Amber Archive Dec 2010 by author
572 messages
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Starting
Tue Nov 30 2010 - 18:00:03 PST,
Ending
Fri Dec 31 2010 - 17:00:04 PST
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Adrian Roitberg
Re: [AMBER] What is the Value of C° (standard concentration) in calculating Free Energy
(Mon Dec 20 2010 - 23:57:20 PST)
Re: [AMBER] (no subject)
(Wed Dec 01 2010 - 08:09:38 PST)
Alex Rodriguez
[AMBER] editing parm in LEAP
(Thu Dec 02 2010 - 08:15:36 PST)
Alex Spasic
[AMBER] Possibly wrong dihedrals assignment in the frcmod.parmbsc0 file
(Wed Dec 22 2010 - 10:26:10 PST)
[AMBER] Possibly wrong dihedrals assignment in the frcmod.parmbsc0 file
(Tue Dec 21 2010 - 09:01:18 PST)
Alice Wang
Re: [AMBER] High STD Value in pbsa
(Sun Dec 05 2010 - 23:48:05 PST)
Re: [AMBER] High STD Value in pbsa
(Sun Dec 05 2010 - 23:24:17 PST)
Re: [AMBER] High STD Value in pbsa
(Sun Dec 05 2010 - 19:12:02 PST)
[AMBER] High STD Value in pbsa
(Sun Dec 05 2010 - 18:26:24 PST)
amit banerjee
Re: [AMBER] Fw: configuring options for Amber tools
(Thu Dec 30 2010 - 22:29:46 PST)
[AMBER] Fw: configuring options for Amber tools
(Thu Dec 30 2010 - 02:16:47 PST)
Andre Serobian
[AMBER] Error with multiple GPU run: kCalculateMolecularVirial
(Sun Dec 19 2010 - 03:05:45 PST)
[AMBER] installing Amber 11 & tools 1.4 on Fedora 14
(Thu Dec 02 2010 - 19:51:14 PST)
Andreas Goetz
Re: [AMBER] RESP Dipole moment
(Wed Dec 22 2010 - 13:07:04 PST)
Re: [AMBER] QM/MM energy terms with DFTB
(Fri Dec 17 2010 - 12:01:32 PST)
Re: [AMBER] QM/MM energy terms with DFTB
(Thu Dec 16 2010 - 14:18:37 PST)
aneesh cna
[AMBER] Regarding Anal energy decomposition
(Tue Dec 21 2010 - 00:51:10 PST)
Re: [AMBER] Regarding energy decomposition
(Sat Dec 11 2010 - 02:24:47 PST)
[AMBER] Regarding energy decomposition
(Wed Dec 08 2010 - 04:40:17 PST)
Anindya Sarkar
Re: [AMBER] Generation of separate crd files
(Tue Dec 21 2010 - 09:14:19 PST)
[AMBER] Generation of separate crd files
(Fri Dec 17 2010 - 09:21:37 PST)
Anselm Horn
Re: [AMBER] phosphorylated residues
(Fri Dec 10 2010 - 07:04:56 PST)
Ashutosh Shandilya
[AMBER] Could not find angle parameter: FE - o - c3
(Wed Dec 22 2010 - 21:15:30 PST)
atila petrosian
[AMBER] can I use ambmask for trajectory file (mdcrd)?
(Thu Dec 30 2010 - 05:39:36 PST)
[AMBER] can I use ambmask for trajectory file (mdcrd)?
(Wed Dec 29 2010 - 06:13:59 PST)
[AMBER] time in ptraj
(Mon Dec 27 2010 - 01:43:51 PST)
[AMBER] maxocc and life time
(Mon Dec 13 2010 - 02:57:40 PST)
[AMBER] comparision of gromacs and amber
(Sat Dec 11 2010 - 04:55:49 PST)
baljinder
Re: [AMBER] phosphorylated residues
(Fri Dec 10 2010 - 21:57:12 PST)
[AMBER] phosphorylated residues
(Fri Dec 10 2010 - 02:54:05 PST)
Beale, John
[AMBER] water molecules
(Wed Dec 22 2010 - 04:48:38 PST)
[AMBER] Closest waters
(Wed Dec 08 2010 - 04:44:42 PST)
[AMBER] Distances between amino acid residues
(Wed Dec 01 2010 - 07:39:54 PST)
Bill Miller III
Re: [AMBER] MMPBSA.py.MPI tests
(Tue Dec 21 2010 - 08:42:19 PST)
Re: [AMBER] MMPBSA.py.MPI tests
(Tue Dec 21 2010 - 07:43:38 PST)
Re: [AMBER] problem with MM-PBSA
(Sun Dec 19 2010 - 04:46:08 PST)
Re: [AMBER] MMPBSA test fail
(Sat Dec 18 2010 - 06:15:24 PST)
Re: [AMBER] MMPBSA test fail
(Sat Dec 18 2010 - 05:49:26 PST)
Re: [AMBER] MMPBSA test fail
(Sat Dec 18 2010 - 05:24:06 PST)
Re: [AMBER] MMPBSA test fail
(Fri Dec 17 2010 - 11:36:24 PST)
Re: [AMBER] MMPBSA test fail
(Fri Dec 17 2010 - 11:16:22 PST)
Re: [AMBER] Error on applying MMPBSA.py Bug Fixes
(Fri Dec 17 2010 - 10:03:20 PST)
Re: [AMBER] MMPBAS.py.MPI
(Fri Dec 17 2010 - 09:04:09 PST)
Re: [AMBER] MMPBAS.py.MPI
(Fri Dec 17 2010 - 08:50:27 PST)
Re: [AMBER] MMPBAS.py.MPI
(Fri Dec 17 2010 - 08:12:12 PST)
Re: [AMBER] MMPBAS.py.MPI
(Fri Dec 17 2010 - 07:59:42 PST)
Re: [AMBER] MMPBSA.py Internal energies
(Wed Dec 15 2010 - 06:06:17 PST)
Re: [AMBER] allocation failure in vector: problem in MMPBSA.py.MPI
(Tue Dec 14 2010 - 04:22:52 PST)
Re: [AMBER] Polyglycine simulation
(Fri Dec 10 2010 - 03:38:51 PST)
Re: [AMBER] Does MMPBSA.py mutant only one residue?
(Thu Dec 09 2010 - 03:40:59 PST)
Re: [AMBER] Error: Sander output is missing values! VDWAALS = *************
(Mon Dec 06 2010 - 20:29:56 PST)
Re: [AMBER] Please help! MM-GBSA per-residue energy calculation.
(Fri Dec 03 2010 - 03:47:35 PST)
Bill Ross
Re: [AMBER] conversion of gromacs trajectory file (xtc) to amber trajectory file (mdcrd) / problem in water molecules
(Wed Dec 29 2010 - 09:46:27 PST)
Re: [AMBER] conversion of gromacs trajectory file (xtc) to amber trajectory file (mdcrd) / problem in water molecules
(Mon Dec 27 2010 - 09:56:00 PST)
Re: [AMBER] conversion of gromacs trajrctory file (xtc) to amber trajectory file (mdcrd) / problem in water moecules.
(Sun Dec 26 2010 - 20:36:28 PST)
Re: [AMBER] conversion of gromacs trajrctory file (xtc) to amber trajectory file (mdcrd) / problem in water moecules.
(Sun Dec 26 2010 - 10:59:22 PST)
Re: [AMBER] RMSD for two trajectories
(Wed Dec 22 2010 - 18:39:45 PST)
Re: [AMBER] RMSD for two trajectories
(Wed Dec 22 2010 - 15:45:05 PST)
Re: [AMBER] Generation of separate crd files
(Fri Dec 17 2010 - 11:55:39 PST)
Re: [AMBER] Residue building and controlling the substitutes
(Thu Dec 16 2010 - 15:53:57 PST)
Re: [AMBER] cnts topology
(Thu Dec 16 2010 - 13:36:10 PST)
Re: [AMBER] Building polymer
(Tue Dec 14 2010 - 11:03:26 PST)
Re: [AMBER] use of packmol in amber
(Tue Dec 14 2010 - 10:24:23 PST)
Re: [AMBER] use of packmol in amber
(Tue Dec 14 2010 - 10:14:35 PST)
Re: [AMBER] use of packmol in amber
(Mon Dec 13 2010 - 20:41:20 PST)
Re: [AMBER] use of packmol in amber
(Mon Dec 13 2010 - 20:16:39 PST)
Re: [AMBER] .mdin file content
(Mon Dec 13 2010 - 15:34:30 PST)
Re: [AMBER] Residues lacking connect0/connect1 - these don't have chain types marked:
(Mon Dec 13 2010 - 11:05:52 PST)
Re: [AMBER] HEME parameters
(Sat Dec 11 2010 - 11:46:21 PST)
Re: [AMBER] HEME parameters
(Sat Dec 11 2010 - 11:29:30 PST)
Re: [AMBER] Residues lacking connect0/connect1 - these don't have chain types marked:
(Sat Dec 11 2010 - 11:23:10 PST)
Re: [AMBER] phosphorylated residues
(Fri Dec 10 2010 - 11:13:42 PST)
Re: [AMBER] phosphorylated residues
(Fri Dec 10 2010 - 10:07:16 PST)
Re: [AMBER] Regarding energy decomposition
(Wed Dec 08 2010 - 10:46:52 PST)
Re: [AMBER] solvatebox
(Tue Dec 07 2010 - 10:26:36 PST)
Re: [AMBER] MMPBSA calculation of a zinc-enzyme
(Thu Dec 02 2010 - 13:56:22 PST)
Re: [AMBER] MMPBSA calculation of a zinc-enzyme
(Thu Dec 02 2010 - 12:20:20 PST)
Re: [AMBER] MMPBSA calculation of a zinc-enzyme
(Thu Dec 02 2010 - 11:47:19 PST)
Bongkeun Kim
Re: [AMBER] Is this output OK from the hybrid remd?
(Wed Dec 22 2010 - 13:12:37 PST)
Re: [AMBER] Is this output OK from the hybrid remd?
(Wed Dec 22 2010 - 11:21:03 PST)
Re: [AMBER] Is this output OK from the hybrid remd?
(Mon Dec 20 2010 - 11:35:10 PST)
Re: [AMBER] Is this output OK from the hybrid remd?
(Mon Dec 20 2010 - 09:30:43 PST)
Re: [AMBER] Is this output OK from the hybrid remd?
(Sun Dec 19 2010 - 11:02:17 PST)
Re: [AMBER] Is this output OK from the hybrid remd?
(Sun Dec 19 2010 - 10:44:03 PST)
Re: [AMBER] Is this output OK from the hybrid remd?
(Sat Dec 18 2010 - 11:23:36 PST)
Re: [AMBER] Is this output OK from the hybrid remd?
(Sat Dec 18 2010 - 08:52:39 PST)
Re: [AMBER] Is this output OK from the hybrid remd?
(Fri Dec 17 2010 - 21:00:14 PST)
Re: [AMBER] Is this output OK from the hybrid remd?
(Fri Dec 17 2010 - 20:33:39 PST)
Re: [AMBER] Is this output OK from the hybrid remd?
(Fri Dec 17 2010 - 08:43:59 PST)
Re: [AMBER] Is this output OK from the hybrid remd?
(Fri Dec 17 2010 - 08:13:47 PST)
[AMBER] Is this output OK from the hybrid remd?
(Fri Dec 17 2010 - 00:13:31 PST)
[AMBER] Map function for custom residue to generate distace restraints?
(Mon Dec 06 2010 - 16:21:02 PST)
Re: [AMBER] How to set up NMR distance restraint between surface and peptide?
(Mon Dec 06 2010 - 15:41:02 PST)
Re: [AMBER] How to set up NMR distance restraint between surface and peptide?
(Mon Dec 06 2010 - 14:31:21 PST)
[AMBER] How to set up NMR distance restraint between surface and peptide?
(Mon Dec 06 2010 - 13:40:13 PST)
Re: [AMBER] energy calculation error after extracting peptide from the explicit water simulation
(Wed Dec 01 2010 - 13:18:25 PST)
Re: [AMBER] energy calculation error after extracting peptide from the explicit water simulation
(Wed Dec 01 2010 - 12:47:49 PST)
[AMBER] energy calculation error after extracting peptide from the explicit water simulation
(Wed Dec 01 2010 - 11:49:04 PST)
Bozell, Joseph John
Re: [AMBER] evaluating physical meaning of Amber results
(Wed Dec 22 2010 - 04:55:46 PST)
[AMBER] evaluating physical meaning of Amber results
(Mon Dec 20 2010 - 13:54:19 PST)
[AMBER] .mdin file content
(Mon Dec 13 2010 - 13:36:15 PST)
Carlos Simmerling
Re: [AMBER] REMD number of replica
(Sun Dec 26 2010 - 09:27:11 PST)
Re: [AMBER] REMD number of replica
(Sat Dec 25 2010 - 08:33:37 PST)
Re: [AMBER] Is this output OK from the hybrid remd?
(Mon Dec 20 2010 - 09:36:41 PST)
Re: [AMBER] Is this output OK from the hybrid remd?
(Sun Dec 19 2010 - 09:16:10 PST)
Re: [AMBER] Is this output OK from the hybrid remd?
(Sat Dec 18 2010 - 10:45:44 PST)
Re: [AMBER] How to study protein-protein complex are stabilized/destabilized upon complexation?
(Tue Dec 14 2010 - 09:29:15 PST)
Re: [AMBER] Problem on nmropt option in amber 11
(Tue Dec 14 2010 - 06:27:32 PST)
Re: [AMBER] REMD replicas blowing up
(Thu Dec 09 2010 - 05:37:19 PST)
Re: [AMBER] REMD replicas blowing up
(Wed Dec 08 2010 - 08:47:00 PST)
Re: [AMBER] (no subject)
(Wed Dec 01 2010 - 13:48:28 PST)
case
Re: [AMBER] about the Sietraj
(Thu Dec 30 2010 - 18:57:19 PST)
Re: [AMBER] Fw: configuring options for Amber tools
(Thu Dec 30 2010 - 05:26:09 PST)
Re: [AMBER] problem with MM-PBSA
(Wed Dec 29 2010 - 06:01:05 PST)
Re: [AMBER] conversion of gromacs trajectory file (xtc) to amber trajectory file (mdcrd) / problem in water molecules
(Wed Dec 29 2010 - 05:57:42 PST)
Re: [AMBER] problem with MM-PBSA
(Tue Dec 28 2010 - 06:19:22 PST)
Re: [AMBER] conversion of gromacs trajectory file (xtc) to amber trajectory file (mdcrd) / problem in water molecules
(Tue Dec 28 2010 - 05:59:42 PST)
Re: [AMBER] QM/MM-MD binding energy
(Mon Dec 27 2010 - 07:54:14 PST)
Re: [AMBER] time in ptraj
(Mon Dec 27 2010 - 06:13:25 PST)
Re: [AMBER] conversion of gromacs trajectory file (xtc) to amber trajectory file (mdcrd) / problem in water molecules
(Mon Dec 27 2010 - 06:12:43 PST)
Re: [AMBER] conversion of gromacs trajrctory file (xtc) to amber trajectory file (mdcrd) / problem in water moecules.
(Mon Dec 27 2010 - 06:02:52 PST)
Re: [AMBER] conversion of gromacs trajrctory file (xtc) to amber trajectory file (mdcrd) / problem in water moecules.
(Sun Dec 26 2010 - 15:34:13 PST)
Re: [AMBER] GAFF polarizability - source
(Fri Dec 24 2010 - 12:46:18 PST)
Re: [AMBER] Using REDUCE
(Wed Dec 22 2010 - 10:51:38 PST)
Re: [AMBER] Possibly wrong dihedrals assignment in the frcmod.parmbsc0 file
(Wed Dec 22 2010 - 10:47:25 PST)
Re: [AMBER] compiling error for amber10 in parallel version with g++4.3.2, gfortan 4.3, mpich or lam or openmpi
(Mon Dec 20 2010 - 20:21:23 PST)
Re: [AMBER] suppose.nab
(Mon Dec 20 2010 - 19:48:33 PST)
Re: [AMBER] suppose.nab
(Mon Dec 20 2010 - 13:16:36 PST)
Re: [AMBER] AmberTools NAB corrections
(Mon Dec 20 2010 - 05:55:12 PST)
Re: [AMBER] Any one reported a drug dissociation barrier could be as high as 100 kcal/mol ?
(Sun Dec 19 2010 - 10:44:38 PST)
Re: [AMBER] j-restrained peptide
(Fri Dec 17 2010 - 11:40:14 PST)
Re: [AMBER] Generation of separate crd files
(Fri Dec 17 2010 - 11:35:41 PST)
Re: [AMBER] error in MD of modeled & docked protein - DAN complex
(Fri Dec 17 2010 - 08:44:49 PST)
Re: [AMBER] Is this output OK from the hybrid remd?
(Fri Dec 17 2010 - 06:19:07 PST)
Re: [AMBER] error in MD of modeled & docked protein - DAN complex
(Fri Dec 17 2010 - 06:07:59 PST)
Re: [AMBER] j-restrained peptide
(Wed Dec 15 2010 - 08:56:12 PST)
Re: [AMBER] j-restrained peptide
(Wed Dec 15 2010 - 08:37:26 PST)
Re: [AMBER] pmemd with mpi number of cpus
(Wed Dec 15 2010 - 06:22:11 PST)
Re: [AMBER] j-restrained peptide
(Wed Dec 15 2010 - 06:00:04 PST)
Re: [AMBER] Entropy calculation of a molecule in water
(Wed Dec 15 2010 - 05:21:24 PST)
Re: [AMBER] Problem on nmropt option in amber 11
(Tue Dec 14 2010 - 07:22:03 PST)
Re: [AMBER] use of packmol in amber
(Tue Dec 14 2010 - 04:44:02 PST)
Re: [AMBER] use of packmol in amber
(Mon Dec 13 2010 - 04:43:29 PST)
Re: [AMBER] problem during MD process
(Sun Dec 12 2010 - 19:53:05 PST)
Re: [AMBER] error on running sander.MPI
(Sun Dec 12 2010 - 06:32:29 PST)
Re: [AMBER] ambpdb error when usind mdcrd file
(Fri Dec 10 2010 - 11:14:34 PST)
Re: [AMBER] Could the energy decomposition be carried out in the AmberTools?
(Fri Dec 10 2010 - 06:32:10 PST)
Re: [AMBER] cyclic peptide
(Thu Dec 09 2010 - 09:45:58 PST)
Re: [AMBER] cyclic peptide
(Thu Dec 09 2010 - 05:03:07 PST)
Re: [AMBER] Tin-foil boundary condition
(Thu Dec 09 2010 - 04:51:09 PST)
Re: [AMBER] 答复: error for antecamber to establish small molecule
(Thu Dec 09 2010 - 04:49:22 PST)
Re: [AMBER] Some errors in the Amber test
(Thu Dec 09 2010 - 04:47:32 PST)
Re: [AMBER] error for antecamber to establish small molecule
(Wed Dec 08 2010 - 07:31:54 PST)
Re: [AMBER] Map function for custom residue to generate distace restraints?
(Mon Dec 06 2010 - 18:48:30 PST)
Re: [AMBER] Installation problem on Mac
(Mon Dec 06 2010 - 07:06:26 PST)
Re: [AMBER] building error of multi-GPU pmemd.cuda
(Mon Dec 06 2010 - 04:47:08 PST)
Re: [AMBER] Query: ABMD
(Mon Dec 06 2010 - 04:39:42 PST)
Re: [AMBER] Query: ABMD
(Sun Dec 05 2010 - 07:01:19 PST)
Re: [AMBER] what is correct atom type descriptor to add binding-site water molecules in tleap
(Thu Dec 02 2010 - 19:41:50 PST)
Re: [AMBER] j-restrained peptide
(Thu Dec 02 2010 - 05:54:35 PST)
Re: [AMBER] (no subject)
(Thu Dec 02 2010 - 05:31:20 PST)
Re: [AMBER] (no subject)
(Wed Dec 01 2010 - 08:05:30 PST)
Catein Catherine
[AMBER] How to define self-rotation of the molecule in VMD when preparing movie of a MD simulation?
(Thu Dec 30 2010 - 06:49:59 PST)
Re: [AMBER] Fw: configuring options for Amber tools
(Thu Dec 30 2010 - 06:47:16 PST)
[AMBER] Are MM-PBSA/GBSA analysis based on MD in implicit or explicit solvent are both aceptable?
(Wed Dec 29 2010 - 07:31:37 PST)
[AMBER] Is MM-PBSA energy for protein-DNA (~ 40 base pairs) as large as -400 kcal/mol reasonable?
(Wed Dec 29 2010 - 07:26:58 PST)
[AMBER] A drug dissociation barrier/energy was found to be as high as 100 kcal/mol.
(Sun Dec 19 2010 - 21:17:31 PST)
[AMBER] Any one reported a drug dissociation barrier could be as high as 100 kcal/mol ?
(Sun Dec 19 2010 - 10:32:36 PST)
[AMBER] How to study protein-protein complex are stabilized/destabilized upon complexation?
(Tue Dec 14 2010 - 09:26:25 PST)
[AMBER] How to define two receptors in MM/GBSA calculation?
(Wed Dec 08 2010 - 08:38:36 PST)
Re: [AMBER] Please help! MM-GBSA per-residue energy calculation.
(Fri Dec 03 2010 - 00:01:03 PST)
[AMBER] Please help! MM-GBSA per-residue energy calculation.
(Thu Dec 02 2010 - 08:43:39 PST)
Re: [AMBER] editing parm in LEAP
(Thu Dec 02 2010 - 08:38:13 PST)
Cenk \(Jenk\) Andac
Re: [AMBER] problem with entropy computations by mm_pbsa_nabnmode
(Sun Dec 05 2010 - 03:22:50 PST)
[AMBER] problem with entropy computations by mm_pbsa_nabnmode
(Sun Dec 05 2010 - 01:17:07 PST)
chicago.ecnu
[AMBER] solvent overlap when "iwrap=1"
(Tue Nov 30 2010 - 20:58:25 PST)
cwt
[AMBER] Some errors in the Amber test
(Wed Dec 08 2010 - 18:14:53 PST)
Re: [AMBER] some problems of restart MD
(Wed Dec 01 2010 - 22:25:30 PST)
[AMBER] some problems of restart MD
(Wed Dec 01 2010 - 18:21:41 PST)
Dachuan Guo
[AMBER] problem during TMD simulation
(Mon Dec 13 2010 - 00:45:10 PST)
Daniel Roe
Re: [AMBER] dissacharide
(Thu Dec 30 2010 - 06:58:56 PST)
Re: [AMBER] Is this output OK from the hybrid remd?
(Wed Dec 22 2010 - 12:35:47 PST)
Re: [AMBER] Is this output OK from the hybrid remd?
(Tue Dec 21 2010 - 14:33:21 PST)
Re: [AMBER] problem of ptraj
(Mon Dec 20 2010 - 08:40:42 PST)
Re: [AMBER] Entropy calculation of a molecule in water
(Thu Dec 16 2010 - 04:53:07 PST)
Re: [AMBER] AmberTools 1.4 serial tests failures
(Fri Dec 03 2010 - 06:48:36 PST)
Re: [AMBER] energy calculation error after extracting peptide from the explicit water simulation
(Thu Dec 02 2010 - 11:29:42 PST)
Re: [AMBER] I've got an error msg, ptraj: double free or corruption
(Thu Dec 02 2010 - 10:54:26 PST)
Re: [AMBER] solvent overlap when "iwrap=1"
(Wed Dec 01 2010 - 06:58:10 PST)
Re: [AMBER] AmberTools serial compilation with intel compiler 12.0.0: final link failed
(Wed Dec 01 2010 - 05:49:29 PST)
Daniel Scott
[AMBER] Issues with Calculating P^2 values with RMS fits
(Thu Dec 16 2010 - 12:05:56 PST)
David Watson
Re: [AMBER] AmberTools 1.4 serial tests failures
(Fri Dec 03 2010 - 07:08:49 PST)
dcerutti.rci.rutgers.edu
Re: [AMBER] solvatebox
(Tue Dec 07 2010 - 10:25:41 PST)
Dean Cuebas
Re: [AMBER] problem during MD process
(Wed Dec 15 2010 - 10:13:53 PST)
Dmitry Mukha
Re: [AMBER] Any one reported a drug dissociation barrier could be as high as 100 kcal/mol ?
(Sun Dec 19 2010 - 10:53:38 PST)
Dmitry Nilov
Re: [AMBER] QM/MM energy terms with DFTB
(Sat Dec 18 2010 - 00:39:52 PST)
Re: [AMBER] torsion parameters in parm99.dat
(Fri Dec 17 2010 - 23:55:44 PST)
Re: [AMBER] torsion parameters in parm99.dat
(Fri Dec 17 2010 - 23:50:01 PST)
Re: [AMBER] SCC-DFTB failure
(Fri Dec 17 2010 - 05:20:14 PST)
Re: [AMBER] QM/MM energy terms with DFTB
(Fri Dec 17 2010 - 04:31:33 PST)
[AMBER] SCC-DFTB failure
(Fri Dec 17 2010 - 03:24:47 PST)
Re: [AMBER] torsion parameters in parm99.dat
(Tue Dec 14 2010 - 23:21:24 PST)
[AMBER] Analytical and empirical parametrization of dihedrals in Amber
(Mon Dec 06 2010 - 00:43:56 PST)
Eliac Brown
[AMBER] Luck or Black Box
(Thu Dec 30 2010 - 20:55:59 PST)
[AMBER] MMPBSA binding energy
(Wed Dec 29 2010 - 17:11:44 PST)
Re: [AMBER] QM/MM-MD binding energy
(Sun Dec 26 2010 - 20:51:28 PST)
Re: [AMBER] QM/MM-MD binding energy
(Sun Dec 26 2010 - 18:42:44 PST)
Re: [AMBER] QM/MM-MD binding energy
(Sun Dec 26 2010 - 09:28:17 PST)
[AMBER] QM/MM-MD binding energy
(Sun Dec 26 2010 - 08:49:51 PST)
[AMBER] RESP Dipole moment
(Tue Dec 21 2010 - 09:31:53 PST)
[AMBER] MMPBSA.py Internal energies
(Wed Dec 15 2010 - 05:58:41 PST)
fancy2012
Re: [AMBER] problem of ptraj
(Sun Dec 26 2010 - 19:28:30 PST)
Re: [AMBER] problem of ptraj
(Mon Dec 20 2010 - 02:32:55 PST)
[AMBER] problem of ptraj
(Sun Dec 19 2010 - 18:54:16 PST)
federica de leo
[AMBER] cnts topology
(Thu Dec 16 2010 - 09:28:22 PST)
filip fratev
Re: [AMBER] GTX470 and Amber 11 Cuda tests
(Sat Dec 25 2010 - 03:09:11 PST)
[AMBER] GTX470 and Amber 11 Cuda tests
(Fri Dec 24 2010 - 23:14:04 PST)
Floris Buelens
[AMBER] sleap loadmol2 bug
(Thu Dec 09 2010 - 04:39:40 PST)
FyD
Re: [AMBER] RESP Dipole moment
(Thu Dec 23 2010 - 02:00:44 PST)
Re: [AMBER] Flip chirality
(Tue Dec 21 2010 - 05:46:12 PST)
Re: [AMBER] cyclic peptide
(Tue Dec 14 2010 - 10:52:39 PST)
Re: [AMBER] problem with resp charge generation with multiple orientations
(Fri Dec 10 2010 - 08:13:40 PST)
Re: [AMBER] problem with resp charge generation with multiple orientations
(Fri Dec 10 2010 - 00:08:04 PST)
Re: [AMBER] cyclic peptide
(Thu Dec 09 2010 - 06:42:34 PST)
Re: [AMBER] cyclic peptide
(Thu Dec 09 2010 - 04:37:43 PST)
Re: [AMBER] using mol2 files with tleap
(Thu Dec 09 2010 - 02:29:41 PST)
Re: [AMBER] : error for antecamber to establish small molecule
(Thu Dec 09 2010 - 02:22:58 PST)
Re: [AMBER] Parameterization of ffamber99sb for octane box
(Wed Dec 08 2010 - 23:47:01 PST)
g t
Re: [AMBER] what is correct atom type descriptor to add binding-site water molecules in tleap
(Fri Dec 03 2010 - 09:10:07 PST)
[AMBER] what is correct atom type descriptor to add binding-site water molecules in tleap
(Thu Dec 02 2010 - 10:51:43 PST)
Gabriel Urquiza
[AMBER] Fwd: simulation terminates for no apparent reason
(Fri Dec 10 2010 - 05:14:22 PST)
Geoffrey Wood
Re: [AMBER] amoeba waters
(Fri Dec 03 2010 - 13:39:11 PST)
[AMBER] amoeba waters
(Fri Dec 03 2010 - 13:12:48 PST)
George Tzotzos
[AMBER] Using REDUCE
(Wed Dec 22 2010 - 10:44:38 PST)
Re: [AMBER] MMPBSA.py.MPI tests
(Tue Dec 21 2010 - 08:45:19 PST)
Re: [AMBER] MMPBSA.py.MPI tests
(Tue Dec 21 2010 - 08:20:45 PST)
[AMBER] MMPBSA.py.MPI tests
(Tue Dec 21 2010 - 07:39:18 PST)
Re: [AMBER] MMPBSA test fail
(Sat Dec 18 2010 - 06:22:17 PST)
Re: [AMBER] MMPBSA test fail
(Sat Dec 18 2010 - 06:11:27 PST)
Re: [AMBER] MMPBSA test fail
(Sat Dec 18 2010 - 05:40:33 PST)
Re: [AMBER] MMPBSA test fail
(Sat Dec 18 2010 - 05:10:58 PST)
Re: [AMBER] MMPBSA test fail
(Sat Dec 18 2010 - 05:06:41 PST)
Re: [AMBER] MMPBSA test fail
(Fri Dec 17 2010 - 11:31:26 PST)
[AMBER] MMPBSA test fail
(Fri Dec 17 2010 - 11:07:17 PST)
Re: [AMBER] Error on applying MMPBSA.py Bug Fixes
(Fri Dec 17 2010 - 10:05:45 PST)
[AMBER] Error on applying MMPBSA.py Bug Fixes
(Fri Dec 17 2010 - 09:58:28 PST)
Re: [AMBER] MMPBAS.py.MPI
(Fri Dec 17 2010 - 08:55:13 PST)
Re: [AMBER] MMPBAS.py.MPI
(Fri Dec 17 2010 - 08:36:36 PST)
Re: [AMBER] MMPBAS.py.MPI
(Fri Dec 17 2010 - 08:02:56 PST)
[AMBER] MMPBAS.py.MPI
(Fri Dec 17 2010 - 07:37:24 PST)
Re: [AMBER] error on running sander.MPI
(Sun Dec 12 2010 - 10:14:34 PST)
Re: [AMBER] error on running sander.MPI
(Sun Dec 12 2010 - 08:10:19 PST)
Re: [AMBER] error on running sander.MPI
(Sun Dec 12 2010 - 06:46:39 PST)
Re: [AMBER] error on running sander.MPI
(Sun Dec 12 2010 - 06:10:10 PST)
[AMBER] error on running sander.MPI
(Sun Dec 12 2010 - 05:59:53 PST)
Re: [AMBER] Installation problem on Mac
(Mon Dec 06 2010 - 07:17:04 PST)
[AMBER] Installation problem on Mac
(Mon Dec 06 2010 - 05:28:29 PST)
Giachetti Andrea - CERM
Re: [AMBER] Problem on nmropt option in amber 11
(Wed Dec 15 2010 - 03:07:42 PST)
Re: [AMBER] Problem on nmropt option in amber 11
(Tue Dec 14 2010 - 06:57:31 PST)
[AMBER] Problem on nmropt option in amber 11
(Tue Dec 14 2010 - 06:24:36 PST)
Gopalakrishnan.R
Re: [AMBER] use of packmol in amber
(Mon Dec 13 2010 - 20:36:07 PST)
Gould, Ian R
Re: [AMBER] Error with multiple GPU run: kCalculateMolecularVirial
(Sun Dec 19 2010 - 05:20:08 PST)
Re: [AMBER] The good choice of the linux system for Amber 11 calculations on Tesla C2050 GPUs ?
(Wed Dec 01 2010 - 11:03:56 PST)
Re: [AMBER] AMBER 11 on multiple GPUs
(Wed Dec 01 2010 - 10:04:34 PST)
Gustavo Seabra
Re: [AMBER] SCC-DFTB failure
(Fri Dec 17 2010 - 04:43:46 PST)
Hopkins, Robert
[AMBER] Box volume calculated by sander
(Sat Dec 04 2010 - 09:48:58 PST)
Hoshin Kim
[AMBER] I've got an error msg, ptraj: double free or corruption
(Wed Dec 01 2010 - 20:46:54 PST)
Re: [AMBER] Serious problem at specific time point
(Wed Dec 01 2010 - 20:34:44 PST)
iccy liu
[AMBER] count number of solvent molecules inside the protein
(Wed Dec 15 2010 - 15:11:24 PST)
Igor Marques
Re: [AMBER] solvatebox
(Tue Dec 07 2010 - 07:39:30 PST)
Re: [AMBER] The good choice of the linux system for Amber 11 calculations on Tesla C2050 GPUs ?
(Thu Dec 02 2010 - 06:10:01 PST)
Re: [AMBER] The good choice of the linux system for Amber 11 calculations on Tesla C2050 GPUs ?
(Wed Dec 01 2010 - 11:57:25 PST)
Igor Sizov
Re: [AMBER] Closest waters
(Mon Dec 13 2010 - 07:44:44 PST)
Jacopo Sgrignani
[AMBER] GTP parameters
(Fri Dec 31 2010 - 09:36:06 PST)
Jan Wahl
[AMBER] using mol2 files with tleap
(Thu Dec 09 2010 - 00:53:14 PST)
Jan.Heyda.seznam.cz
[AMBER] GAFF polarizability - source
(Fri Dec 24 2010 - 08:53:40 PST)
Janzsó Gábor
Re: [AMBER] REMD replicas blowing up
(Thu Dec 09 2010 - 09:18:19 PST)
Re: [AMBER] REMD replicas blowing up
(Wed Dec 08 2010 - 08:57:37 PST)
Re: [AMBER] REMD replicas blowing up
(Wed Dec 08 2010 - 08:44:27 PST)
Jarmila Husby
Re: [AMBER] running amber in amazon ec2 cloud environment
(Tue Dec 14 2010 - 03:00:55 PST)
Re: [AMBER] running amber in amazon ec2 cloud environment
(Tue Dec 14 2010 - 02:38:38 PST)
[AMBER] force constant parameters in amberports
(Mon Dec 06 2010 - 06:11:52 PST)
Jason Swails
Re: [AMBER] GTP parameters
(Fri Dec 31 2010 - 16:09:39 PST)
Re: [AMBER] how to add phosphate group in protein
(Thu Dec 30 2010 - 08:42:28 PST)
Re: [AMBER] Fw: configuring options for Amber tools
(Thu Dec 30 2010 - 08:35:13 PST)
Re: [AMBER] MMPBSA binding energy
(Wed Dec 29 2010 - 21:01:16 PST)
Re: [AMBER] Are MM-PBSA/GBSA analysis based on MD in implicit or explicit solvent are both aceptable?
(Wed Dec 29 2010 - 10:46:50 PST)
Re: [AMBER] Is MM-PBSA energy for protein-DNA (~ 40 base pairs) as large as -400 kcal/mol reasonable?
(Wed Dec 29 2010 - 10:42:01 PST)
Re: [AMBER] flag dihedrals in the .prmtop
(Wed Dec 29 2010 - 00:24:04 PST)
Re: [AMBER] QM/MM-MD binding energy
(Sun Dec 26 2010 - 21:23:18 PST)
Re: [AMBER] QM/MM-MD binding energy
(Sun Dec 26 2010 - 20:26:18 PST)
Re: [AMBER] conversion of gromacs trajrctory file (xtc) to amber trajectory file (mdcrd) / problem in water moecules.
(Sun Dec 26 2010 - 15:38:06 PST)
Re: [AMBER] QM/MM-MD binding energy
(Sun Dec 26 2010 - 15:06:20 PST)
Re: [AMBER] Is this output OK from the hybrid remd?
(Mon Dec 20 2010 - 09:37:34 PST)
Re: [AMBER] Is this output OK from the hybrid remd?
(Mon Dec 20 2010 - 08:53:51 PST)
Re: [AMBER] Any one reported a drug dissociation barrier could be as high as 100 kcal/mol ?
(Sun Dec 19 2010 - 21:36:03 PST)
Re: [AMBER] problem of ptraj
(Sun Dec 19 2010 - 21:25:02 PST)
Re: [AMBER] MMPBSA test fail
(Sat Dec 18 2010 - 11:45:05 PST)
Re: [AMBER] Is this output OK from the hybrid remd?
(Sat Dec 18 2010 - 04:16:13 PST)
Re: [AMBER] Is this output OK from the hybrid remd?
(Fri Dec 17 2010 - 19:37:41 PST)
Re: [AMBER] QM/MM energy terms with DFTB
(Fri Dec 17 2010 - 18:02:49 PST)
Re: [AMBER] Generation of separate crd files
(Fri Dec 17 2010 - 17:52:18 PST)
Re: [AMBER] MMPBSA test fail
(Fri Dec 17 2010 - 16:39:05 PST)
Re: [AMBER] Is this output OK from the hybrid remd?
(Fri Dec 17 2010 - 04:32:56 PST)
Re: [AMBER] Issues with Calculating P^2 values with RMS fits
(Thu Dec 16 2010 - 21:32:02 PST)
Re: [AMBER] NAMD cal with AMBER forces: Polarizable parameters in AMBER
(Thu Dec 16 2010 - 11:44:53 PST)
Re: [AMBER] restart md simulation from different points
(Thu Dec 16 2010 - 11:38:41 PST)
Re: [AMBER] allocation failure in vector: problem in MMPBSA.py.MPI
(Thu Dec 16 2010 - 06:58:07 PST)
Re: [AMBER] allocation failure in vector: problem in MMPBSA.py.MPI
(Wed Dec 15 2010 - 12:39:07 PST)
Re: [AMBER] allocation failure in vector: problem in MMPBSA.py.MPI
(Wed Dec 15 2010 - 09:47:38 PST)
Re: [AMBER] allocation failure in vector: problem in MMPBSA.py.MPI
(Wed Dec 15 2010 - 07:40:22 PST)
Re: [AMBER] torsion parameters in parm99.dat
(Wed Dec 15 2010 - 06:55:56 PST)
Re: [AMBER] Building polymer
(Tue Dec 14 2010 - 10:47:11 PST)
Re: [AMBER] cyclic peptide
(Tue Dec 14 2010 - 06:38:31 PST)
Re: [AMBER] .mdin file content
(Mon Dec 13 2010 - 14:54:15 PST)
Re: [AMBER] error regarding periodic prmtop
(Mon Dec 13 2010 - 09:13:06 PST)
Re: [AMBER] error regarding periodic prmtop
(Sun Dec 12 2010 - 22:19:30 PST)
Re: [AMBER] error on running sander.MPI
(Sun Dec 12 2010 - 09:33:33 PST)
Re: [AMBER] Residues lacking connect0/connect1 - these don't have chain types marked:
(Sat Dec 11 2010 - 10:34:36 PST)
Re: [AMBER] phosphorylated residues
(Fri Dec 10 2010 - 11:30:55 PST)
Re: [AMBER] compile pmemd using gcc
(Fri Dec 10 2010 - 11:27:32 PST)
Re: [AMBER] phosphorylated residues
(Fri Dec 10 2010 - 11:01:50 PST)
Re: [AMBER] compile pmemd using gcc
(Fri Dec 10 2010 - 09:55:54 PST)
Re: [AMBER] Fwd: simulation terminates for no apparent reason
(Fri Dec 10 2010 - 07:55:29 PST)
Re: [AMBER] phosphorylated residues
(Fri Dec 10 2010 - 07:36:21 PST)
Re: [AMBER] Could the energy decomposition be carried out in the AmberTools?
(Thu Dec 09 2010 - 17:45:24 PST)
Re: [AMBER] Does MMPBSA.py mutant only one residue?
(Thu Dec 09 2010 - 07:35:47 PST)
Re: [AMBER] How to define two receptors in MM/GBSA calculation?
(Wed Dec 08 2010 - 08:45:30 PST)
Re: [AMBER] How to define two receptors in MM/GBSA calculation?
(Wed Dec 08 2010 - 08:43:36 PST)
Re: [AMBER] Closest waters
(Wed Dec 08 2010 - 06:27:36 PST)
Re: [AMBER] Illegal CONECT record in pdb file / The file contained 1 atoms not in residue templates
(Wed Dec 08 2010 - 06:21:47 PST)
Re: [AMBER] Error: Sander output is missing values! VDWAALS = *************
(Tue Dec 07 2010 - 11:15:40 PST)
Re: [AMBER] pmemd.cuda on Snow Leopard 10.6.5
(Tue Dec 07 2010 - 07:43:20 PST)
Re: [AMBER] What can we do with velocities file ?
(Mon Dec 06 2010 - 18:31:46 PST)
Re: [AMBER] How to set up NMR distance restraint between surface and peptide?
(Mon Dec 06 2010 - 16:30:43 PST)
Re: [AMBER] How to set up NMR distance restraint between surface and peptide?
(Mon Dec 06 2010 - 14:16:58 PST)
Re: [AMBER] Installation problem on Mac
(Mon Dec 06 2010 - 13:08:13 PST)
Re: [AMBER] questions on molsurf program
(Mon Dec 06 2010 - 09:29:07 PST)
Re: [AMBER] Installation problem on Mac
(Mon Dec 06 2010 - 09:03:40 PST)
Re: [AMBER] building error of multi-GPU pmemd.cuda
(Mon Dec 06 2010 - 08:55:03 PST)
Re: [AMBER] hydrogen bond analysis of gromacs simulation by amber (direct and water mediated HB)
(Mon Dec 06 2010 - 08:49:48 PST)
Re: [AMBER] High STD Value in pbsa
(Sun Dec 05 2010 - 18:51:37 PST)
Re: [AMBER] hydrogen bond analysis of gromacs simulation by amber (direct and water mediated HB)
(Sun Dec 05 2010 - 11:26:40 PST)
Re: [AMBER] amoeba waters
(Fri Dec 03 2010 - 13:49:47 PST)
Re: [AMBER] amoeba waters
(Fri Dec 03 2010 - 13:17:59 PST)
Re: [AMBER] Please help! MM-GBSA per-residue energy calculation.
(Thu Dec 02 2010 - 09:27:32 PST)
Re: [AMBER] editing parm in LEAP
(Thu Dec 02 2010 - 09:26:44 PST)
Re: [AMBER] editing parm in LEAP
(Thu Dec 02 2010 - 08:21:10 PST)
Re: [AMBER] some problems of restart MD
(Thu Dec 02 2010 - 06:57:38 PST)
Re: [AMBER] some problems of restart MD
(Wed Dec 01 2010 - 20:43:59 PST)
Re: [AMBER] (no subject)
(Wed Dec 01 2010 - 13:44:58 PST)
Re: [AMBER] energy calculation error after extracting peptide from the explicit water simulation
(Wed Dec 01 2010 - 12:55:26 PST)
Re: [AMBER] energy calculation error after extracting peptide from the explicit water simulation
(Wed Dec 01 2010 - 12:31:16 PST)
Re: [AMBER] Distances between amino acid residues
(Wed Dec 01 2010 - 08:55:32 PST)
Re: [AMBER] solvent overlap when "iwrap=1"
(Wed Dec 01 2010 - 06:40:00 PST)
Re: [AMBER] AmberTools serial compilation with intel compiler 12.0.0: final link failed
(Wed Dec 01 2010 - 06:29:59 PST)
Jio M
[AMBER] reference for gbsa = 2
(Mon Dec 13 2010 - 06:25:03 PST)
Re: [AMBER] error regarding periodic prmtop
(Sun Dec 12 2010 - 23:24:26 PST)
[AMBER] error regarding periodic prmtop
(Sun Dec 12 2010 - 20:55:13 PST)
Jiri Sponer
Re: [AMBER] Benzene Stacking in AMBER
(Wed Dec 01 2010 - 02:40:31 PST)
John S
[AMBER] Flip chirality
(Mon Dec 20 2010 - 10:21:50 PST)
[AMBER] Residue building and controlling the substitutes
(Thu Dec 16 2010 - 15:39:48 PST)
[AMBER] force field
(Thu Dec 16 2010 - 15:30:46 PST)
[AMBER] Building polymer
(Tue Dec 14 2010 - 08:48:19 PST)
[AMBER] Atomic fluctuation
(Sat Dec 11 2010 - 22:36:06 PST)
Re: [AMBER] Trajectory
(Thu Dec 09 2010 - 14:52:19 PST)
Jorgen Simonsen
[AMBER] restart md simulation from different points
(Thu Dec 16 2010 - 08:45:29 PST)
Re: [AMBER] compile pmemd using gcc
(Fri Dec 10 2010 - 11:05:08 PST)
[AMBER] compile pmemd using gcc
(Fri Dec 10 2010 - 09:53:26 PST)
Jose Borreguero
[AMBER] where are the parameters controlling the cis/trans configuration of Proline ?
(Fri Dec 31 2010 - 09:32:06 PST)
Kalpesh Sharma
[AMBER] Work Smarter, Not Harder - I will earn for you - You sit and relax.
(Tue Dec 07 2010 - 20:43:59 PST)
kamlesh sahu
Re: [AMBER] Error: Sander output is missing values! VDWAALS = *************
(Tue Dec 07 2010 - 21:06:37 PST)
[AMBER] Error: Sander output is missing values! VDWAALS = *************
(Mon Dec 06 2010 - 20:21:46 PST)
Karan Mehra
Re: [AMBER] HEME parameters
(Sat Dec 11 2010 - 11:24:31 PST)
Re: [AMBER] HEME parameters
(Fri Dec 10 2010 - 13:37:33 PST)
[AMBER] HEME parameters
(Thu Dec 09 2010 - 17:38:21 PST)
Karl N. Kirschner
Re: [AMBER] comparision of gromacs and amber
(Mon Dec 13 2010 - 02:05:26 PST)
Kevin Hauser
Re: [AMBER] Is MM-PBSA energy for protein-DNA (~ 40 base pairs) as large as -400 kcal/mol reasonable?
(Wed Dec 29 2010 - 08:02:42 PST)
Khaled Barakat
[AMBER] MM-PBSA with DELPHI
(Sat Dec 04 2010 - 17:00:25 PST)
Kshatresh Dutta Dubey
Re: [AMBER] Query: ABMD
(Sun Dec 05 2010 - 20:43:58 PST)
[AMBER] Query: ABMD
(Sun Dec 05 2010 - 01:29:38 PST)
kurisaki ikuo
[AMBER] Are there polarized ion models in Amber?
(Mon Dec 13 2010 - 17:55:22 PST)
[AMBER] Tin-foil boundary condition
(Wed Dec 08 2010 - 20:51:14 PST)
leila karami
[AMBER] conversion of gromacs trajectory file (xtc) to amber trajectory file (mdcrd) / problem in water molecules
(Thu Dec 30 2010 - 02:34:03 PST)
Re: [AMBER] conversion of gromacs trajectory file (xtc) to amber trajectory file (mdcrd) / problem in water molecules
(Wed Dec 29 2010 - 22:43:25 PST)
[AMBER] conversion of gromacs trajectory file (xtc) to amber trajectory file (mdcrd) / problem in water molecules
(Wed Dec 29 2010 - 02:47:59 PST)
[AMBER] conversion of gromacs trajectory file (xtc) to amber trajectory file (mdcrd) / problem in water molecules
(Mon Dec 27 2010 - 10:27:54 PST)
[AMBER] conversion of gromacs trajectory file (xtc) to amber trajectory file (mdcrd) / problem in water molecules
(Mon Dec 27 2010 - 06:40:14 PST)
[AMBER] conversion of gromacs trajectory file (xtc) to amber trajectory file (mdcrd) / problem in water molecules
(Mon Dec 27 2010 - 01:28:03 PST)
[AMBER] conversion of gromacs trajrctory file (xtc) to amber trajectory file (mdcrd) / problem in water moecules.
(Sun Dec 26 2010 - 07:47:01 PST)
[AMBER] watershell / number of waters and which waters?
(Sun Dec 26 2010 - 06:01:07 PST)
[AMBER] conversion of gromacs trajrctory file (xtc) to amber trajectory file (mdcrd) / problem in water moecules.
(Sun Dec 26 2010 - 03:24:02 PST)
[AMBER] watershell / number of waters and which waters?
(Mon Dec 20 2010 - 03:05:19 PST)
[AMBER] reordering of atoms in mdcrd file
(Sun Dec 19 2010 - 10:28:29 PST)
[AMBER] Residues lacking connect0/connect1 - these don't have chain types marked:
(Sun Dec 12 2010 - 01:05:47 PST)
[AMBER] Residues lacking connect0/connect1 - these don't have chain types marked:
(Sat Dec 11 2010 - 03:33:37 PST)
[AMBER] Illegal CONECT record in pdb file / The file contained 1 atoms not in residue templates
(Tue Dec 07 2010 - 06:40:47 PST)
[AMBER] solvatebox
(Tue Dec 07 2010 - 04:00:09 PST)
[AMBER] hydrogen bond analysis of gromacs simulation by amber (direct and water mediated HB)
(Mon Dec 06 2010 - 22:26:01 PST)
[AMBER] hydrogen bond analysis of gromacs simulation by amber (direct and water mediated HB)
(Mon Dec 06 2010 - 00:13:35 PST)
[AMBER] hydrogen bond analysis of gromacs simulation by amber (direct and water mediated HB)
(Sun Dec 05 2010 - 00:56:07 PST)
Lishan Yao
Re: [AMBER] GLYCAM with FF99SB
(Tue Nov 30 2010 - 19:41:47 PST)
[AMBER] GLYCAM with FF99SB
(Tue Nov 30 2010 - 17:55:16 PST)
lnedialkova.gmail.com
[AMBER] ambpdb error when usind mdcrd file
(Fri Dec 10 2010 - 09:50:23 PST)
[AMBER] Umbrella Sampling
(Wed Dec 08 2010 - 10:18:02 PST)
Logan Ahlstrom
[AMBER] Using offsets to image with ptraj
(Mon Dec 13 2010 - 12:17:36 PST)
Re: [AMBER] Translate command with ptraj
(Sun Dec 12 2010 - 06:27:41 PST)
Re: [AMBER] Atomic fluctuation
(Sun Dec 12 2010 - 06:24:11 PST)
Re: [AMBER] Translate command with ptraj
(Sat Dec 11 2010 - 19:06:51 PST)
Re: [AMBER] Translate command with ptraj
(Sat Dec 11 2010 - 15:22:36 PST)
[AMBER] Translate command with ptraj
(Fri Dec 10 2010 - 17:21:24 PST)
Lucio Ferella
Re: [AMBER] GRID-enabled web portal for the use of the AMBER
(Thu Dec 16 2010 - 05:05:25 PST)
M. L. Dodson
Re: [AMBER] water molecules
(Wed Dec 22 2010 - 06:04:20 PST)
Re: [AMBER] use of packmol in amber
(Wed Dec 15 2010 - 06:46:29 PST)
Re: [AMBER] use of packmol in amber
(Tue Dec 14 2010 - 11:06:18 PST)
Re: [AMBER] use of packmol in amber
(Tue Dec 14 2010 - 06:09:19 PST)
M. Shahid
Re: [AMBER] using mol2 files with tleap
(Thu Dec 09 2010 - 01:37:11 PST)
Re: [AMBER] pmemd.cuda on Snow Leopard 10.6.5
(Tue Dec 07 2010 - 13:05:20 PST)
Re: [AMBER] pmemd.cuda on Snow Leopard 10.6.5
(Tue Dec 07 2010 - 04:33:57 PST)
Re: [AMBER] Installation problem on Mac
(Mon Dec 06 2010 - 07:44:27 PST)
manoj singh
Re: [AMBER] Luck or Black Box
(Thu Dec 30 2010 - 21:40:11 PST)
Marek Maly
Re: [AMBER] Building polymer
(Tue Dec 14 2010 - 11:47:26 PST)
Re: [AMBER] The good choice of the linux system for Amber 11 calculations on Tesla C2050 GPUs ?
(Thu Dec 02 2010 - 06:59:17 PST)
Re: [AMBER] The good choice of the linux system for Amber 11 calculations on Tesla C2050 GPUs ?
(Thu Dec 02 2010 - 02:34:01 PST)
Re: [AMBER] The good choice of the linux system for Amber 11 calculations on Tesla C2050 GPUs ?
(Thu Dec 02 2010 - 02:26:18 PST)
[AMBER] The good choice of the linux system for Amber 11 calculations on Tesla C2050 GPUs ?
(Wed Dec 01 2010 - 10:50:14 PST)
Mark Foster
Re: [AMBER] suppose.nab
(Mon Dec 20 2010 - 13:54:27 PST)
[AMBER] suppose.nab
(Mon Dec 20 2010 - 11:53:08 PST)
Markus Kaukonen
Re: [AMBER] QM/MM-MD binding energy
(Sun Dec 26 2010 - 09:46:58 PST)
Re: [AMBER] QM/MM-MD binding energy
(Sun Dec 26 2010 - 09:23:12 PST)
[AMBER] AmberTools NAB corrections
(Mon Dec 20 2010 - 05:32:00 PST)
Re: [AMBER] QM/MM energy terms with DFTB
(Sat Dec 18 2010 - 07:29:51 PST)
[AMBER] QM/MM energy terms with DFTB
(Thu Dec 16 2010 - 07:49:50 PST)
Re: [AMBER] Entropy calculation of a molecule in water
(Thu Dec 16 2010 - 00:02:21 PST)
[AMBER] Entropy calculation of a molecule in water
(Wed Dec 15 2010 - 02:07:31 PST)
Maryam Hamzehee
Re: [AMBER] problem with MM-PBSA
(Tue Dec 28 2010 - 09:37:53 PST)
[AMBER] problem with MM-PBSA
(Tue Dec 28 2010 - 03:17:03 PST)
[AMBER] RMSD for two trajectories
(Wed Dec 22 2010 - 04:31:26 PST)
Re: [AMBER] problem with MM-PBSA
(Mon Dec 20 2010 - 05:30:41 PST)
[AMBER] problem with MM-PBSA
(Sun Dec 19 2010 - 03:06:33 PST)
Maryam Hamzehee via LinkedIn
[AMBER] Join my network on LinkedIn
(Thu Dec 23 2010 - 05:34:44 PST)
Masakazu SEKIJIMA
[AMBER] building error of multi-GPU pmemd.cuda
(Sun Dec 05 2010 - 23:30:19 PST)
michelle.dupont.ulg.ac.be
[AMBER] compiling error for amber10 in parallel version with g++4.3.2, gfortan 4.3, mpich or lam or openmpi
(Mon Dec 20 2010 - 07:52:49 PST)
mish
Re: [AMBER] allocation failure in vector: problem in MMPBSA.py.MPI
(Wed Dec 15 2010 - 03:11:14 PST)
Re: [AMBER] allocation failure in vector: problem in MMPBSA.py.MPI
(Tue Dec 14 2010 - 04:35:23 PST)
[AMBER] allocation failure in vector: problem in MMPBSA.py.MPI
(Tue Dec 14 2010 - 04:11:48 PST)
Niel Henriksen
Re: [AMBER] RMSD for two trajectories
(Wed Dec 22 2010 - 17:20:30 PST)
Nilmeier, Jerome P.
Re: [AMBER] (no subject)
(Thu Dec 02 2010 - 16:05:26 PST)
Re: [AMBER] (no subject)
(Wed Dec 01 2010 - 14:03:52 PST)
Re: [AMBER] (no subject)
(Wed Dec 01 2010 - 13:41:28 PST)
Re: [AMBER] (no subject)
(Wed Dec 01 2010 - 13:20:22 PST)
Nitu Bansal
Re: [AMBER] HEME parameters
(Fri Dec 10 2010 - 21:16:30 PST)
Re: [AMBER] HEME parameters
(Fri Dec 10 2010 - 04:33:28 PST)
Oliver Grant
Re: [AMBER] conversion of gromacs trajrctory file (xtc) to amber trajectory file (mdcrd) / problem in water moecules.
(Sun Dec 26 2010 - 07:33:36 PST)
Re: [AMBER] solvatebox
(Tue Dec 07 2010 - 07:21:47 PST)
Re: [AMBER] Illegal CONECT record in pdb file / The file contained 1 atoms not in residue templates
(Tue Dec 07 2010 - 07:20:16 PST)
parasu raman
[AMBER] top and crd-reg..............
(Tue Nov 30 2010 - 20:05:14 PST)
Per Jr. Greisen
Re: [AMBER] Flip chirality
(Mon Dec 20 2010 - 10:26:35 PST)
Qizhi Cui
Re: [AMBER] about the Sietraj
(Fri Dec 31 2010 - 16:48:38 PST)
Ray Luo
Re: [AMBER] questions on molsurf program
(Mon Dec 06 2010 - 10:29:36 PST)
Re: [AMBER] High STD Value in pbsa
(Mon Dec 06 2010 - 10:05:18 PST)
Ray Luo, Ph.D.
Re: [AMBER] High STD Value in pbsa
(Sun Dec 05 2010 - 22:06:35 PST)
Richard Owczarzy
Re: [AMBER] evaluating physical meaning of Amber results
(Mon Dec 20 2010 - 15:13:54 PST)
Re: [AMBER] suppose.nab
(Mon Dec 20 2010 - 12:58:11 PST)
Re: [AMBER] running amber in amazon ec2 cloud environment
(Tue Dec 14 2010 - 06:17:14 PST)
Re: [AMBER] .mdin file content
(Mon Dec 13 2010 - 15:28:25 PST)
Rilei Yu
[AMBER] native number of contacts
(Fri Dec 24 2010 - 07:17:49 PST)
ros
Re: [AMBER] Closest waters
(Wed Dec 08 2010 - 05:41:50 PST)
Re: [AMBER] The good choice of the linux system for Amber 11 calculations on Tesla C2050 GPUs ?
(Wed Dec 01 2010 - 11:23:50 PST)
Ross Walker
[AMBER] Test Message - Do not reply.
(Tue Dec 21 2010 - 23:35:20 PST)
Re: [AMBER] Error with multiple GPU run: kCalculateMolecularVirial
(Sun Dec 19 2010 - 08:22:59 PST)
Re: [AMBER] QM/MM energy terms with DFTB
(Thu Dec 16 2010 - 14:17:35 PST)
Re: [AMBER] pmemd with mpi number of cpus
(Wed Dec 15 2010 - 11:59:54 PST)
Re: [AMBER] Problems compiling pmemd.cuda.MPI for InfiniBand
(Tue Dec 14 2010 - 15:49:29 PST)
Re: [AMBER] running amber in amazon ec2 cloud environment
(Tue Dec 14 2010 - 08:31:27 PST)
Re: [AMBER] error on running sander.MPI
(Sun Dec 12 2010 - 10:22:19 PST)
Re: [AMBER] error on running sander.MPI
(Sun Dec 12 2010 - 10:09:04 PST)
Re: [AMBER] Fwd: simulation terminates for no apparent reason
(Fri Dec 10 2010 - 11:07:12 PST)
Re: [AMBER] (no subject)
(Wed Dec 01 2010 - 13:38:45 PST)
Re: [AMBER] The good choice of the linux system for Amber 11 calculations on Tesla C2050 GPUs ?
(Wed Dec 01 2010 - 11:12:01 PST)
Re: [AMBER] AMBER 11 on multiple GPUs
(Wed Dec 01 2010 - 10:14:51 PST)
[AMBER] AMBER 11 on multiple GPUs
(Wed Dec 01 2010 - 09:51:31 PST)
Re: [AMBER] AmberTools serial compilation with intel compiler 12.0.0: final link failed
(Wed Dec 01 2010 - 09:03:53 PST)
Rossella Noschese
Re: [AMBER] j-restrained peptide
(Mon Dec 20 2010 - 02:44:34 PST)
Re: [AMBER] j-restrained peptide
(Wed Dec 15 2010 - 09:33:53 PST)
Re: [AMBER] j-restrained peptide
(Wed Dec 15 2010 - 08:49:24 PST)
Re: [AMBER] j-restrained peptide
(Wed Dec 15 2010 - 08:15:07 PST)
Re: [AMBER] cyclic peptide
(Tue Dec 14 2010 - 05:29:46 PST)
Re: [AMBER] cyclic peptide
(Thu Dec 09 2010 - 07:31:22 PST)
[AMBER] cyclic peptide
(Thu Dec 09 2010 - 02:50:41 PST)
Re: [AMBER] j-restrained peptide
(Thu Dec 02 2010 - 06:08:33 PST)
Re: [AMBER] small organic molecule
(Thu Dec 02 2010 - 01:31:54 PST)
Re: [AMBER] j-restrained peptide
(Thu Dec 02 2010 - 01:30:13 PST)
Sangita Kachhap
Re: [AMBER] how to add phosphate group in protein
(Thu Dec 30 2010 - 08:48:54 PST)
[AMBER] how to add phosphate group in protein
(Thu Dec 30 2010 - 01:45:02 PST)
Re: [AMBER] REMD number of replica
(Mon Dec 27 2010 - 08:25:30 PST)
Re: [AMBER] REMD number of replica
(Sat Dec 25 2010 - 11:07:49 PST)
[AMBER] REMD number of replica
(Sat Dec 25 2010 - 04:53:28 PST)
Re: [AMBER] error in MD of modeled & docked protein - DAN complex
(Fri Dec 17 2010 - 10:04:33 PST)
Re: [AMBER] error in MD of modeled & docked protein - DAN complex
(Fri Dec 17 2010 - 08:27:34 PST)
[AMBER] error in MD of modeled & docked protein - DAN complex
(Thu Dec 16 2010 - 01:22:38 PST)
Sasha Buzko
Re: [AMBER] Problems compiling pmemd.cuda.MPI for InfiniBand
(Tue Dec 14 2010 - 15:57:08 PST)
[AMBER] Problems compiling pmemd.cuda.MPI for InfiniBand
(Tue Dec 14 2010 - 15:02:02 PST)
Senthil Natesan
Re: [AMBER] questions on molsurf program
(Mon Dec 06 2010 - 09:42:04 PST)
[AMBER] questions on molsurf program
(Mon Dec 06 2010 - 07:36:33 PST)
Sergio R Aragon
Re: [AMBER] GTX470 and Amber 11 Cuda tests
(Sat Dec 25 2010 - 10:41:14 PST)
Re: [AMBER] Fwd: simulation terminates for no apparent reason
(Fri Dec 10 2010 - 10:15:33 PST)
setyanto md
Re: [AMBER] RMSD for two trajectories
(Wed Dec 22 2010 - 18:04:46 PST)
[AMBER] What can we do with velocities file ?
(Mon Dec 06 2010 - 18:03:28 PST)
Simon Becker
Re: [AMBER] problem during TMD simulation
(Mon Dec 13 2010 - 01:23:48 PST)
Stefano Pieraccini
[AMBER] pmemd with mpi number of cpus
(Wed Dec 15 2010 - 03:26:38 PST)
steinbrt.rci.rutgers.edu
[AMBER] vdW parameters
(Mon Dec 06 2010 - 23:49:26 PST)
Su Qiu
Re: [AMBER] Distances between amino acid residues
(Wed Dec 01 2010 - 18:46:36 PST)
subrata paul
[AMBER] rdf
(Thu Dec 30 2010 - 07:26:53 PST)
[AMBER] dissacharide
(Thu Dec 30 2010 - 04:49:42 PST)
Re: [AMBER] use of packmol in amber
(Tue Dec 14 2010 - 23:13:58 PST)
Re: [AMBER] use of packmol in amber
(Tue Dec 14 2010 - 03:23:58 PST)
Re: [AMBER] use of packmol in amber
(Mon Dec 13 2010 - 20:29:39 PST)
Re: [AMBER] use of packmol in amber
(Mon Dec 13 2010 - 19:57:29 PST)
[AMBER] use of packmol in amber
(Mon Dec 13 2010 - 02:43:03 PST)
sunita gupta
[AMBER] What is the Value of C° (standard concentration) in calculating Free Energy
(Mon Dec 20 2010 - 22:56:52 PST)
[AMBER] What is the Value of C° (standard concentration)
(Tue Nov 30 2010 - 21:43:03 PST)
Sushil Mishra
Re: [AMBER] allocation failure in vector: problem in MMPBSA.py.MPI
(Wed Dec 15 2010 - 23:01:33 PST)
Re: [AMBER] allocation failure in vector: problem in MMPBSA.py.MPI
(Wed Dec 15 2010 - 12:26:05 PST)
Re: [AMBER] allocation failure in vector: problem in MMPBSA.py.MPI
(Wed Dec 15 2010 - 07:49:55 PST)
Tatyana Shubina
[AMBER] 25th Molecular Modelling Workshop 2011 Announcement
(Thu Dec 23 2010 - 07:20:44 PST)
Thomas Cheatham III
Re: [AMBER] Translate command with ptraj
(Sat Dec 11 2010 - 16:19:14 PST)
Thomas Schlesier
Re: [AMBER] problem with resp charge generation with multiple orientations
(Mon Dec 13 2010 - 02:01:19 PST)
Re: [AMBER] problem with resp charge generation with multiple orientations
(Fri Dec 10 2010 - 04:26:10 PST)
[AMBER] problem with resp charge generation with multiple orientations
(Thu Dec 09 2010 - 13:10:21 PST)
Timothy J Giese
Re: [AMBER] Installation problem on Mac
(Mon Dec 06 2010 - 06:00:59 PST)
Re: [AMBER] AmberTools 1.4 serial tests failures
(Fri Dec 03 2010 - 06:53:14 PST)
Tomáš Kučera
[AMBER] running amber in amazon ec2 cloud environment
(Tue Dec 14 2010 - 01:58:46 PST)
Vitaly Chaban
Re: [AMBER] cnts topology
(Thu Dec 16 2010 - 15:18:19 PST)
Re: [AMBER] comparision of gromacs and amber
(Sat Dec 11 2010 - 07:19:53 PST)
Vlad Cojocaru
Re: [AMBER] AmberTools 1.4 serial tests failures
(Sat Dec 04 2010 - 05:32:44 PST)
[AMBER] 'final link failed' error independent of intel compiler version
(Sat Dec 04 2010 - 03:11:32 PST)
Re: [AMBER] AmberTools 1.4 serial tests failures
(Fri Dec 03 2010 - 07:32:49 PST)
Re: [AMBER] AmberTools 1.4 serial tests failures
(Fri Dec 03 2010 - 07:01:23 PST)
[AMBER] AmberTools 1.4 serial tests failures
(Fri Dec 03 2010 - 06:27:07 PST)
Re: [AMBER] installing Amber 11 & tools 1.4 on Fedora 14
(Fri Dec 03 2010 - 00:38:02 PST)
Re: [AMBER] AmberTools serial compilation with intel compiler 12.0.0: final link failed
(Wed Dec 01 2010 - 07:33:58 PST)
[AMBER] AmberTools serial compilation with intel compiler 12.0.0: final link failed
(Wed Dec 01 2010 - 03:34:24 PST)
Wei Zhang
Re: [AMBER] sleap loadmol2 bug
(Wed Dec 15 2010 - 23:27:41 PST)
Xiao Ju Zhang
[AMBER] NAMD cal with AMBER forces: Polarizable parameters in AMBER
(Thu Dec 16 2010 - 11:22:16 PST)
XiaoJu Zhang
Re: [AMBER] force field
(Thu Dec 16 2010 - 18:51:19 PST)
xqkong
Re: [AMBER] torsion parameters in parm99.dat
(Sat Dec 18 2010 - 04:02:30 PST)
Re: [AMBER] torsion parameters in parm99.dat
(Fri Dec 17 2010 - 18:01:11 PST)
Re: [AMBER] torsion parameters in parm99.dat
(Fri Dec 17 2010 - 17:57:27 PST)
[AMBER] torsion parameters in parm99.dat
(Tue Dec 14 2010 - 22:42:19 PST)
xuemeiwang1103
[AMBER] about the Sietraj
(Thu Dec 30 2010 - 17:11:47 PST)
[AMBER] about the Sietraj
(Sun Dec 26 2010 - 22:22:44 PST)
yan zhang
[AMBER] MM-PBSA energy-decomposition
(Wed Dec 01 2010 - 22:15:59 PST)
Yao-Chi Chen
Re: [AMBER] Could the energy decomposition be carried out in the AmberTools?
(Thu Dec 09 2010 - 22:48:28 PST)
[AMBER] Could the energy decomposition be carried out in the AmberTools?
(Thu Dec 09 2010 - 17:23:19 PST)
YUVRAJ UBOVEJA
[AMBER] Polyglycine simulation
(Fri Dec 10 2010 - 02:28:53 PST)
Re: [AMBER] Parameterization of ffamber99sb for octane box
(Wed Dec 08 2010 - 20:21:21 PST)
Z.Xiao
Re: [AMBER] flag dihedrals in the .prmtop
(Wed Dec 29 2010 - 01:38:23 PST)
[AMBER] flag dihedrals in the .prmtop
(Tue Dec 28 2010 - 23:43:24 PST)
zhihong ke
[AMBER] MMPBSA calculation for chlorine anion
(Wed Dec 08 2010 - 11:25:19 PST)
Re: [AMBER] MMPBSA calculation of a zinc-enzyme
(Thu Dec 02 2010 - 12:33:31 PST)
Re: [AMBER] MMPBSA calculation of a zinc-enzyme
(Thu Dec 02 2010 - 12:14:42 PST)
[AMBER] MMPBSA calculation of a zinc-enzyme
(Thu Dec 02 2010 - 09:53:06 PST)
Zhou Gong
[AMBER] 答复: error for antecamber to establish small molecule
(Wed Dec 08 2010 - 18:33:02 PST)
[AMBER] error for antecamber to establish small molecule
(Wed Dec 08 2010 - 06:58:49 PST)
zjxu
Re: [AMBER] comparision of gromacs and amber
(Sat Dec 11 2010 - 05:49:49 PST)
Re: [AMBER] Does MMPBSA.py mutant only one residue?
(Thu Dec 09 2010 - 18:05:11 PST)
Re: [AMBER] Does MMPBSA.py mutant only one residue?
(Thu Dec 09 2010 - 04:45:09 PST)
[AMBER] Does MMPBSA.py mutant only one residue?
(Wed Dec 08 2010 - 23:31:39 PST)
蒋峻峰
Re: [AMBER] problem during MD process
(Wed Dec 15 2010 - 17:38:26 PST)
Re: [AMBER] problem during MD process
(Mon Dec 13 2010 - 00:06:41 PST)
[AMBER] problem during MD process
(Sun Dec 12 2010 - 18:09:16 PST)
Last message date
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Fri Dec 31 2010 - 17:00:04 PST
Archived on
: Fri Nov 22 2024 - 05:54:09 PST
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