format error from mmpbsa.py
(Sun Jun 12 2011 - 09:41:40 PDT)
Re: [AMBER] format error from mmpbsa.py
(Sat Jun 11 2011 - 20:02:20 PDT)
Re: [AMBER] format error from mmpbsa.py
(Sat Jun 11 2011 - 15:57:27 PDT)
Re: [AMBER] Amber Compilation error
(Fri Jun 10 2011 - 22:48:22 PDT)
Re: [AMBER] Question about INTRAmolecular restraint
(Fri Jun 10 2011 - 21:43:42 PDT)
Re: [AMBER] Problems Compiling Amber10
(Fri Jun 10 2011 - 21:34:57 PDT)
Re: [AMBER] Alanine scanning
(Fri Jun 10 2011 - 07:02:04 PDT)
Re: [AMBER] Using PQR files produced by PDB2PQR as input for tleap/xleap
(Thu Jun 09 2011 - 09:47:10 PDT)
Re: [AMBER] Loadin AMBER9 in linux
(Tue Jun 07 2011 - 08:11:36 PDT)
Re: [AMBER] PMEMD does not support intermolecular PRFs
(Tue Jun 07 2011 - 08:08:26 PDT)
Re: [AMBER] PMEMD does not support intermolecular PRFs
(Mon Jun 06 2011 - 23:12:09 PDT)
Re: [AMBER] Calculating energies
(Mon Jun 06 2011 - 06:02:07 PDT)
Re: [AMBER] Problem with make test.serial Amber 9
(Mon Jun 06 2011 - 05:58:28 PDT)
Re: [AMBER] AmberTools 1.5 installation problem
(Thu Jun 02 2011 - 09:27:32 PDT)
Re: [AMBER] Question about the influence of trajectory format (ioutfm) on results - part 2
(Wed Jun 01 2011 - 06:00:09 PDT)
Jennifer L. Muzyka
Re: [AMBER] trouble installing Amber 10
(Wed Jun 22 2011 - 08:06:09 PDT)
Re: [AMBER] trouble installing Amber 10
(Wed Jun 22 2011 - 06:17:34 PDT)
[AMBER] trouble installing Amber 10
(Tue Jun 21 2011 - 13:45:41 PDT)
Jerome Golebiowski
Re: [AMBER] restraints file
(Wed Jun 22 2011 - 00:29:39 PDT)
Jianyin Shao
Re: [AMBER] PTRAJ clustering
(Fri Jun 10 2011 - 23:51:57 PDT)
Re: [AMBER] PTRAJ clustering
(Tue Jun 07 2011 - 08:50:55 PDT)
Re: [AMBER] PTRAJ clustering
(Tue Jun 07 2011 - 08:44:21 PDT)
Jiri Sponer
Re: [AMBER] regarding pi-pi interaction
(Tue Jun 07 2011 - 03:28:00 PDT)
Re: [AMBER] Force fields for DNA, what to choose?
(Thu Jun 02 2011 - 09:09:47 PDT)
Jiri Wiesner
Re: [AMBER] Amber 11 and AmberTools 1.5 on Debian 6
(Sun Jun 12 2011 - 07:59:46 PDT)
Joachim Reichelt
Re: [AMBER] Sirius software
(Wed Jun 22 2011 - 00:51:58 PDT)
Joel Dockray
[AMBER] Antechamber: Failure to calculate Mulliken partial charges using a Tripos MOL2 input file
(Sat Jun 18 2011 - 17:09:32 PDT)
John S
Re: [AMBER] Error mmpbsa
(Mon Jun 27 2011 - 19:44:53 PDT)
[AMBER] Error mmpbsa
(Sun Jun 26 2011 - 20:29:24 PDT)
[AMBER] error running mmpbsa
(Sun Jun 26 2011 - 14:26:54 PDT)
Joseph Seemiller
[AMBER] Units of SMD Simulation Output
(Mon Jun 06 2011 - 13:16:44 PDT)
Julian Zachmann
Re: [AMBER] Ligand Minimization with Simulated Annealing
(Mon Jun 06 2011 - 07:42:00 PDT)
[AMBER] Ligand Minimization with Simulated Annealing
(Mon Jun 06 2011 - 07:24:51 PDT)
Re: [AMBER] Delete Solvatebox
(Wed Jun 01 2011 - 12:32:47 PDT)
[AMBER] Delete Solvatebox
(Wed Jun 01 2011 - 12:12:12 PDT)
Jyotsna Bhat
[AMBER] missing residue
(Wed Jun 15 2011 - 01:34:52 PDT)
Katrine Kirkeby Skeby
[AMBER] ptraj cluster
(Wed Jun 22 2011 - 04:21:58 PDT)
kaustubh joshi
[AMBER] query with multocomponent system
(Tue Jun 28 2011 - 07:49:29 PDT)
Keith Yarem
[AMBER] Non-periodic behavior of NMR restraints upon restart in a periodic system
(Tue Jun 21 2011 - 09:57:00 PDT)
Kevin Hauser
Re: [AMBER] Ligand Minimization with Simulated Annealing
(Mon Jun 06 2011 - 10:10:41 PDT)
Kevin Olsson
[AMBER] Natural Language Angle Restraint
(Mon Jun 27 2011 - 13:50:15 PDT)
Kshatresh Dutta Dubey
Re: [AMBER] Sander Error
(Fri Jun 24 2011 - 01:12:06 PDT)
Re: [AMBER] Amber 10: Compilation error
(Sun Jun 12 2011 - 21:09:56 PDT)
[AMBER] Amber Compilation error
(Fri Jun 10 2011 - 22:38:53 PDT)
[AMBER] Amber 10: Compilation error
(Fri Jun 10 2011 - 04:51:34 PDT)
kurisaki
Re: [AMBER] Kinetic energy in mdout file is not identical to that calculated from mdvel file.
(Tue Jun 28 2011 - 04:01:23 PDT)
[AMBER] Kinetic energy in mdout file is not identical to that calculated from mdvel file.
(Tue Jun 28 2011 - 01:19:29 PDT)
Re: [AMBER] Negative value of SASA calculated by surf command in cpptraj
(Sun Jun 12 2011 - 19:49:30 PDT)
Re: [AMBER] Negative value of SASA calculated by surf command in cpptraj
(Sun Jun 12 2011 - 19:29:19 PDT)
[AMBER] Negative value of SASA calculated by surf command in cpptraj
(Sun Jun 05 2011 - 20:30:54 PDT)
[AMBER] Error message for cpptraj
(Tue May 31 2011 - 22:01:51 PDT)
Lachele Foley (Lists)
Re: [AMBER] Glycam Parameters for O-SIALIC ACID
(Tue Jun 28 2011 - 10:51:29 PDT)
Re: [AMBER] Glycam Parameters for O-SIALIC ACID
(Mon Jun 27 2011 - 14:21:18 PDT)
Re: [AMBER] Glycam Parameters for O-SIALIC ACID
(Sat Jun 25 2011 - 05:49:42 PDT)
Re: [AMBER] installing ambertools
(Fri Jun 24 2011 - 13:54:09 PDT)
Re: [AMBER] Glycam Parameters for O-SIALIC ACID
(Fri Jun 24 2011 - 09:10:41 PDT)
Re: [AMBER] tleap error in reading structure generated from GLYCAM web
(Fri Jun 24 2011 - 07:09:50 PDT)
lnedialkova.gmail.com
[AMBER] Question on the construction of a topology file
(Fri Jun 24 2011 - 14:31:24 PDT)
Lorenzo Gontrani
Re: [AMBER] Gromacs to Amber trajectory
(Thu Jun 16 2011 - 09:10:06 PDT)
Re: [AMBER] Question about INTRAmolecular restraint
(Sat Jun 11 2011 - 12:58:20 PDT)
[AMBER] Question about INTRAmolecular restraint
(Fri Jun 10 2011 - 09:52:29 PDT)
Re: [AMBER] Question about the influence of trajectory format (ioutfm) on results - part 2
(Wed Jun 01 2011 - 08:34:18 PDT)
[AMBER] Question about the influence of trajectory format (ioutfm) on results - part 2
(Wed Jun 01 2011 - 03:11:53 PDT)
[AMBER] Sorry again..this is right
(Wed Jun 01 2011 - 02:52:43 PDT)
[AMBER] Binary reported data were wrong..
(Wed Jun 01 2011 - 02:48:11 PDT)
[AMBER] Question about the influence of trajectory format (ioutfm) on results
(Wed Jun 01 2011 - 02:43:55 PDT)
Mahmoud A. A. Ibrahim
Re: [AMBER] Bug - AMBER Atom type - iodine
(Wed Jun 01 2011 - 11:23:35 PDT)
Re: [AMBER] Bug - AMBER Atom type - iodine
(Wed Jun 01 2011 - 11:15:58 PDT)
[AMBER] Bug - AMBER Atom type - iodine
(Wed Jun 01 2011 - 10:30:11 PDT)
manikanthan bhavaraju
[AMBER] Nmode with amber8
(Tue Jun 28 2011 - 14:47:52 PDT)
[AMBER] Recompiling amber 8 on IBM
(Tue Jun 28 2011 - 13:54:30 PDT)
[AMBER] Nmode calculations using Amber 8
(Tue Jun 21 2011 - 17:19:52 PDT)
[AMBER] Nmode calculations using Amber 8
(Tue Jun 21 2011 - 12:29:14 PDT)
Manish
[AMBER] CHAMBER prmtop
(Mon Jun 27 2011 - 09:41:02 PDT)
Mannan
[AMBER] pairwise RMSD
(Tue Jun 28 2011 - 01:26:53 PDT)
Marc van der Kamp
Re: [AMBER] alanine mutagenisis in amber
(Wed Jun 22 2011 - 00:18:11 PDT)
Re: [AMBER] unexpected behavior of ambpdb
(Fri Jun 03 2011 - 08:36:07 PDT)
Marek Maly
Re: [AMBER] DIELC constant for normal mode analyses in vacuum ?
(Fri Jun 24 2011 - 08:56:37 PDT)
Re: [AMBER] DIELC constant for normal mode analyses in vacuum ?
(Thu Jun 23 2011 - 13:51:43 PDT)
Re: [AMBER] DIELC constant for normal mode analyses in vacuum ?
(Thu Jun 23 2011 - 07:40:19 PDT)
[AMBER] DIELC constant for normal mode analyses in vacuum ?
(Thu Jun 23 2011 - 05:55:04 PDT)
Re: [AMBER] Solid surface simulation in Amber - the recommended approach ?
(Mon Jun 20 2011 - 11:53:55 PDT)
Re: [AMBER] Estimation of free energy of solvation ?
(Wed Jun 15 2011 - 08:38:33 PDT)
Re: [AMBER] Estimation of free energy of solvation ?
(Wed Jun 15 2011 - 08:36:52 PDT)
Re: [AMBER] Estimation of free energy of solvation ?
(Wed Jun 15 2011 - 08:12:41 PDT)
Re: [AMBER] Estimation of free energy of solvation ?
(Wed Jun 15 2011 - 07:46:15 PDT)
[AMBER] Estimation of free energy of solvation ?
(Wed Jun 15 2011 - 07:19:37 PDT)
Re: [AMBER] Problem with two jobs on one GPU
(Wed Jun 08 2011 - 03:46:21 PDT)
[AMBER] Problem with two jobs on one GPU
(Mon Jun 06 2011 - 03:24:15 PDT)
Maria
Re: [AMBER] AMBER 11 and Ambertools 1.5 Installs failing tests for mmpbsa_py
(Thu Jun 23 2011 - 06:58:26 PDT)
[AMBER] AMBER 11 and Ambertools 1.5 Installs failing tests for mmpbsa_py
(Wed Jun 22 2011 - 14:18:47 PDT)
Mariano Rech
Re: [AMBER] pairwise RMSD
(Tue Jun 28 2011 - 02:35:12 PDT)
Re: [AMBER] Interpreting the distance covariance matrix
(Tue Jun 14 2011 - 17:22:03 PDT)
Re: [AMBER] Fwd: Interpreting the distance covariance matrix
(Tue Jun 14 2011 - 14:42:33 PDT)
Re: [AMBER] Fwd: Interpreting the distance covariance matrix
(Tue Jun 14 2011 - 14:40:01 PDT)
Mark Williamson
Re: [AMBER] VMD-Chamber interface
(Thu Jun 30 2011 - 02:59:15 PDT)
Re: [AMBER] CHAMBER prmtop
(Mon Jun 27 2011 - 11:27:17 PDT)
Re: [AMBER] format error from mmpbsa.py
(Mon Jun 13 2011 - 02:58:25 PDT)
Massimiliano Porrini
Re: [AMBER] restraints file
(Wed Jun 22 2011 - 01:51:08 PDT)
[AMBER] restraints file
(Tue Jun 21 2011 - 08:51:51 PDT)
Matias Factorovich
Re: [AMBER] running a MD with a innert gas
(Sat Jun 11 2011 - 11:07:46 PDT)
[AMBER] running a MD with a innert gas
(Fri Jun 10 2011 - 10:08:32 PDT)
Maura Catherine Mooney
Re: [AMBER] PMEMD does not support intermolecular PRFs
(Fri Jun 17 2011 - 07:37:19 PDT)
Re: [AMBER] PMEMD does not support intermolecular PRFs
(Thu Jun 16 2011 - 19:05:22 PDT)
Re: [AMBER] PMEMD does not support intermolecular PRFs
(Thu Jun 16 2011 - 07:54:49 PDT)
Re: [AMBER] PMEMD does not support intermolecular PRFs
(Thu Jun 16 2011 - 07:39:25 PDT)
Re: [AMBER] PMEMD does not support intermolecular PRFs
(Thu Jun 16 2011 - 06:54:33 PDT)
Re: [AMBER] PMEMD does not support intermolecular PRFs
(Tue Jun 07 2011 - 05:22:15 PDT)
Re: [AMBER] PMEMD does not support intermolecular PRFs
(Mon Jun 06 2011 - 08:10:50 PDT)
[AMBER] PMEMD does not support intermolecular PRFs
(Sun Jun 05 2011 - 08:44:43 PDT)
MD
[AMBER] velocity auto correlation function; resident time;
(Thu Jun 16 2011 - 21:38:57 PDT)
[AMBER] velocity auto correlation function; resident time;
(Thu Jun 16 2011 - 13:00:23 PDT)
Michael Zimmermann
[AMBER] ptraj, alignment, and rmsd
(Wed Jun 15 2011 - 13:13:35 PDT)
mish
Re: [AMBER] Glycam Parameters for O-SIALIC ACID
(Tue Jun 28 2011 - 09:19:59 PDT)
Re: [AMBER] Glycam Parameters for O-SIALIC ACID
(Sat Jun 25 2011 - 09:18:41 PDT)
[AMBER] Glycam Parameters for O-SIALIC ACID
(Fri Jun 24 2011 - 08:21:00 PDT)
Re: [AMBER] tleap error in reading structure generated from GLYCAM web
(Fri Jun 24 2011 - 07:21:05 PDT)
[AMBER] tleap error in reading structure generated from GLYCAM web
(Fri Jun 24 2011 - 01:58:11 PDT)
Re: [AMBER] non-bonded cutoff in the case of REMD in explicit solvent
(Wed Jun 08 2011 - 01:55:11 PDT)
[AMBER] non-bonded cutoff in the case of REMD in explicit solvent
(Wed Jun 08 2011 - 01:20:10 PDT)
Mo Chen
[AMBER] VMD-Chamber interface
(Wed Jun 29 2011 - 13:20:19 PDT)
[AMBER] Inquiry about installing AMBER
(Tue Jun 28 2011 - 08:33:19 PDT)
Mr. Joseph S. Castle
[AMBER] software assistance
(Tue Jun 28 2011 - 06:05:57 PDT)
Nadine Utz
Re: [AMBER] re-image
(Thu Jun 09 2011 - 07:04:25 PDT)
najmul arfin
[AMBER] Fwd:
(Thu Jun 30 2011 - 22:21:32 PDT)
Nitu Bansal
Re: [AMBER] prep files ATP-MG++ and for phosphorylated threonine
(Mon Jun 06 2011 - 10:26:55 PDT)
[AMBER] prep files ATP-MG++ and for phosphorylated threonine
(Sun Jun 05 2011 - 13:12:37 PDT)
Pablo I. D. Dans Puiggròs
Re: [AMBER] re-image
(Thu Jun 09 2011 - 06:53:09 PDT)
Re: [AMBER] re-image
(Thu Jun 09 2011 - 06:34:54 PDT)
pamodeo
[AMBER] AmberTools 1.5 gnu compilation fails under FC15
(Mon Jun 20 2011 - 13:11:22 PDT)
Paul S. Nerenberg
Re: [AMBER] RED
(Fri Jun 03 2011 - 14:30:31 PDT)
peker milas
Re: [AMBER] trouble installing Amber 10
(Wed Jun 22 2011 - 06:53:53 PDT)
Re: [AMBER] Solid surface simulation in Amber - the recommended approach ?
(Tue Jun 21 2011 - 05:03:09 PDT)
Re: [AMBER] Solid surface simulation in Amber - the recommended approach ?
(Mon Jun 20 2011 - 10:17:17 PDT)
pirincn
Re: [AMBER] mm_pbsa.pl with Fe(III) ion
(Thu Jun 23 2011 - 11:33:20 PDT)
[AMBER] mm_pbsa.pl with Fe(III) ion
(Thu Jun 23 2011 - 05:38:54 PDT)
Pooja Khurana
[AMBER] Restraint Minimization
(Wed Jun 15 2011 - 03:01:19 PDT)
Praapti Jayaswal
Re: [AMBER] sander terminates abruptly
(Thu Jun 02 2011 - 21:39:41 PDT)
Re: [AMBER] sander terminates abruptly
(Thu Jun 02 2011 - 04:08:35 PDT)
[AMBER] sander terminates abruptly
(Wed Jun 01 2011 - 21:01:36 PDT)
Prajwal Nandekar
[AMBER] Request for Amber Heme parameter file
(Tue Jun 21 2011 - 04:25:57 PDT)
Qian Wang
Re: [AMBER] amber10 output
(Thu Jun 16 2011 - 15:15:42 PDT)
Re: [AMBER] amber10 output
(Thu Jun 16 2011 - 14:41:17 PDT)
[AMBER] amber10 output
(Thu Jun 16 2011 - 13:42:09 PDT)
r smith
[AMBER] water test with pmemd.amba
(Mon Jun 13 2011 - 07:33:27 PDT)
[AMBER] water test with pmemd.amba
(Wed Jun 08 2011 - 08:26:38 PDT)
[AMBER] sander.mpi with amoeba?
(Wed Jun 08 2011 - 07:19:07 PDT)
Raja Pandian
[AMBER] MMPBSA
(Thu Jun 30 2011 - 03:56:01 PDT)
[AMBER] Gromacs to Amber trajectory
(Thu Jun 16 2011 - 07:20:12 PDT)
Raman Parkesh
Re: [AMBER] RNA duplex
(Tue Jun 28 2011 - 17:50:51 PDT)
Ray Luo, Ph.D.
Re: [AMBER] Error mmpbsa
(Thu Jun 30 2011 - 23:00:44 PDT)
Re: [AMBER] mm_pbsa.pl with Fe(III) ion
(Thu Jun 23 2011 - 10:47:50 PDT)
Re: [AMBER] SANDER BOMB
(Thu Jun 09 2011 - 08:53:27 PDT)
Re: [AMBER] MM-PBSA/GBSA of charged molecules
(Tue Jun 07 2011 - 10:55:28 PDT)
Richard Owczarzy
[AMBER] AmberTools 1.5 + Amber 11 installation - bugfixes conflicts?
(Thu Jun 23 2011 - 07:17:59 PDT)
Robert Duke
Re: [AMBER] About difference between Sander and Pmemd
(Fri Jun 17 2011 - 09:16:11 PDT)
Re: [AMBER] About difference between Sander and Pmemd
(Thu Jun 16 2011 - 20:10:51 PDT)
Re: [AMBER] RAM requirements
(Wed Jun 01 2011 - 10:29:21 PDT)
Re: [AMBER] RAM requirements
(Wed Jun 01 2011 - 10:25:29 PDT)
Ross Walker
Re: [AMBER] VMD-Chamber interface
(Thu Jun 30 2011 - 02:05:11 PDT)
Re: [AMBER] AMBER9- error in LEaP while learning MMPBSA tutorial
(Wed Jun 29 2011 - 02:02:41 PDT)
Re: [AMBER] ptraj in parallel
(Tue Jun 28 2011 - 11:35:10 PDT)
Re: [AMBER] Problems Compiling Amber11 Parallel GPU
(Mon Jun 27 2011 - 08:08:59 PDT)
Re: [AMBER] Sirius software
(Tue Jun 21 2011 - 08:35:26 PDT)
Re: [AMBER] System temperature
(Wed Jun 15 2011 - 16:00:04 PDT)
Re: [AMBER] Parallel compilation of AmberTools1.5 failed
(Wed Jun 15 2011 - 02:09:53 PDT)
Re: [AMBER] question about amber
(Tue Jun 14 2011 - 01:33:08 PDT)
Re: [AMBER] Restart problems with pmemd.cuda
(Mon Jun 13 2011 - 09:08:52 PDT)
Re: [AMBER] About "Must have more residues than processors"
(Mon Jun 13 2011 - 07:36:46 PDT)
Re: [AMBER] Problem with two jobs on one GPU
(Mon Jun 06 2011 - 09:23:08 PDT)
Re: [AMBER] PMEMD does not support intermolecular PRFs
(Sun Jun 05 2011 - 22:12:55 PDT)
Re: [AMBER] Choosing the number of replicas in NEB
(Fri Jun 03 2011 - 09:32:23 PDT)
Re: [AMBER] CHAMBER and making PDB files
(Wed Jun 01 2011 - 10:49:55 PDT)
Re: [AMBER] Bug - AMBER Atom type - iodine
(Wed Jun 01 2011 - 10:37:35 PDT)
Re: [AMBER] Zotac GTX 580 3 GB
(Wed Jun 01 2011 - 10:20:17 PDT)
Re: [AMBER] RAM requirements
(Wed Jun 01 2011 - 10:16:49 PDT)
Re: [AMBER] Zotac GTX 580 3 GB
(Wed Jun 01 2011 - 09:01:29 PDT)
Re: [AMBER] Zotac GTX 580 3 GB
(Wed Jun 01 2011 - 08:57:39 PDT)
Sajeewa Pemasinghe
Re: [AMBER] Fwd: warning in ptraj check coordinates()
(Fri Jun 17 2011 - 11:53:09 PDT)
[AMBER] Fwd: warning in ptraj check coordinates()
(Fri Jun 17 2011 - 11:21:49 PDT)
[AMBER] warning in ptraj check coordinates()
(Wed Jun 15 2011 - 09:17:21 PDT)
Re: [AMBER] Interpreting the distance covariance matrix
(Tue Jun 14 2011 - 18:09:15 PDT)
Re: [AMBER] Interpreting the distance covariance matrix
(Tue Jun 14 2011 - 16:49:04 PDT)
Re: [AMBER] Fwd: Interpreting the distance covariance matrix
(Tue Jun 14 2011 - 16:48:05 PDT)
Re: [AMBER] Interpreting the distance covariance matrix
(Tue Jun 14 2011 - 15:42:22 PDT)
Re: [AMBER] Interpreting the distance covariance matrix
(Tue Jun 14 2011 - 15:35:07 PDT)
[AMBER] Fwd: Interpreting the distance covariance matrix
(Tue Jun 14 2011 - 09:32:31 PDT)
[AMBER] Interpreting the distance covariance matrix
(Mon Jun 13 2011 - 15:48:39 PDT)
Sander B.
Re: [AMBER] PTRAJ clustering
(Wed Jun 08 2011 - 01:11:42 PDT)
[AMBER] PTRAJ clustering
(Tue Jun 07 2011 - 07:40:12 PDT)
Sasha Buzko
Re: [AMBER] Sirius software
(Wed Jun 22 2011 - 10:23:10 PDT)
Re: [AMBER] Sirius software
(Tue Jun 21 2011 - 10:21:11 PDT)
Scott Le Grand
Re: [AMBER] CUDA 4.0 RC
(Thu Jun 23 2011 - 09:49:18 PDT)
Re: [AMBER] Does anyone know a screening program of hardware validity for GeForce GTX board?
(Wed Jun 08 2011 - 10:26:04 PDT)
Re: [AMBER] Problem with two jobs on one GPU
(Mon Jun 06 2011 - 09:58:52 PDT)
Re: [AMBER] Zotac GTX 580 3 GB
(Wed Jun 01 2011 - 10:29:22 PDT)
Re: [AMBER] Zotac GTX 580 3 GB
(Wed Jun 01 2011 - 08:59:50 PDT)
Re: [AMBER] Zotac GTX 580 3 GB
(Wed Jun 01 2011 - 07:40:40 PDT)
Seibold, Stephen
[AMBER] RED
(Fri Jun 03 2011 - 14:11:43 PDT)
[AMBER] CHAMBER and making PDB files
(Wed Jun 01 2011 - 10:34:55 PDT)
Senthil Natesan
Re: [AMBER] simulation of small molecule with organic solvent and water
(Fri Jun 03 2011 - 07:12:05 PDT)
[AMBER] simulation of small molecule with organic solvent and water
(Thu Jun 02 2011 - 08:03:35 PDT)
Sergey Samsonov
[AMBER] Free energy perturbation of Ca2+ ion
(Fri Jun 10 2011 - 06:50:37 PDT)
Sergio R Aragon
Re: [AMBER] System temperature
(Wed Jun 22 2011 - 12:25:32 PDT)
Re: [AMBER] System temperature
(Wed Jun 22 2011 - 11:47:25 PDT)
Re: [AMBER] Residue numbering
(Thu Jun 16 2011 - 12:01:29 PDT)
Re: [AMBER] Problem related to the load PDB/missing residues problem
(Tue Jun 14 2011 - 23:56:20 PDT)
Re: [AMBER] Interpreting the distance covariance matrix
(Tue Jun 14 2011 - 16:40:41 PDT)
Re: [AMBER] Interpreting the distance covariance matrix
(Tue Jun 14 2011 - 15:16:28 PDT)
[AMBER] Leap question/suggestion for leap developers
(Sun Jun 12 2011 - 12:23:14 PDT)
Sheau Chen Lee
Re: [AMBER] AMBER9- error in LEaP while learning MMPBSA tutorial
(Thu Jun 30 2011 - 00:28:58 PDT)
[AMBER] AMBER9- error in LEaP while learning MMPBSA tutorial
(Tue Jun 28 2011 - 20:23:25 PDT)
Shesh Nath
[AMBER] Amber
(Wed Jun 15 2011 - 05:34:36 PDT)
[AMBER] Hairpin
(Tue Jun 14 2011 - 02:42:46 PDT)
[AMBER] Installation problem
(Tue Jun 07 2011 - 23:42:46 PDT)
Siavoush Dastmalchi
[AMBER] Amber 11 and AmberTools 1.5 on Debian 6
(Sun Jun 12 2011 - 04:10:24 PDT)
Re: [AMBER] AmberTools 1.5 installation problem
(Thu Jun 02 2011 - 10:39:56 PDT)
Re: [AMBER] AmberTools 1.5 installation problem
(Thu Jun 02 2011 - 09:02:02 PDT)
Re: [AMBER] AmberTools 1.5 installation problem
(Thu Jun 02 2011 - 08:21:16 PDT)
[AMBER] AmberTools 1.5 installation problem
(Thu Jun 02 2011 - 04:22:42 PDT)
Sindrila Dutta banik
Re: [AMBER] Problem related to Missing amino acids in pdb
(Tue Jun 14 2011 - 23:11:57 PDT)
[AMBER] Problem related to Missing amino acids in pdb
(Tue Jun 14 2011 - 23:06:31 PDT)
[AMBER] Problem related to the load PDB
(Tue Jun 14 2011 - 22:57:18 PDT)
[AMBER] Problem related to the load PDB
(Tue Jun 14 2011 - 22:47:57 PDT)
[AMBER] Problem related to the residue template and add ion
(Mon Jun 13 2011 - 09:01:36 PDT)
[AMBER] Problem related to teh residue template and add ion
(Fri Jun 10 2011 - 08:18:13 PDT)
[AMBER] Problem related to the residue template and add ion
(Thu Jun 09 2011 - 05:27:54 PDT)
[AMBER] Problem related to teh residue template and add ion
(Thu Jun 09 2011 - 03:47:16 PDT)
[AMBER] Problem related with the Ptraj
(Sat Jun 04 2011 - 04:14:08 PDT)
souvik sur
[AMBER] Installation of Amber 9 : Problem
(Wed Jun 15 2011 - 23:15:36 PDT)
Re: [AMBER] Installation Problem : Amber 9
(Wed Jun 15 2011 - 23:06:36 PDT)
[AMBER] Installation Problem : Amber 9
(Wed Jun 15 2011 - 05:41:21 PDT)
Re: [AMBER] Loadin AMBER9 in linux
(Sat Jun 11 2011 - 04:29:35 PDT)
Re: [AMBER] Loadin AMBER9 in linux
(Sat Jun 11 2011 - 02:23:51 PDT)
Re: [AMBER] Loadin AMBER9 in linux
(Fri Jun 10 2011 - 04:47:07 PDT)
Re: [AMBER] Loadin AMBER9 in linux
(Fri Jun 10 2011 - 02:56:23 PDT)
Re: [AMBER] Loadin AMBER9 in linux
(Wed Jun 08 2011 - 23:23:31 PDT)
Re: [AMBER] Loadin AMBER9 in linux
(Wed Jun 08 2011 - 02:31:36 PDT)
Re: [AMBER] Loadin AMBER9 in linux
(Wed Jun 08 2011 - 00:26:26 PDT)
Re: [AMBER] Loadin AMBER9 in linux
(Wed Jun 08 2011 - 00:10:55 PDT)
Re: [AMBER] Loadin AMBER9 in linux
(Tue Jun 07 2011 - 23:42:51 PDT)
Re: [AMBER] Loadin AMBER9 in linux
(Tue Jun 07 2011 - 10:15:31 PDT)
Re: [AMBER] Loadin AMBER9 in linux
(Tue Jun 07 2011 - 03:44:19 PDT)
Re: [AMBER] Loadin AMBER9 in linux
(Tue Jun 07 2011 - 03:14:26 PDT)
[AMBER] Loadin AMBER9 in linux
(Tue Jun 07 2011 - 03:08:00 PDT)
steinbrt.rci.rutgers.edu
Re: [AMBER] Estimation of free energy of solvation ?
(Wed Jun 15 2011 - 08:36:21 PDT)
Re: [AMBER] Estimation of free energy of solvation ?
(Wed Jun 15 2011 - 07:58:10 PDT)
subrata paul
[AMBER] hydration number
(Tue Jun 14 2011 - 23:38:26 PDT)
[AMBER] bin size for rdf
(Wed Jun 08 2011 - 09:23:05 PDT)
Takeshi Baba
Re: [AMBER] netcdf
(Tue Jun 28 2011 - 00:02:38 PDT)
[AMBER] netcdf
(Mon Jun 27 2011 - 21:08:51 PDT)
Re: [AMBER] How to prepare ATP with Antechamber?
(Tue Jun 21 2011 - 02:05:03 PDT)
[AMBER] Resp charge
(Sat Jun 18 2011 - 01:18:51 PDT)
tdo.chem.ucsb.edu
Re: [AMBER] ptraj: Could not find target 300.000000 in any of the replica trajectories
(Wed Jun 15 2011 - 07:20:26 PDT)
Re: [AMBER] ptraj: Could not find target 300.000000 in any of the replica trajectories
(Wed Jun 15 2011 - 06:57:43 PDT)
[AMBER] ptraj: Could not find target 300.000000 in any of the replica trajectories
(Wed Jun 15 2011 - 06:49:23 PDT)
[AMBER] High-temperature output in REMD
(Sun Jun 12 2011 - 18:16:44 PDT)
TH Chew
Re: [AMBER] Loadin AMBER9 in linux
(Sat Jun 11 2011 - 22:30:56 PDT)
Re: [AMBER] Loadin AMBER9 in linux
(Sat Jun 11 2011 - 02:32:24 PDT)
Re: [AMBER] Loadin AMBER9 in linux
(Fri Jun 10 2011 - 07:07:39 PDT)
Re: [AMBER] Loadin AMBER9 in linux
(Thu Jun 09 2011 - 06:49:59 PDT)
Re: [AMBER] Loadin AMBER9 in linux
(Wed Jun 08 2011 - 05:56:56 PDT)
Re: [AMBER] Loadin AMBER9 in linux
(Wed Jun 08 2011 - 00:45:12 PDT)
Re: [AMBER] Loadin AMBER9 in linux
(Wed Jun 08 2011 - 00:17:32 PDT)
Re: [AMBER] Loadin AMBER9 in linux
(Tue Jun 07 2011 - 23:47:29 PDT)
Re: [AMBER] Loadin AMBER9 in linux
(Tue Jun 07 2011 - 03:54:02 PDT)
Re: [AMBER] Loadin AMBER9 in linux
(Tue Jun 07 2011 - 03:11:23 PDT)
Re: [AMBER] Problem with make test.serial Amber 9
(Mon Jun 06 2011 - 22:20:39 PDT)
[AMBER] Problem with make test.serial Amber 9
(Mon Jun 06 2011 - 03:17:09 PDT)
Thomas Cheatham
Re: [AMBER] Fwd: warning in ptraj check coordinates()
(Fri Jun 17 2011 - 11:30:09 PDT)
Re: [AMBER] algorithm for rms
(Fri Jun 17 2011 - 08:20:18 PDT)
Re: [AMBER] ptraj: cluster
(Thu Jun 02 2011 - 07:21:37 PDT)
Re: [AMBER] ptraj: cluster
(Thu Jun 02 2011 - 06:36:10 PDT)
Thomas Cheatham III
Re: [AMBER] how to assess the convergence of the clustering
(Tue Jun 28 2011 - 14:36:56 PDT)
Re: [AMBER] Entropy Decomposition
(Fri Jun 24 2011 - 14:14:19 PDT)
Re: [AMBER] About the coordinates of input or output files
(Fri Jun 24 2011 - 13:39:21 PDT)
Thomas Evangelidis
Re: [AMBER] NMR chemical shift restraints for an intrinsically disordered peptide
(Thu Jun 23 2011 - 09:22:28 PDT)
[AMBER] NMR chemical shift restraints for an intrinsically disordered peptide
(Thu Jun 23 2011 - 02:32:06 PDT)
Thomas Gaillard
[AMBER] small inconsistencies in parm99.dat and parm94.dat
(Fri Jun 17 2011 - 02:43:23 PDT)
Re: [AMBER] rmsd calculation
(Tue Jun 07 2011 - 03:32:52 PDT)
tong Zhu
[AMBER] NMR restraints file format
(Wed Jun 01 2011 - 03:07:57 PDT)
Toshifumi Yui
Re: [AMBER] DIELC constant for normal mode analyses in vacuum ?
(Fri Jun 24 2011 - 00:11:34 PDT)
tsurma.umich.edu
Re: [AMBER] ff03 force field
(Thu Jun 30 2011 - 09:27:04 PDT)
[AMBER] ff03 force field
(Tue Jun 28 2011 - 11:07:19 PDT)
victor ma
Re: [AMBER] energy decomposition with mmpbsa.py
(Mon Jun 06 2011 - 10:12:51 PDT)
[AMBER] energy decomposition with mmpbsa.py
(Mon Jun 06 2011 - 10:07:29 PDT)
Vivek Shankar Bharadwaj
[AMBER] Issues with Generating Prep File from Gaussian output using Antechamber
(Fri Jun 10 2011 - 13:44:22 PDT)
Re: [AMBER] AMBER11 Installation on FEDORA 15
(Wed Jun 01 2011 - 18:06:18 PDT)
Xiao Chen
Re: [AMBER] Bfactor calculation in cpptraj
(Fri Jun 17 2011 - 02:54:51 PDT)
Re: [AMBER] Bfactor calculation in cpptraj
(Thu Jun 16 2011 - 01:26:44 PDT)
[AMBER] Bfactor calculation in cpptraj
(Wed Jun 15 2011 - 00:28:37 PDT)
Re: [AMBER] keyword ref
(Tue Jun 14 2011 - 21:22:43 PDT)
Re: [AMBER] keyword ref
(Tue Jun 14 2011 - 20:38:33 PDT)
[AMBER] keyword ref
(Mon Jun 13 2011 - 03:39:23 PDT)
[AMBER] CPPTRAJ- segmentation fault
(Thu Jun 09 2011 - 21:00:17 PDT)
Re: [AMBER] rmsd calculation
(Tue Jun 07 2011 - 21:55:53 PDT)
Re: [AMBER] rmsd calculation
(Tue Jun 07 2011 - 21:48:43 PDT)
Re: [AMBER] rmsd calculation
(Tue Jun 07 2011 - 04:04:09 PDT)
[AMBER] rmsd calculation
(Tue Jun 07 2011 - 02:03:57 PDT)
Re: [AMBER] production run duration
(Fri Jun 03 2011 - 01:53:44 PDT)
[AMBER] production run duration
(Thu Jun 02 2011 - 21:46:54 PDT)
Xioling Chuang
[AMBER] Amoeba with water and ions (2)
(Mon Jun 20 2011 - 19:05:48 PDT)
Re: [AMBER] Amoeba with water and ion
(Sun Jun 19 2011 - 07:49:18 PDT)
[AMBER] Amoeba with water and ion
(Fri Jun 17 2011 - 23:07:10 PDT)
Re: [AMBER] Parallel compilation of AmberTools1.5 failed (2)
(Thu Jun 16 2011 - 08:08:29 PDT)
Re: [AMBER] Parallel compilation of AmberTools1.5 failed (2)
(Thu Jun 16 2011 - 03:38:37 PDT)
Re: [AMBER] Parallel compilation of AmberTools1.5 failed
(Wed Jun 15 2011 - 22:06:59 PDT)
Re: [AMBER] Parallel compilation of AmberTools1.5 failed
(Tue Jun 14 2011 - 22:56:03 PDT)
[AMBER] Parallel compilation of AmberTools1.5 failed
(Tue Jun 14 2011 - 20:24:28 PDT)
Re: [AMBER] Compile Python error
(Tue Jun 14 2011 - 08:23:46 PDT)
Re: [AMBER] Compile Python error
(Tue Jun 14 2011 - 01:37:29 PDT)
Re: [AMBER] Compile Python error
(Mon Jun 13 2011 - 23:40:00 PDT)
Re: [AMBER] Compile Python error
(Mon Jun 13 2011 - 21:22:50 PDT)
[AMBER] Compile Python error
(Mon Jun 13 2011 - 19:21:04 PDT)
[AMBER] Can Amoeba force field be used with divalent ions?
(Mon Jun 13 2011 - 04:02:05 PDT)
[AMBER] SANDER BOMB
(Thu Jun 09 2011 - 07:41:29 PDT)
Zhi Wang
Re: [AMBER] format error from mmpbsa.py
(Sun Jun 12 2011 - 02:02:06 PDT)
Re: [AMBER] format error from mmpbsa.py
(Sun Jun 12 2011 - 01:31:05 PDT)
[AMBER] format error from mmpbsa.py
(Sat Jun 11 2011 - 14:01:38 PDT)
Zhu Tong
[AMBER] saving the first solvent shell molecules by Ptraj
(Mon Jun 27 2011 - 05:24:21 PDT)
zw258.cam.ac.uk
Re: [AMBER] format error from mmpbsa.py
(Mon Jun 13 2011 - 05:18:30 PDT)
Re: [AMBER] format error from mmpbsa.py
(Mon Jun 13 2011 - 03:25:41 PDT)
付婷
[AMBER] mmpbsa-bad atom (metal ions)
(Thu Jun 02 2011 - 17:59:26 PDT)
Last message date
:
Fri Jul 01 2011 - 02:00:03 PDT
Archived on
: Fri Apr 26 2024 - 05:54:23 PDT
789 messages
sort by
: [
thread
] [ author ] [
date
] [
subject
] [
attachment
]
Custom Search
