Amber Archive Jul 2009 by author
577 messages
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Starting
Mon Jul 06 2009 - 12:26:26 PDT,
Ending
Wed Aug 19 2009 - 19:59:29 PDT
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Adrian Roitberg
Re: [AMBER] Protonated or not
(Fri Jul 31 2009 - 10:32:50 PDT)
AL Olson
[AMBER] vlimit error after heating restart
(Fri Jul 17 2009 - 07:26:05 PDT)
Alan
Re: [AMBER] Compiling AmberTools 1.2 with intel compilers for Mac Osx in 64 bits
(Thu Jul 30 2009 - 06:39:03 PDT)
[AMBER] Compiling AmberTools 1.2 with intel compilers for Mac Osx in 64 bits
(Wed Jul 29 2009 - 09:00:42 PDT)
[AMBER] Re: bugfix 10 failing for ambertools1.2
(Mon Jul 20 2009 - 01:25:55 PDT)
[AMBER] bugfix 10 failing for ambertools1.2
(Mon Jul 20 2009 - 01:14:16 PDT)
[AMBER] different results for antechamber/mopac for the same input
(Wed Jul 15 2009 - 15:05:07 PDT)
Re: [AMBER] antechamber
(Thu Jul 02 2009 - 03:16:55 PDT)
Re: [AMBER] antechamber
(Wed Jul 01 2009 - 04:37:40 PDT)
albert albert
Re: [AMBER] Removed proton in protein (Advanced Tutorials A1 old)
(Fri Jul 31 2009 - 12:27:02 PDT)
[AMBER] Removed proton in protein (Advanced Tutorials A1 old)
(Sun Jul 26 2009 - 23:57:20 PDT)
Re: [AMBER] unsolved verbosity when running minimization
(Wed Jul 08 2009 - 04:10:43 PDT)
[AMBER] unsolved verbosity when running minimization
(Mon Jul 06 2009 - 12:09:02 PDT)
Aldo Humberto Romero
[AMBER] Amber10, Serial compilation with ifort
(Sun Jul 12 2009 - 13:57:40 PDT)
Alison Saunders
[AMBER] Error in Sander Output File
(Tue Jul 28 2009 - 10:00:12 PDT)
Re: [AMBER] Trouble saving amberparm files
(Mon Jul 13 2009 - 14:43:40 PDT)
Re: [AMBER] Trouble saving amberparm files
(Mon Jul 13 2009 - 14:06:12 PDT)
[AMBER] Trouble saving amberparm files
(Mon Jul 13 2009 - 10:07:28 PDT)
Re: [AMBER] Acetylate and Amidate
(Wed Jul 08 2009 - 15:47:59 PDT)
[AMBER] Acetylate and Amidate
(Wed Jul 08 2009 - 15:19:44 PDT)
amoreno.wesleyan.edu
[AMBER] Replacing DNA base with analog
(Thu Jul 23 2009 - 07:20:08 PDT)
Andrew Olson
Re: [AMBER] Holding ligand rigid for minimization
(Tue Jul 14 2009 - 11:23:31 PDT)
[AMBER] Holding ligand rigid for minimization
(Tue Jul 14 2009 - 08:23:01 PDT)
[AMBER] Holding ligand rigid for minimization
(Tue Jul 14 2009 - 08:14:38 PDT)
Re: [AMBER] ligand/protein minimization
(Mon Jul 13 2009 - 10:10:18 PDT)
Re: [AMBER] ligand/protein minimization
(Mon Jul 13 2009 - 08:53:11 PDT)
[AMBER] ligand/protein minimization
(Fri Jul 10 2009 - 14:00:26 PDT)
Re: [AMBER] Antechamber prep question
(Fri Jul 10 2009 - 06:33:09 PDT)
Re: [AMBER] Antechamber prep question
(Thu Jul 09 2009 - 10:00:19 PDT)
Re: [AMBER] Antechamber prep question
(Thu Jul 09 2009 - 08:22:18 PDT)
[AMBER] Antechamber prep question
(Thu Jul 09 2009 - 07:39:25 PDT)
Andrew Voronkov
Re: [AMBER] The Right Neutralization Procedure and Ionic Strength Calculation ?
(Tue Jul 28 2009 - 21:19:41 PDT)
Re: [AMBER] only ff94 and ff99 for GBSA?
(Mon Jul 27 2009 - 23:12:15 PDT)
Re: [AMBER] only ff94 and ff99 for GBSA?
(Mon Jul 27 2009 - 09:41:27 PDT)
[AMBER] amino acids caps for truncated proteins
(Thu Jul 16 2009 - 09:31:18 PDT)
Re: [AMBER] MPI process terminated unexpectedly forrtl: error (69): process interrupted (SIGINT)
(Wed Jul 08 2009 - 03:05:52 PDT)
[AMBER] MPI process terminated unexpectedly forrtl: error (69): process interrupted (SIGINT)
(Wed Jul 08 2009 - 02:39:03 PDT)
aneesh cna
[AMBER] Regarding Hbond interactions
(Tue Jul 21 2009 - 23:30:10 PDT)
Ashish Runthala
Re: [AMBER] Non-Standard Amino Acid Residue LEAP ERROR
(Thu Jul 30 2009 - 20:40:45 PDT)
Re: [AMBER] ambpdb problem
(Thu Jul 30 2009 - 20:44:10 PDT)
Re: [AMBER] Am I doing the right thing
(Tue Jul 28 2009 - 20:44:59 PDT)
Re: [AMBER] Am I doing the right thing
(Tue Jul 28 2009 - 18:35:09 PDT)
Re: [AMBER] Question on REST and VALUE1 keywords
(Tue Jul 28 2009 - 18:26:19 PDT)
Re: [AMBER] Using idecomp=3 with igb=10 (PB)
(Tue Jul 28 2009 - 07:33:02 PDT)
Re: [AMBER] Removed proton in protein (Advanced Tutorials A1 old)
(Tue Jul 28 2009 - 06:08:48 PDT)
Re: [AMBER] Removed proton in protein (Advanced Tutorials A1 old)
(Tue Jul 28 2009 - 03:28:40 PDT)
Re: [AMBER] Removed proton in protein (Advanced Tutorials A1 old)
(Mon Jul 27 2009 - 02:09:23 PDT)
Re: [AMBER] DNA + intercalator
(Fri Jul 24 2009 - 20:12:27 PDT)
Aust, Susanne
AW: [AMBER] Steered MD---more than one pair of atoms
(Tue Jul 07 2009 - 23:47:56 PDT)
Bala subramanian
Re: [AMBER] ouput trajectory of only CA atom
(Wed Jul 08 2009 - 08:01:27 PDT)
[AMBER] ouput trajectory of only CA atom
(Wed Jul 08 2009 - 06:24:56 PDT)
Re: [AMBER] amber9 in fedora10
(Thu Jul 02 2009 - 01:05:55 PDT)
Re: [AMBER] amber9 in fedora10
(Thu Jul 02 2009 - 00:02:54 PDT)
[AMBER] amber9 in fedora10
(Wed Jul 01 2009 - 07:09:15 PDT)
balaji nagarajan
RE: [AMBER] rmsd_ptraj
(Wed Jul 08 2009 - 22:50:10 PDT)
[AMBER] rmsd_ptraj
(Wed Jul 08 2009 - 21:19:56 PDT)
RE: [AMBER] rmsd_dna
(Wed Jul 08 2009 - 18:55:53 PDT)
[AMBER] rmsd_dna
(Wed Jul 08 2009 - 09:15:02 PDT)
Beale, John
[AMBER] (no subject)
(Mon Jul 13 2009 - 10:35:46 PDT)
Ben Roberts
Re: [AMBER] charge not zero on group: RESP
(Sat Jul 18 2009 - 05:45:10 PDT)
bharat lakhani
[AMBER] query
(Fri Jul 31 2009 - 00:42:04 PDT)
[AMBER] Normal mode analysis of water
(Thu Jul 30 2009 - 02:27:19 PDT)
Re: [AMBER] command for RESP fitting
(Mon Jul 20 2009 - 00:01:23 PDT)
[AMBER] command for RESP fitting
(Thu Jul 16 2009 - 00:10:33 PDT)
[AMBER] Please help me out
(Wed Jul 15 2009 - 03:43:21 PDT)
Bill Ross
Re: [AMBER] Am I doing the right thing
(Tue Jul 28 2009 - 19:39:48 PDT)
Re: [AMBER] residues lacking connect0/connect1
(Mon Jul 27 2009 - 09:40:31 PDT)
Re: [AMBER] Removed proton in protein (Advanced Tutorials A1 old)
(Mon Jul 27 2009 - 09:17:29 PDT)
Re: [AMBER] DNA + intercalator
(Fri Jul 24 2009 - 16:03:06 PDT)
Re: [AMBER] Alpha-L-Methys Fucose structure problem bond 0fA.d.C1 OME.d.O "S"
(Wed Jul 15 2009 - 09:53:41 PDT)
Re: [AMBER] Acetylate and Amidate
(Wed Jul 08 2009 - 16:13:09 PDT)
Biswaranjan Meher
Re: [AMBER] Langevin Dynamics in AMBER10
(Thu Jul 23 2009 - 16:12:59 PDT)
[AMBER] Langevin Dynamics in AMBER10
(Thu Jul 23 2009 - 14:54:58 PDT)
Bokun Cho
[AMBER] Re: Ambertools 1.2 installation error
(Sun Jul 26 2009 - 23:51:49 PDT)
Brothers, Michael Charles
RE: [AMBER] Non-Standard Amino Acid Residue LEAP ERROR
(Fri Jul 31 2009 - 10:36:10 PDT)
[AMBER] Non-Standard Amino Acid Residue LEAP ERROR
(Thu Jul 30 2009 - 15:28:43 PDT)
[AMBER] Syntax Bellymask
(Fri Jul 10 2009 - 16:59:01 PDT)
RE: [AMBER] Tleap input error, atom not found in residue template
(Tue Jul 07 2009 - 09:08:00 PDT)
[AMBER] Tleap input error, atom not found in residue template
(Mon Jul 06 2009 - 18:25:00 PDT)
Carlos Simmerling
Re: [AMBER] Question on REST and VALUE1 keywords
(Tue Jul 28 2009 - 14:14:20 PDT)
Re: [AMBER] nonbon.f question
(Mon Jul 27 2009 - 12:34:20 PDT)
Re: [AMBER] Langevin Dynamics in AMBER10
(Fri Jul 24 2009 - 05:01:28 PDT)
Re: [AMBER] Langevin Dynamics in AMBER10
(Thu Jul 23 2009 - 14:57:44 PDT)
Re: [AMBER] IGB=7 vs IGB=5
(Tue Jul 21 2009 - 06:51:22 PDT)
Re: [AMBER] Box shape change
(Sun Jul 19 2009 - 06:51:44 PDT)
Re: [AMBER] Box shape change
(Sun Jul 19 2009 - 04:40:03 PDT)
Re: [AMBER] Box shape change
(Sat Jul 18 2009 - 18:35:41 PDT)
Re: [AMBER] unexplained blow-up at restart
(Mon Jul 13 2009 - 03:24:23 PDT)
Re: [AMBER] problem with energy calculations
(Sun Jul 12 2009 - 07:15:39 PDT)
Re: [AMBER] problem with energy calculations
(Sun Jul 12 2009 - 06:42:35 PDT)
Re: [AMBER] unexplained blow-up at restart
(Fri Jul 10 2009 - 10:58:15 PDT)
Re: [AMBER] problem with energy calculations
(Fri Jul 10 2009 - 10:25:56 PDT)
Re: [AMBER] unexplained blow-up at restart
(Fri Jul 10 2009 - 10:25:10 PDT)
Re: [AMBER] unexplained blow-up at restart
(Fri Jul 10 2009 - 10:02:39 PDT)
TMD: was: Re: [AMBER] charges in topology file
(Fri Jul 10 2009 - 09:36:30 PDT)
Re: [AMBER] implicit solvent (GB version2) MD simulation
(Fri Jul 10 2009 - 08:57:57 PDT)
Re: [AMBER] EPtot for Alpha-L- methyl fucose
(Fri Jul 10 2009 - 06:57:34 PDT)
Re: [AMBER] Restrained backbone conformation MD simulation"
(Fri Jul 10 2009 - 04:47:20 PDT)
Re: [AMBER] unexplained blow-up at restart
(Fri Jul 10 2009 - 03:55:51 PDT)
Re: [AMBER] Acetylate and Amidate
(Thu Jul 09 2009 - 04:52:28 PDT)
Re: [AMBER] Acetylate and Amidate
(Wed Jul 08 2009 - 15:22:58 PDT)
Re: [AMBER] rmsd_dna
(Wed Jul 08 2009 - 11:21:29 PDT)
Re: [AMBER] ouput trajectory of only CA atom
(Wed Jul 08 2009 - 07:41:25 PDT)
Re: [AMBER] unsolved verbosity when running minimization
(Wed Jul 08 2009 - 04:34:20 PDT)
Re: [AMBER] unsolved verbosity when running minimization
(Mon Jul 06 2009 - 12:28:08 PDT)
Re: [AMBER] The problem of restart file
(Wed Jul 01 2009 - 05:49:32 PDT)
case
Re: [AMBER] Normal mode analysis of water
(Thu Jul 30 2009 - 07:11:23 PDT)
Re: [AMBER] error in antechamber
(Mon Jul 27 2009 - 21:23:54 PDT)
Re: [AMBER] only ff94 and ff99 for GBSA?
(Mon Jul 27 2009 - 10:05:48 PDT)
Re: [AMBER] Output forces in Sander
(Mon Jul 27 2009 - 08:11:30 PDT)
Re: [AMBER] Re: bugfix 10 failing for ambertools1.2
(Mon Jul 27 2009 - 08:03:24 PDT)
Re: [AMBER] thymidine monophosphate parametrization
(Mon Jul 27 2009 - 07:47:38 PDT)
Re: [AMBER] Re: Ambertools 1.2 installation error
(Mon Jul 27 2009 - 07:38:28 PDT)
Re: [AMBER] cpin error
(Fri Jul 24 2009 - 12:41:00 PDT)
Re: [AMBER] amber10 parallel compiling error
(Wed Jul 22 2009 - 19:15:50 PDT)
Re: [AMBER] setting AMBERHOME
(Wed Jul 22 2009 - 19:15:34 PDT)
Re: [AMBER] Steered MD.....SHAKE error!!
(Fri Jul 17 2009 - 05:01:03 PDT)
Re: [AMBER] diffusion coeficients
(Fri Jul 17 2009 - 04:59:41 PDT)
Re: [AMBER] File conversion for from Amber to Charmm
(Fri Jul 17 2009 - 04:53:06 PDT)
Re: [AMBER] Disappearing common atoms in Amber 10 with TI
(Fri Jul 17 2009 - 04:41:39 PDT)
Re: [AMBER] Umbrella Sampling
(Thu Jul 16 2009 - 13:03:29 PDT)
Re: [AMBER] query regarding FE4S4
(Thu Jul 16 2009 - 04:45:06 PDT)
Re: [AMBER] carbonic anhydrase (CA) simulation
(Thu Jul 16 2009 - 04:36:17 PDT)
Re: [AMBER] different results for antechamber/mopac for the same input
(Thu Jul 16 2009 - 04:30:08 PDT)
Re: [AMBER] Please help me out
(Wed Jul 15 2009 - 12:55:21 PDT)
Re: [AMBER] Equilibrium water density
(Wed Jul 15 2009 - 12:53:54 PDT)
Re: [AMBER] Could not find bond parameter for O2 - ca
(Tue Jul 14 2009 - 20:28:02 PDT)
Re: [AMBER] Counterion release and Free energy of binding ?
(Tue Jul 14 2009 - 20:10:18 PDT)
Re: [AMBER] ptraj mask selection
(Mon Jul 13 2009 - 11:10:46 PDT)
Re: [AMBER] unexplained blow-up at restart
(Mon Jul 13 2009 - 09:51:46 PDT)
[AMBER] Re: reference re. size of dt
(Mon Jul 13 2009 - 09:56:46 PDT)
Re: [AMBER] ligand/protein minimization
(Mon Jul 13 2009 - 09:29:06 PDT)
Re: [AMBER] Peptide bond broken
(Sun Jul 12 2009 - 19:35:35 PDT)
Re: [AMBER] ligand/protein minimization
(Sun Jul 12 2009 - 19:32:29 PDT)
Re: [AMBER] amber dihedral format
(Sun Jul 12 2009 - 14:49:12 PDT)
Re: [AMBER] Antechamber prep question
(Thu Jul 09 2009 - 11:54:44 PDT)
Re: [AMBER] Antechamber prep question
(Thu Jul 09 2009 - 09:48:44 PDT)
Re: [AMBER] Antechamber prep question
(Thu Jul 09 2009 - 08:16:17 PDT)
Re: [AMBER] charged or not
(Thu Jul 09 2009 - 08:10:14 PDT)
Re: [AMBER] ff parameters
(Thu Jul 09 2009 - 06:23:31 PDT)
Re: [AMBER] amber10 installation problem
(Thu Jul 09 2009 - 05:38:01 PDT)
Re: [AMBER] amber10 installation problem
(Wed Jul 08 2009 - 04:56:19 PDT)
Re: [AMBER] Installing of amber10
(Wed Jul 08 2009 - 04:42:02 PDT)
Re: [AMBER] H-bond vs. VdW
(Mon Jul 06 2009 - 10:29:49 PDT)
Re: [AMBER] need charges of FE-S cluster
(Mon Jul 06 2009 - 05:35:19 PDT)
Re: [AMBER] Boundary Condition Problem
(Sat Jul 04 2009 - 06:45:45 PDT)
Re: [AMBER] default integration scheme in 7 vs. 10
(Thu Jul 02 2009 - 04:37:17 PDT)
Re: [AMBER] Steps for NMR structure minimization
(Wed Jul 01 2009 - 05:48:13 PDT)
Re: [AMBER] antechamber
(Wed Jul 01 2009 - 05:04:02 PDT)
Catein Catherine
[AMBER] What is the meaning of "rms first *"
(Thu Jul 30 2009 - 20:49:17 PDT)
RE: [AMBER] PCA analysis: the first vector is the movement of whole molecule.
(Thu Jul 30 2009 - 20:46:49 PDT)
[AMBER] PCA analysis: the first vector is the movement of whole molecule.
(Thu Jul 30 2009 - 03:37:49 PDT)
[AMBER] Re: MM-PBSA test jobs error messages (Can i fix the problem without recompile the amber?)
(Wed Jul 29 2009 - 02:39:02 PDT)
[AMBER] RE: MM-PBSA test jobs error messages (with bugfix.all)
(Tue Jul 28 2009 - 22:50:50 PDT)
[AMBER] How to visualize PCA results without IED?
(Tue Jul 28 2009 - 02:30:22 PDT)
[AMBER] RE: MM-PBSA test jobs error messages
(Tue Jul 28 2009 - 02:24:31 PDT)
[AMBER] MM-PBSA cannot finish without error message.
(Thu Jul 23 2009 - 02:57:00 PDT)
[AMBER] Is rmsd ~ 3 A reasonable for a 4ns simulation?
(Wed Jul 08 2009 - 02:45:41 PDT)
Chris Whittleston
Re: [AMBER] Using idecomp=3 with igb=10 (PB)
(Tue Jul 28 2009 - 03:54:09 PDT)
[AMBER] Using idecomp=3 with igb=10 (PB)
(Mon Jul 27 2009 - 13:04:14 PDT)
Christof Jaeger
Re: [AMBER] ptraj-radial distribution function
(Thu Jul 16 2009 - 01:22:02 PDT)
Chunliyan
[AMBER] Manganese bondi radii for mm/pbsa calculation
(Fri Jul 10 2009 - 06:39:51 PDT)
[AMBER] radius for Manganese ion
(Fri Jul 10 2009 - 06:39:51 PDT)
[AMBER] manganese bondi radii for mm_pbsa calculation
(Fri Jul 10 2009 - 06:39:51 PDT)
[AMBER] Manganese
(Fri Jul 10 2009 - 06:39:51 PDT)
[AMBER] Manganese bondi radii
(Fri Jul 10 2009 - 06:39:51 PDT)
Cihan Aydin
RE: [AMBER] ptraj - cluster
(Fri Jul 17 2009 - 07:22:37 PDT)
[AMBER] ptraj - cluster
(Wed Jul 15 2009 - 22:55:07 PDT)
Re: [AMBER] RE: suggestions
(Mon Jul 06 2009 - 18:29:22 PDT)
Re: [AMBER] H-bond vs. VdW
(Mon Jul 06 2009 - 08:13:39 PDT)
[AMBER] Leap Questions...
(Sat Jul 04 2009 - 18:41:39 PDT)
Clark, Tiffany D
[AMBER] vertex atom mismatch
(Fri Jul 31 2009 - 06:14:15 PDT)
David Dubins
[AMBER] Installing Amber10 on Ubuntu
(Wed Jul 29 2009 - 11:50:12 PDT)
David Mobley
[AMBER] Re: bug in antechamber
(Mon Jul 13 2009 - 10:41:01 PDT)
[AMBER] bug in antechamber
(Wed Jul 08 2009 - 09:19:12 PDT)
David Watson
Re: [AMBER] Compiling AmberTools 1.2 with intel compilers for Mac Osx in 64 bits
(Thu Jul 30 2009 - 12:10:39 PDT)
Re: [AMBER] Compiling AmberTools 1.2 with intel compilers for Mac Osx in 64 bits
(Wed Jul 29 2009 - 09:21:50 PDT)
[AMBER] Compiling AMBER 10 (parallel, MPICH2) on Mac OS X Intel w/gcc, ifort, icc
(Thu Jul 23 2009 - 13:03:59 PDT)
Re: [AMBER] how to launch XLEaP from SSH Secure Shell?
(Wed Jul 22 2009 - 17:30:12 PDT)
[AMBER] Compiling Amber 10 (serial) on Mac OS X 10.5.7 w/ gcc, Intel Fortan 11.0 and MKL 10.0
(Tue Jul 21 2009 - 14:20:36 PDT)
Duggan, Brendan M.
[AMBER] RE: DCCM
(Mon Jul 20 2009 - 07:29:46 PDT)
RE: [AMBER] DCCM
(Wed Jul 15 2009 - 09:06:57 PDT)
E.M.
[AMBER] RESP fit
(Fri Jul 17 2009 - 16:00:08 PDT)
[AMBER] Re: Request to mailing list AMBER rejected
(Mon Jul 13 2009 - 20:37:46 PDT)
felix
Re: [AMBER] diffusion coeficients
(Fri Jul 17 2009 - 06:41:43 PDT)
[AMBER] diffusion coeficients
(Fri Jul 17 2009 - 01:15:35 PDT)
Frank X. Vázquez
[AMBER] Output forces in Sander
(Tue Jul 21 2009 - 14:58:36 PDT)
FyD
Re: [AMBER] Removed proton in protein (Advanced Tutorials A1 old)
(Tue Jul 28 2009 - 04:59:51 PDT)
Re: [AMBER] only ff94 and ff99 for GBSA?
(Tue Jul 28 2009 - 00:32:52 PDT)
Re: [AMBER] loading a mol2 file in xleap
(Mon Jul 27 2009 - 06:44:50 PDT)
Re: [AMBER] Could not find type: MG Parameter file was not saved. though it was loaded
(Sun Jul 26 2009 - 22:03:00 PDT)
Re: [AMBER] loading a mol2 file in xleap
(Fri Jul 24 2009 - 13:00:41 PDT)
Re: [AMBER] radical simulation
(Fri Jul 24 2009 - 03:27:34 PDT)
Re: [AMBER] questions about RESP
(Thu Jul 23 2009 - 10:49:23 PDT)
Re: [AMBER] saquinavir parameterization with antechamber
(Thu Jul 23 2009 - 00:29:57 PDT)
Re: [AMBER] saquinavir parameterization with antechamber
(Wed Jul 22 2009 - 11:41:21 PDT)
Re: [AMBER] questions about RESP
(Mon Jul 20 2009 - 13:46:04 PDT)
Re: [AMBER] RE: charge not zero on group:''''.respin1 attached
(Sun Jul 19 2009 - 00:41:17 PDT)
Re: [AMBER] RESP fit
(Fri Jul 17 2009 - 23:29:56 PDT)
Re: [AMBER] amino acids caps for truncated proteins
(Thu Jul 16 2009 - 09:58:32 PDT)
Re: [AMBER] command for RESP fitting
(Thu Jul 16 2009 - 07:34:28 PDT)
Re: [AMBER] questions about RESP
(Thu Jul 16 2009 - 07:27:44 PDT)
Re: [AMBER] GAFF and NME, ACE terminal res
(Wed Jul 15 2009 - 23:25:03 PDT)
Re: [AMBER] R.E.D. help please
(Wed Jul 15 2009 - 09:35:57 PDT)
Re: [AMBER] non standard residue
(Tue Jul 14 2009 - 13:01:32 PDT)
Re: [AMBER] GAFF and NME, ACE terminal res
(Tue Jul 14 2009 - 00:40:00 PDT)
Re: [AMBER] non standard residue
(Mon Jul 13 2009 - 23:47:00 PDT)
Re: [AMBER] help needed for HID
(Mon Jul 13 2009 - 13:27:13 PDT)
Re: [AMBER] R.E.D intra-mcc and reorientation
(Sat Jul 11 2009 - 01:05:56 PDT)
Re: [AMBER] Peptide bond broken
(Fri Jul 10 2009 - 23:58:06 PDT)
Re: [AMBER] Antechamber prep question
(Fri Jul 10 2009 - 08:24:08 PDT)
Re: [AMBER] Antechamber prep question
(Thu Jul 09 2009 - 22:52:12 PDT)
Re: [AMBER] Zinc ion, help
(Wed Jul 08 2009 - 02:43:26 PDT)
Re: [AMBER] non standard residue
(Tue Jul 07 2009 - 00:50:09 PDT)
Re: [AMBER] RED: Charge derivation of transtion state analogue
(Sun Jul 05 2009 - 23:45:13 PDT)
Re: [AMBER] RED: Charge derivation of transtion state analogue
(Sun Jul 05 2009 - 23:29:11 PDT)
Re: [AMBER] RED: Charge derivation of transtion state analogue
(Sun Jul 05 2009 - 02:39:13 PDT)
[AMBER] Re: [q4md-fft] Charge calculation or non standard residue
(Sun Jul 05 2009 - 01:30:50 PDT)
Re: [AMBER] H-bond vs. VdW
(Fri Jul 03 2009 - 22:01:58 PDT)
[AMBER] Re: Error in REDIII
(Fri Jul 03 2009 - 07:59:30 PDT)
Re: [AMBER] antechamber
(Wed Jul 01 2009 - 23:33:46 PDT)
Re: [AMBER] antechamber
(Wed Jul 01 2009 - 05:26:39 PDT)
Ganesh Krishnan
Re: [AMBER] R.E.D intra-mcc and reorientation
(Sat Jul 11 2009 - 15:56:18 PDT)
[AMBER] R.E.D intra-mcc and reorientation
(Fri Jul 10 2009 - 15:00:35 PDT)
gilbert.bluemarble.net
Re: [AMBER] Antechamber prep question
(Fri Jul 10 2009 - 06:10:32 PDT)
Re: [AMBER] antechamber
(Wed Jul 01 2009 - 05:11:17 PDT)
Giorgos Lamprinidis
Re: [AMBER] Need help for PMEMD 10 installation
(Tue Jul 14 2009 - 00:29:09 PDT)
Re: [AMBER] MM-PBSA problem
(Mon Jul 06 2009 - 01:07:14 PDT)
[AMBER] MM-PBSA problem
(Fri Jul 03 2009 - 06:50:36 PDT)
Guillermo Mulliert Carlín
Re: [AMBER] vertex atom mismatch
(Fri Jul 31 2009 - 07:33:46 PDT)
gunajyoti das
[AMBER] (no subject)
(Sun Jul 19 2009 - 08:13:01 PDT)
[AMBER] (no subject)
(Sun Jul 19 2009 - 08:14:20 PDT)
Gustavo Seabra
Re: [AMBER] reference re. determining size of timestep
(Fri Jul 17 2009 - 09:53:46 PDT)
Re: Fw: [AMBER] Re: pls help and suggest
(Fri Jul 17 2009 - 09:50:59 PDT)
Re: [AMBER] QMMM outupts
(Thu Jul 09 2009 - 09:58:30 PDT)
[AMBER] Re: pls help and suggest
(Thu Jul 09 2009 - 09:14:42 PDT)
Hannes Kopitz
Re: [AMBER] Using idecomp=3 with igb=10 (PB)
(Tue Jul 28 2009 - 05:47:15 PDT)
Re: [AMBER] Using idecomp=3 with igb=10 (PB)
(Tue Jul 28 2009 - 03:09:01 PDT)
Re: [AMBER] question of mm_pbsa
(Fri Jul 10 2009 - 02:36:44 PDT)
Hannes Loeffler
RE: [AMBER] PCA analysis: the first vector is the movement of whole molecule.
(Fri Jul 31 2009 - 00:27:54 PDT)
Re: [AMBER] PCA analysis: the first vector is the movement of whole molecule.
(Thu Jul 30 2009 - 03:52:48 PDT)
Re: [AMBER] How to visualize PCA results without IED?
(Tue Jul 28 2009 - 03:12:04 PDT)
[AMBER] nasty memory bug in calculatePrincipalAxis
(Mon Jul 20 2009 - 01:30:38 PDT)
Harald Lanig
[AMBER] Molecular Modeling Workshop and Model(l)ing'09 in Erlangen, Germany
(Tue Jul 14 2009 - 07:02:16 PDT)
Hemant Kumar
Re: [AMBER] Box shape change
(Sun Jul 19 2009 - 10:38:43 PDT)
Re: [AMBER] Box shape change
(Sun Jul 19 2009 - 05:05:04 PDT)
Re: [AMBER] Box shape change
(Sun Jul 19 2009 - 04:00:18 PDT)
[AMBER] Box shape change
(Sat Jul 18 2009 - 12:38:46 PDT)
RE: [AMBER] Umbrella Sampling
(Sat Jul 18 2009 - 12:28:19 PDT)
[AMBER] Umbrella Sampling
(Thu Jul 16 2009 - 11:01:40 PDT)
Hlengisizwe Ndlovu
[AMBER] Steered MD.....SHAKE error!!
(Fri Jul 17 2009 - 01:50:11 PDT)
[AMBER] vlimit exceeded....nscu_SMD!!
(Thu Jul 16 2009 - 05:53:50 PDT)
[AMBER] Steered MD---more than one pair of atoms
(Tue Jul 07 2009 - 06:27:59 PDT)
Hopkins, Robert
RE: [Subject Filtered] Re: [AMBER] PMEMD in a Cygwin Environment 8%
(Thu Jul 23 2009 - 13:37:12 PDT)
[AMBER] PMEMD in a Cygwin Environment
(Tue Jul 14 2009 - 12:48:41 PDT)
Hugh Heldenbrand
Re: [AMBER] Exclamation marks in trajectory
(Mon Jul 13 2009 - 11:52:37 PDT)
[AMBER] Exclamation marks in trajectory
(Mon Jul 13 2009 - 08:16:26 PDT)
hwu.clarku.edu
[AMBER] Question on REST and VALUE1 keywords
(Tue Jul 28 2009 - 14:06:34 PDT)
Jeffrey
Re: [AMBER] radical simulation
(Sun Jul 26 2009 - 05:28:39 PDT)
[AMBER] radical simulation
(Fri Jul 24 2009 - 00:34:53 PDT)
Re: [AMBER] questions about RESP
(Thu Jul 23 2009 - 05:51:34 PDT)
Re: [AMBER] questions about RESP
(Mon Jul 20 2009 - 00:42:29 PDT)
[AMBER] questions about RESP
(Wed Jul 15 2009 - 23:57:28 PDT)
[AMBER] TMD: solvation and equilibration questions
(Fri Jul 10 2009 - 18:07:55 PDT)
Re: [AMBER] charges in topology file
(Fri Jul 10 2009 - 09:20:01 PDT)
Re: [AMBER] The problem of restart file
(Wed Jul 01 2009 - 07:07:08 PDT)
[AMBER] The problem of restart file
(Wed Jul 01 2009 - 05:15:34 PDT)
Jianyin Shao
Re: [AMBER] ptraj mask selection
(Mon Jul 13 2009 - 12:02:03 PDT)
Re: [AMBER] ptraj mask selection
(Mon Jul 13 2009 - 10:57:23 PDT)
Jio M
Re: [AMBER] ambpdb problem
(Fri Jul 31 2009 - 00:11:32 PDT)
[AMBER] ambpdb problem
(Thu Jul 30 2009 - 12:12:10 PDT)
[AMBER] pdb file no bond and charges
(Tue Jul 28 2009 - 23:28:48 PDT)
[AMBER] residues lacking connect0/connect1
(Mon Jul 27 2009 - 09:10:06 PDT)
[AMBER] -a flag :RESP
(Sun Jul 19 2009 - 03:48:20 PDT)
[AMBER] RE: charge not zero on group:''''.respin1 attached
(Sat Jul 18 2009 - 07:40:18 PDT)
[AMBER] charge not zero on group: RESP
(Fri Jul 17 2009 - 22:14:58 PDT)
Re: [AMBER] GAFF and NME, ACE terminal res
(Wed Jul 15 2009 - 21:29:08 PDT)
[AMBER] GAFF and NME, ACE terminal res
(Mon Jul 13 2009 - 13:51:06 PDT)
[AMBER] suitable force field
(Wed Jul 08 2009 - 00:14:12 PDT)
[AMBER] suitable force field
(Wed Jul 08 2009 - 03:06:35 PDT)
Jordan Monnet
Re: [AMBER] ambpdb problem
(Fri Jul 31 2009 - 07:30:54 PDT)
Re: [AMBER] ambpdb problem
(Thu Jul 30 2009 - 12:32:57 PDT)
Re: [AMBER] Can I get the torsion angle between base-pairs using ptraj ?
(Wed Jul 15 2009 - 15:56:12 PDT)
Re: [AMBER] ouput trajectory of only CA atom
(Wed Jul 08 2009 - 09:03:32 PDT)
Jun Dong
Re: [AMBER] RE: pmemd parallel
(Wed Jul 15 2009 - 08:00:49 PDT)
RE: [AMBER] Need help for PMEMD 10 installation
(Mon Jul 13 2009 - 11:10:34 PDT)
RE: [AMBER] Need help for PMEMD 10 installation
(Fri Jul 10 2009 - 10:25:03 PDT)
[AMBER] Need help for PMEMD 10 installation
(Fri Jul 10 2009 - 09:05:49 PDT)
Keith Van Nostrand
Re: [AMBER] Regarding Running QM/MM NEB with PM3-PDDG using Amber10
(Wed Jul 22 2009 - 08:58:08 PDT)
Re: [AMBER] Regarding Running QM/MM NEB with PM3-PDDG using Amber10
(Thu Jul 16 2009 - 14:08:04 PDT)
[AMBER] Regarding Running QM/MM NEB with PM3-PDDG using Amber10
(Fri Jul 10 2009 - 08:27:12 PDT)
Khavrutskii, Ilja
Re: [AMBER] Disappearing common atoms in Amber 10 with TI
(Mon Jul 20 2009 - 04:46:38 PDT)
Re: [AMBER] Disappearing common atoms in Amber 10 with TI
(Thu Jul 16 2009 - 14:02:10 PDT)
[AMBER] Disappearing common atoms in Amber 10 with TI
(Thu Jul 16 2009 - 06:38:43 PDT)
Kristina Furse
RE: [AMBER] Replacing DNA base with analog
(Thu Jul 23 2009 - 07:36:26 PDT)
RE: [AMBER] question of ibelly used in pmemd
(Tue Jul 21 2009 - 09:27:29 PDT)
RE: [AMBER] question of ibelly used in pmemd
(Tue Jul 21 2009 - 06:53:21 PDT)
RE: [AMBER] question of ibelly used in pmemd
(Mon Jul 20 2009 - 09:56:26 PDT)
RE: [AMBER] ntt=3 and ibelly=1
(Fri Jul 17 2009 - 09:41:29 PDT)
[AMBER] ntt=3 and ibelly=1
(Thu Jul 16 2009 - 09:07:23 PDT)
Lake, Thomas
RE: [AMBER] problem with energy calculations
(Sun Jul 12 2009 - 06:35:33 PDT)
Lan JIN
Re: [AMBER] amber10 installation problem
(Fri Jul 10 2009 - 00:41:34 PDT)
Re: [AMBER] amber10 installation problem
(Wed Jul 08 2009 - 19:46:22 PDT)
[AMBER] amber10 installation problem
(Tue Jul 07 2009 - 23:49:05 PDT)
Mahmoud A. A. Ibrahim
Re: [AMBER] problem with the energetics of the system
(Sun Jul 12 2009 - 03:37:37 PDT)
[AMBER] problem with the energetics of the system
(Sat Jul 11 2009 - 16:23:13 PDT)
[AMBER] Zinc ion, help
(Tue Jul 07 2009 - 07:26:48 PDT)
Manish Kumar
Re: [AMBER] Simulation with United atom force field in Implicit solvent.
(Sun Jul 26 2009 - 11:22:40 PDT)
[AMBER] Simulation with United atom force field in Implicit solvent.
(Sat Jul 25 2009 - 20:55:42 PDT)
Re: [AMBER] radical simulation
(Fri Jul 24 2009 - 00:48:01 PDT)
Re: [AMBER] Re: MM-PBSA delphi.crg and delphi.siz
(Thu Jul 23 2009 - 00:10:51 PDT)
[AMBER] Patching terminal
(Tue Jul 21 2009 - 16:53:54 PDT)
Re: [AMBER] Re: MM-PBSA delphi.crg and delphi.siz
(Mon Jul 20 2009 - 14:11:20 PDT)
Re: [AMBER] Re: MM-PBSA delphi.crg and delphi.siz
(Sun Jul 19 2009 - 12:36:35 PDT)
[AMBER] Re: MM-PBSA delphi.crg and delphi.siz
(Thu Jul 09 2009 - 20:33:01 PDT)
[AMBER] MM-PBSA delphi.crg and delphi.siz
(Wed Jul 08 2009 - 14:29:40 PDT)
Mannan
[AMBER] Could not find type: MG Parameter file was not saved. though it was loaded
(Sun Jul 26 2009 - 20:49:54 PDT)
[AMBER] Could not find type: MG Parameter file was not saved.
(Sat Jul 25 2009 - 20:41:24 PDT)
manoj singh
Re: [AMBER] RED: Charge derivation of transtion state analogue
(Sun Jul 05 2009 - 22:03:27 PDT)
[AMBER] RED: Charge derivation of transtion state analogue
(Sat Jul 04 2009 - 23:10:57 PDT)
Marek Maly
Re: [AMBER] The Right Neutralization Procedure and Ionic Strength Calculation ?
(Fri Jul 17 2009 - 11:37:02 PDT)
[AMBER] The Right Neutralization Procedure and Ionic Strength Calculation ?
(Fri Jul 17 2009 - 09:34:44 PDT)
Re: [AMBER] Counterion release and Free energy of binding ?
(Fri Jul 17 2009 - 04:10:40 PDT)
[AMBER] Counterion release and Free energy of binding ?
(Tue Jul 14 2009 - 15:27:18 PDT)
Re: [AMBER] Nonstandard molecules simulated with parm99EP ?
(Wed Jul 01 2009 - 09:02:29 PDT)
Re: [AMBER] Nonstandard molecules simulated with parm99EP ?
(Wed Jul 01 2009 - 08:47:04 PDT)
Marius Retegan
Re: [AMBER] help needed for HID
(Sun Jul 12 2009 - 11:24:40 PDT)
Markus Kaukonen
Re: [AMBER] need charges of FE-S cluster
(Tue Jul 21 2009 - 11:50:39 PDT)
Massimiliano Bonomi
[AMBER] PLUMED release 1.1.0 available
(Tue Jul 28 2009 - 01:10:39 PDT)
Matthias Negri
[AMBER] MM/PBSA, MM/GBSA and NMODE Analysis
(Wed Jul 29 2009 - 03:55:46 PDT)
Mengjuei Hsieh
[AMBER] Re: problem of installation of amber10
(Wed Jul 29 2009 - 12:41:52 PDT)
Re: [AMBER] error in antechamber
(Mon Jul 27 2009 - 15:29:06 PDT)
Re: [AMBER] errors of PMEMD installation
(Sat Jul 25 2009 - 20:10:11 PDT)
Re: 回复： [AMBER] errors of PMEMD installation
(Fri Jul 24 2009 - 11:12:00 PDT)
Re: 回复： [AMBER] errors of PMEMD installation
(Fri Jul 24 2009 - 01:41:05 PDT)
Re: [AMBER] errors of PMEMD installation
(Thu Jul 23 2009 - 12:25:27 PDT)
moitrayee.mbu.iisc.ernet.in
RE: [AMBER] Problem with amber9 installation
(Tue Jul 14 2009 - 00:02:39 PDT)
[AMBER] Problem with amber9 installation
(Mon Jul 13 2009 - 13:31:18 PDT)
Myeong Lee
[AMBER] How to read md trajectory for each time slice as an input coordinate
(Mon Jul 27 2009 - 01:16:47 PDT)
[AMBER] Can I get the torsion angle between base-pairs using ptraj ?
(Wed Jul 15 2009 - 14:51:02 PDT)
[AMBER] Equilibrium water density
(Wed Jul 15 2009 - 01:58:52 PDT)
[AMBER] How to fix specific atoms? (not residue)
(Sat Jul 11 2009 - 04:46:06 PDT)
[AMBER] QMMM outupts
(Tue Jul 07 2009 - 10:13:27 PDT)
nam kim
Re: [AMBER] amber10 parallel compiling error
(Thu Jul 23 2009 - 21:32:14 PDT)
Re: [AMBER] amber10 parallel compiling error
(Tue Jul 21 2009 - 10:06:32 PDT)
Re: [AMBER] amber10 parallel compiling error
(Mon Jul 20 2009 - 15:53:24 PDT)
Re: [AMBER] amber10 parallel compiling error
(Mon Jul 20 2009 - 11:34:41 PDT)
Re: [AMBER] amber10 parallel compiling error
(Mon Jul 20 2009 - 11:15:16 PDT)
Re: [AMBER] amber10 parallel compiling error
(Mon Jul 20 2009 - 10:24:14 PDT)
[AMBER] amber10 parallel compiling error
(Sat Jul 18 2009 - 10:19:39 PDT)
[AMBER] amber10 parallel compiling error
(Thu Jul 16 2009 - 17:50:57 PDT)
Nancy
[AMBER] ptraj-radial distribution function
(Wed Jul 15 2009 - 23:34:12 PDT)
Naser Alijabbari
Re: [AMBER] Re: mpirun noticed that process rank 1 ... on signal 1 (Hangup).
(Tue Jul 14 2009 - 09:30:55 PDT)
[AMBER] Re: mpirun noticed that process rank 1 ... on signal 1 (Hangup).
(Tue Jul 14 2009 - 03:49:14 PDT)
[AMBER] mpirun noticed that process rank 1 ... on signal 1 (Hangup).
(Tue Jul 14 2009 - 03:41:39 PDT)
Neha Gandhi
[AMBER] Re: non aminoacid Residue
(Mon Jul 06 2009 - 01:43:56 PDT)
[AMBER] non standard residue
(Mon Jul 06 2009 - 01:07:35 PDT)
nicholus bhattacharjee
Re: [AMBER] Am I doing the right thing
(Tue Jul 28 2009 - 21:36:31 PDT)
[AMBER] Am I doing the right thing
(Tue Jul 28 2009 - 10:20:57 PDT)
Nicolas SAPAY
Re: [AMBER] Compilation error with pmemd (amber10) on fedora9 64 bits
(Fri Jul 31 2009 - 05:55:18 PDT)
[AMBER] Compilation error with pmemd (amber10) on fedora9 64 bits
(Fri Jul 31 2009 - 02:41:21 PDT)
Niel Henriksen
[AMBER] RE: Average structure over simulation
(Mon Jul 27 2009 - 07:56:40 PDT)
oguz gurbulak
[AMBER] ff parameters
(Wed Jul 08 2009 - 07:35:40 PDT)
Oliver Kuhn
Re: [AMBER] saquinavir parameterization with antechamber
(Thu Jul 23 2009 - 01:06:00 PDT)
Re: [AMBER] saquinavir parameterization with antechamber
(Thu Jul 23 2009 - 00:02:49 PDT)
[AMBER] saquinavir parameterization with antechamber
(Wed Jul 22 2009 - 08:42:49 PDT)
Olotu Odunayo
RE: [AMBER] RE: Average structure over simulation
(Mon Jul 27 2009 - 08:47:20 PDT)
[AMBER] Average structure over simulation
(Mon Jul 27 2009 - 06:38:59 PDT)
RE: [AMBER] Equilibration step
(Wed Jul 22 2009 - 23:52:50 PDT)
RE: [AMBER] Equilibration step
(Wed Jul 22 2009 - 09:46:12 PDT)
RE: [AMBER] Equilibration step
(Wed Jul 22 2009 - 09:41:13 PDT)
[AMBER] Equilibration step
(Wed Jul 22 2009 - 02:47:37 PDT)
Organization
[AMBER] [ALERT]: It's the time to come out on streets and stop the complete nation on it's place - Take immediate actions at once with full force.
(Wed Jul 22 2009 - 12:13:37 PDT)
Pansy Patel
Re: [AMBER] query
(Fri Jul 31 2009 - 07:41:05 PDT)
Patrick Gedeon
Re: [AMBER] ptraj mask selection
(Mon Jul 13 2009 - 12:58:18 PDT)
[AMBER] ptraj mask selection
(Sun Jul 12 2009 - 20:45:56 PDT)
[AMBER] Re: Directory - GAFF Parameter File?
(Mon Jul 06 2009 - 16:38:57 PDT)
[AMBER] Directory - GAFF Parameter File?
(Mon Jul 06 2009 - 16:31:49 PDT)
Paul Brandt
[AMBER] reference re. determining size of timestep
(Thu Jul 09 2009 - 11:07:50 PDT)
[AMBER] default integration scheme in 7 vs. 10
(Wed Jul 01 2009 - 13:48:46 PDT)
Paul Mortenson
[AMBER] rdparm bug?
(Tue Jul 07 2009 - 09:29:44 PDT)
Pepe` Falahat
[AMBER] Boundary Condition Problem
(Sat Jul 04 2009 - 05:10:59 PDT)
Peter Varnai
[AMBER] pmemd/bintraj and ifort 10.1.0.21
(Wed Jul 01 2009 - 11:28:30 PDT)
Prem Prakash Pathak
[AMBER] Restrained backbone conformation MD simulation"
(Fri Jul 10 2009 - 04:27:38 PDT)
Qinghua Liao
[AMBER] problem from xleap
(Fri Jul 31 2009 - 07:38:18 PDT)
Re: [AMBER] error in antechamber
(Mon Jul 27 2009 - 22:13:49 PDT)
Re: [AMBER] error in antechamber
(Mon Jul 27 2009 - 18:02:26 PDT)
[AMBER] error in antechamber
(Mon Jul 27 2009 - 04:57:50 PDT)
Re: 回复： [AMBER] errors of PMEMD installation
(Fri Jul 24 2009 - 18:24:10 PDT)
Re: 回复： [AMBER] errors of PMEMD installation
(Fri Jul 24 2009 - 02:59:03 PDT)
Re: 回复： [AMBER] errors of PMEMD installation
(Fri Jul 24 2009 - 02:18:44 PDT)
[AMBER] mailing list
(Thu Jul 23 2009 - 18:45:50 PDT)
R. A.
Re: [AMBER] antechamber
(Thu Jul 02 2009 - 17:35:42 PDT)
Re: [AMBER] antechamber
(Wed Jul 01 2009 - 17:46:19 PDT)
[AMBER] antechamber
(Wed Jul 01 2009 - 02:19:54 PDT)
[AMBER] antechamber
(Wed Jul 01 2009 - 02:17:51 PDT)
Raja Pandian
[AMBER] DCCM
(Tue Jul 07 2009 - 04:05:20 PDT)
Ray Luo
Re: [AMBER] MM/PBSA, MM/GBSA and NMODE Analysis
(Wed Jul 29 2009 - 17:25:14 PDT)
Re: [AMBER] Simulation with United atom force field in Implicit solvent.
(Sun Jul 26 2009 - 00:09:07 PDT)
Re: [AMBER] Re: MM-PBSA delphi.crg and delphi.siz
(Tue Jul 21 2009 - 07:24:40 PDT)
Re: [AMBER] Re: MM-PBSA delphi.crg and delphi.siz
(Sun Jul 19 2009 - 15:45:29 PDT)
Re: [AMBER] question of mm_pbsa
(Fri Jul 10 2009 - 09:47:12 PDT)
Re: [AMBER] Re: MM-PBSA delphi.crg and delphi.siz
(Fri Jul 10 2009 - 09:32:18 PDT)
Rilei Yu
[AMBER] installing of amber10 problem
(Wed Jul 08 2009 - 01:47:13 PDT)
[AMBER] Installing of amber10
(Wed Jul 08 2009 - 01:34:24 PDT)
[AMBER] calculation of the solvent accessibility
(Sat Jul 04 2009 - 01:54:23 PDT)
Rizwan Tai
[AMBER] nonbon.f question
(Mon Jul 27 2009 - 12:30:12 PDT)
[AMBER] nonbon.f question
(Mon Jul 20 2009 - 12:31:17 PDT)
Robert Duke
Re: [AMBER] Compilation error with pmemd (amber10) on fedora9 64 bits
(Fri Jul 31 2009 - 05:33:52 PDT)
Re: [AMBER] MPI error
(Wed Jul 29 2009 - 05:05:57 PDT)
Re: [AMBER] how to launch XLEaP from SSH Secure Shell?
(Wed Jul 22 2009 - 16:07:24 PDT)
Re: [AMBER] question of ibelly used in pmemd
(Tue Jul 21 2009 - 07:16:21 PDT)
Re: [AMBER] question of ibelly used in pmemd
(Tue Jul 21 2009 - 06:15:20 PDT)
Re: [AMBER] question of ibelly used in pmemd
(Mon Jul 20 2009 - 10:55:23 PDT)
Re: [AMBER] question of ibelly used in pmemd
(Mon Jul 20 2009 - 10:10:03 PDT)
Re: [AMBER] question of ibelly used in pmemd
(Mon Jul 20 2009 - 09:42:08 PDT)
Re: [AMBER] question of ibelly used in pmemd
(Mon Jul 20 2009 - 08:53:50 PDT)
Re: [AMBER] question of ibelly used in pmemd
(Mon Jul 20 2009 - 07:42:15 PDT)
Re: [AMBER] question of ibelly used in pmemd
(Fri Jul 17 2009 - 08:48:41 PDT)
Re: [AMBER] question of ibelly used in pmemd
(Wed Jul 15 2009 - 14:56:00 PDT)
Re: [AMBER] question of ibelly used in pmemd
(Wed Jul 15 2009 - 11:22:23 PDT)
Re: [AMBER] PMEMD in a Cygwin Environment
(Tue Jul 14 2009 - 13:16:46 PDT)
Re: [AMBER] Need help for PMEMD 10 installation
(Tue Jul 14 2009 - 04:50:26 PDT)
Re: [AMBER] pmemd/bintraj and ifort 10.1.0.21
(Wed Jul 01 2009 - 11:54:52 PDT)
Rodrigo Galindo
Re: [AMBER] Installing Amber10 on Ubuntu
(Wed Jul 29 2009 - 12:49:33 PDT)
[AMBER] DNA + intercalator
(Fri Jul 24 2009 - 15:22:35 PDT)
Ross Walker
[AMBER] RE: Questions about QMMM
(Tue Jul 21 2009 - 15:47:49 PDT)
[AMBER] RE: the copper paramter
(Mon Jul 20 2009 - 14:38:14 PDT)
RE: [AMBER] Tutorial A3
(Mon Jul 20 2009 - 12:03:44 PDT)
RE: [AMBER] amber10 parallel compiling error
(Mon Jul 20 2009 - 10:33:08 PDT)
RE: [AMBER] question of ibelly used in pmemd
(Mon Jul 20 2009 - 10:32:08 PDT)
RE: [AMBER] Different machines
(Sun Jul 19 2009 - 09:28:52 PDT)
RE: [AMBER] production phase
(Thu Jul 16 2009 - 20:56:13 PDT)
RE: [AMBER] ntt=3 and ibelly=1
(Thu Jul 16 2009 - 20:44:47 PDT)
RE: [AMBER] amber10 parallel compiling error
(Thu Jul 16 2009 - 20:43:15 PDT)
RE: [AMBER] IDIVF and PN
(Thu Jul 16 2009 - 20:40:11 PDT)
RE: [AMBER] Regarding Running QM/MM NEB with PM3-PDDG using Amber10
(Thu Jul 16 2009 - 20:34:13 PDT)
RE: [AMBER] question of ibelly used in pmemd
(Wed Jul 15 2009 - 18:32:07 PDT)
RE: [AMBER] Re: mpirun noticed that process rank 1 ... on signal 1 (Hangup).
(Tue Jul 14 2009 - 05:33:49 PDT)
[AMBER] RE: pmemd parallel
(Tue Jul 14 2009 - 05:24:06 PDT)
RE: [AMBER] Problem with amber9 installation
(Mon Jul 13 2009 - 20:34:54 PDT)
RE: [AMBER] Exclamation marks in trajectory
(Mon Jul 13 2009 - 12:20:37 PDT)
RE: [AMBER] Need help for PMEMD 10 installation
(Mon Jul 13 2009 - 12:18:26 PDT)
RE: [AMBER] Exclamation marks in trajectory
(Mon Jul 13 2009 - 11:13:17 PDT)
RE: [AMBER] Amber10, Serial compilation with ifort
(Sun Jul 12 2009 - 14:41:07 PDT)
Re: [AMBER] problem with the energetics of the system
(Sat Jul 11 2009 - 16:52:42 PDT)
RE: [AMBER] Need help for PMEMD 10 installation
(Fri Jul 10 2009 - 11:52:13 PDT)
RE: [AMBER] Need help for PMEMD 10 installation
(Fri Jul 10 2009 - 09:26:29 PDT)
RE: [AMBER] Regarding Running QM/MM NEB with PM3-PDDG using Amber10
(Fri Jul 10 2009 - 09:21:11 PDT)
RE: [AMBER] AMBER windows version ?
(Thu Jul 09 2009 - 15:45:49 PDT)
RE: [AMBER] rmsd_ptraj
(Wed Jul 08 2009 - 21:35:59 PDT)
RE: [AMBER] MPI process terminated unexpectedly forrtl: error (69): process interrupted (SIGINT)
(Wed Jul 08 2009 - 08:01:24 PDT)
RE: [AMBER] Principle Questions
(Tue Jul 07 2009 - 16:42:42 PDT)
RE: [AMBER] Tleap input error, atom not found in residue template
(Mon Jul 06 2009 - 21:28:46 PDT)
[AMBER] RE: suggestions
(Mon Jul 06 2009 - 18:01:51 PDT)
[AMBER] RE: question about TUTORIAL A1
(Mon Jul 06 2009 - 09:58:47 PDT)
RE: [AMBER] Re: non aminoacid Residue
(Mon Jul 06 2009 - 09:21:44 PDT)
RE: [AMBER] Leap Questions...
(Sun Jul 05 2009 - 21:01:34 PDT)
[AMBER] RE: ask for help (zn parameters)
(Sun Jul 05 2009 - 19:56:50 PDT)
[AMBER] RE: question about TUTORIAL A1
(Sun Jul 05 2009 - 19:29:38 PDT)
RE: [AMBER] default integration scheme in 7 vs. 10
(Wed Jul 01 2009 - 14:29:12 PDT)
RE: [AMBER] amber9 in fedora10
(Wed Jul 01 2009 - 09:36:33 PDT)
Rubben Torella
Re: [AMBER] MM-PBSA problem
(Fri Jul 03 2009 - 06:57:09 PDT)
Rukman Hertadi
RE: [AMBER] cpin error
(Mon Jul 27 2009 - 22:22:18 PDT)
[AMBER] cpin error
(Fri Jul 24 2009 - 00:18:52 PDT)
s. Bill
[AMBER] Metalloproteins - Ligand Protonation
(Fri Jul 31 2009 - 11:01:42 PDT)
[AMBER] Protonated or not
(Fri Jul 31 2009 - 10:15:32 PDT)
Re: Solved it thanks [AMBER] RED.III: Invalid Optimization OUTPUT
(Wed Jul 29 2009 - 05:14:02 PDT)
[AMBER] RED.III: Invalid Optimization OUTPUT
(Wed Jul 29 2009 - 01:37:27 PDT)
[AMBER] QM/MM
(Mon Jul 27 2009 - 23:44:15 PDT)
[AMBER] Tutorial A3
(Sun Jul 19 2009 - 12:33:58 PDT)
[AMBER] which keyword
(Sun Jul 19 2009 - 05:21:23 PDT)
[AMBER] Different machines
(Sun Jul 19 2009 - 02:55:48 PDT)
[AMBER] production phase
(Thu Jul 16 2009 - 05:18:25 PDT)
[AMBER] IDIVF and PN
(Thu Jul 16 2009 - 05:11:27 PDT)
[AMBER] R.E.D. help please
(Wed Jul 15 2009 - 07:11:46 PDT)
[AMBER] help needed for HID
(Sun Jul 12 2009 - 11:16:08 PDT)
[AMBER] amber dihedral format
(Sun Jul 12 2009 - 07:05:23 PDT)
[AMBER] charged or not
(Thu Jul 09 2009 - 05:33:05 PDT)
s_bill36.yahoo.co.uk
[AMBER] Principle Questions
(Tue Jul 07 2009 - 00:50:53 PDT)
Sally Pias
Re: [AMBER] unexplained blow-up at restart
(Mon Jul 13 2009 - 09:11:08 PDT)
Re: [AMBER] unexplained blow-up at restart
(Mon Jul 13 2009 - 00:01:29 PDT)
Re: [AMBER] unexplained blow-up at restart
(Fri Jul 10 2009 - 11:59:24 PDT)
Re: [AMBER] unexplained blow-up at restart
(Fri Jul 10 2009 - 10:20:27 PDT)
Re: [AMBER] unexplained blow-up at restart
(Fri Jul 10 2009 - 09:31:59 PDT)
Re: [AMBER] unexplained blow-up at restart
(Fri Jul 10 2009 - 08:29:01 PDT)
[AMBER] unexplained blow-up at restart
(Fri Jul 10 2009 - 01:02:42 PDT)
Santosh Mogurampelly
[AMBER] pulling two atoms in SMD
(Tue Jul 28 2009 - 05:10:12 PDT)
Scott Brozell
Re: [AMBER] Compiling Amber 10 (serial) on Mac OS X 10.5.7 w/ gcc, Intel Fortan 11.0 and MKL 10.0
(Wed Jul 22 2009 - 12:52:59 PDT)
Seetin, Matthew
RE: [AMBER] Umbrella Sampling
(Thu Jul 16 2009 - 13:13:59 PDT)
Sergey Samsonov
[AMBER] xleap facility to insert a residue
(Fri Jul 24 2009 - 06:07:27 PDT)
Shozeb Haider
Re: [AMBER] How to visualize PCA results without IED?
(Tue Jul 28 2009 - 04:02:22 PDT)
[AMBER] position v time graph
(Wed Jul 15 2009 - 11:21:35 PDT)
Shubhra Gupta
Re: [AMBER] Alpha-L-Methys Fucose structure problem bond 0fA.d.C1 OME.d.O "S"
(Wed Jul 15 2009 - 05:38:34 PDT)
Re: [AMBER] Peptide bond broken
(Sun Jul 12 2009 - 21:17:31 PDT)
Siddharth Rastogi
Re: [AMBER] AMBER windows version ?
(Thu Jul 09 2009 - 16:17:33 PDT)
[AMBER] AMBER windows version ?
(Thu Jul 09 2009 - 14:14:05 PDT)
Simon Becker
Re: [AMBER] unexplained blow-up at restart
(Fri Jul 10 2009 - 06:24:13 PDT)
steinbrt.rci.rutgers.edu
Re: [AMBER] QM/MM
(Tue Jul 28 2009 - 00:19:32 PDT)
Re: [AMBER] Disappearing common atoms in Amber 10 with TI
(Mon Jul 20 2009 - 05:05:24 PDT)
Re: [AMBER] Disappearing common atoms in Amber 10 with TI
(Fri Jul 17 2009 - 01:53:19 PDT)
Re: [AMBER] Disappearing common atoms in Amber 10 with TI
(Thu Jul 16 2009 - 07:09:39 PDT)
Re: [AMBER] Coordinate resetting (SHAKE) cannot be accomplished,
(Thu Jul 16 2009 - 02:01:15 PDT)
subarna thakur
[AMBER] ESP charges of Fe4S4
(Tue Jul 21 2009 - 22:19:48 PDT)
[AMBER] query regarding FE4S4
(Thu Jul 16 2009 - 00:14:27 PDT)
[AMBER] need charges of FE-S cluster
(Mon Jul 06 2009 - 03:44:05 PDT)
suhaib sh
Re: [AMBER] Re: MM-PBSA delphi.crg and delphi.siz
(Fri Jul 10 2009 - 07:17:52 PDT)
[AMBER] missing Halogen parameters (radii) for PBSA/GBSA calculations - PB Bomb in pb_aaradi(): No radius assigned for atom
(Thu Jul 02 2009 - 06:18:05 PDT)
Sushil Mishra
[AMBER] file truncated : Output file truncated during equilibration of salivated complex in MM-PBSA
(Mon Jul 20 2009 - 05:26:27 PDT)
[AMBER] Output file truncated during equilibration of salivated complex in MM-PBSA
(Mon Jul 20 2009 - 03:40:51 PDT)
[AMBER] MM-PBSA tail: equil.out: file truncated during equilibration of salivated complex
(Mon Jul 20 2009 - 01:32:32 PDT)
Re: [AMBER] Alpha-L-Methys Fucose structure problem bond 0fA.d.C1 OME.d.O "S"
(Wed Jul 15 2009 - 06:58:13 PDT)
[AMBER] Alpha-L-Methys Fucose structure problem bond 0fA.d.C1 OME.d.O "S"
(Wed Jul 15 2009 - 03:36:26 PDT)
[AMBER] calculation of binding energy for lectin and fucuse..
(Fri Jul 10 2009 - 11:26:20 PDT)
Re: [AMBER] EPtot for Alpha-L- methyl fucose
(Fri Jul 10 2009 - 07:12:28 PDT)
[AMBER] EPtot for Alpha-L- methyl fucose
(Fri Jul 10 2009 - 06:47:26 PDT)
Syed Tarique Moin
Re: [AMBER] Peptide bond broken
(Mon Jul 13 2009 - 06:20:02 PDT)
[AMBER] Peptide bond broken
(Fri Jul 10 2009 - 11:19:02 PDT)
Taufik Al-Sarraj
[AMBER] H-bond vs. VdW
(Fri Jul 03 2009 - 11:48:12 PDT)
Thomas Cheatham
Re: [AMBER] Regarding Hbond interactions
(Thu Jul 23 2009 - 15:57:57 PDT)
RE: [AMBER] rmsd_ptraj
(Thu Jul 09 2009 - 00:08:53 PDT)
Thomas Cheatham III
Re: [AMBER] The Right Neutralization Procedure and Ionic Strength Calculation ?
(Fri Jul 17 2009 - 09:50:15 PDT)
Thomas Lake
Re: [AMBER] problem with energy calculations
(Sun Jul 12 2009 - 07:10:58 PDT)
[AMBER] problem with energy calculations
(Fri Jul 10 2009 - 09:13:55 PDT)
Thomas Patko
Re: [AMBER] how to launch XLEaP from SSH Secure Shell?
(Wed Jul 22 2009 - 17:47:51 PDT)
Tom Joseph
Re: [AMBER] problem from xleap
(Fri Jul 31 2009 - 09:41:49 PDT)
Re: [AMBER] how to launch XLEaP from SSH Secure Shell?
(Wed Jul 22 2009 - 16:24:56 PDT)
Re: [AMBER] Equilibration step
(Wed Jul 22 2009 - 12:05:58 PDT)
Re: [AMBER] Equilibration step
(Wed Jul 22 2009 - 05:35:15 PDT)
Re: [AMBER] Trouble saving amberparm files
(Mon Jul 13 2009 - 14:14:39 PDT)
Re: [AMBER] Trouble saving amberparm files
(Mon Jul 13 2009 - 14:13:14 PDT)
Re: [AMBER] Trouble saving amberparm files
(Mon Jul 13 2009 - 13:16:27 PDT)
Re: [AMBER] How to fix specific atoms? (not residue)
(Sat Jul 11 2009 - 15:01:04 PDT)
Toshifumi Yui
Re: [AMBER] amber10 parallel compiling error
(Mon Jul 20 2009 - 22:46:11 PDT)
vallespardojl.chem.leidenuniv.nl
Re: [AMBER] loading a mol2 file in xleap
(Mon Jul 27 2009 - 05:40:13 PDT)
[AMBER] loading a mol2 file in xleap
(Fri Jul 24 2009 - 10:40:13 PDT)
vhakkim boy
[AMBER] MPI error
(Wed Jul 29 2009 - 02:44:35 PDT)
[AMBER] carbonic anhydrase (CA) simulation
(Thu Jul 16 2009 - 00:03:23 PDT)
Vishal Maingi
Fw: [AMBER] Re: pls help and suggest
(Thu Jul 09 2009 - 11:45:21 PDT)
[AMBER] unable to read MM charges (no reply yet)
(Mon Jul 06 2009 - 20:32:07 PDT)
[AMBER] unable to read MM charges
(Mon Jul 06 2009 - 02:32:29 PDT)
vitor.felix
Re: [AMBER] Compiling Amber 10 (serial) on Mac OS X 10.5.7 w/ gcc, Intel Fortan 11.0 and MKL 10.0
(Tue Jul 21 2009 - 20:15:06 PDT)
Vlad Cojocaru
Re: [AMBER] How to visualize PCA results without IED?
(Tue Jul 28 2009 - 03:42:05 PDT)
Re: [AMBER] How to visualize PCA results without IED?
(Tue Jul 28 2009 - 02:58:50 PDT)
Re: [AMBER] ouput trajectory of only CA atom
(Wed Jul 08 2009 - 08:07:30 PDT)
Wei Huang
RE: [AMBER] ptraj - cluster
(Fri Jul 17 2009 - 05:34:00 PDT)
workalemahu berhanu
[AMBER] implicit solvent (GB version2) MD simulation
(Fri Jul 10 2009 - 08:53:47 PDT)
xiaoqin huang
RE: [AMBER] question of ibelly used in pmemd
(Mon Jul 20 2009 - 10:39:16 PDT)
RE: [AMBER] question of ibelly used in pmemd
(Mon Jul 20 2009 - 10:20:36 PDT)
RE: [AMBER] question of ibelly used in pmemd
(Mon Jul 20 2009 - 09:28:42 PDT)
RE: [AMBER] question of ibelly used in pmemd
(Mon Jul 20 2009 - 08:20:32 PDT)
RE: [AMBER] question of ibelly used in pmemd
(Mon Jul 20 2009 - 07:21:20 PDT)
RE: [AMBER] question of ibelly used in pmemd
(Fri Jul 17 2009 - 07:54:55 PDT)
RE: [AMBER] question of ibelly used in pmemd
(Fri Jul 17 2009 - 07:36:06 PDT)
RE: [AMBER] question of ibelly used in pmemd
(Wed Jul 15 2009 - 14:28:52 PDT)
[AMBER] question of ibelly used in pmemd
(Wed Jul 15 2009 - 10:34:20 PDT)
xueqin pang
[AMBER] how to choose exclusion policy for GPCR
(Tue Jul 28 2009 - 19:12:33 PDT)
Yana Berezovskaya
[AMBER] how to launch XLEaP from SSH Secure Shell?
(Wed Jul 22 2009 - 15:44:45 PDT)
Ye MEI
[AMBER] equivalent atoms
(Mon Jul 20 2009 - 21:56:52 PDT)
Yogesh Aher
[AMBER] File conversion for from Amber to Charmm
(Thu Jul 16 2009 - 23:45:11 PDT)
Re: [AMBER] Could not find bond parameter for O2 - ca
(Thu Jul 16 2009 - 23:37:52 PDT)
[AMBER] Could not find bond parameter for O2 - ca
(Tue Jul 14 2009 - 05:53:35 PDT)
Youn Kyeung Lee
[AMBER] ptraj grid option
(Tue Jul 21 2009 - 00:15:11 PDT)
Yvonne.Westermaier.unige.ch
Re: [AMBER] thymidine monophosphate parametrization
(Tue Jul 28 2009 - 05:10:43 PDT)
[AMBER] thymidine monophosphate parametrization
(Fri Jul 24 2009 - 08:18:18 PDT)
Zhongjie Liang
答复: [AMBER] Coordinate resetting (SHAKE) cannot be accomplished,
(Thu Jul 16 2009 - 02:16:02 PDT)
[AMBER] Coordinate resetting (SHAKE) cannot be accomplished,
(Thu Jul 16 2009 - 01:37:29 PDT)
廖青华
回复： [AMBER] errors of PMEMD installation
(Thu Jul 23 2009 - 18:27:51 PDT)
[AMBER] errors of PMEMD installation
(Wed Jul 22 2009 - 07:28:45 PDT)
回复： [AMBER] amber10 parallel compiling error
(Thu Jul 16 2009 - 18:27:05 PDT)
回复： [AMBER] question of mm_pbsa
(Sat Jul 11 2009 - 17:03:33 PDT)
回复： [AMBER] question of mm_pbsa
(Fri Jul 10 2009 - 18:22:25 PDT)
回复： [AMBER] question of mm_pbsa
(Fri Jul 10 2009 - 17:50:55 PDT)
[AMBER] question of mm_pbsa
(Thu Jul 09 2009 - 18:49:40 PDT)
回复： [AMBER] missing Halogen parameters (radii) for PBSA/GBSA calculations - PB Bomb in pb_aaradi(): No radius assigned for atom
(Thu Jul 02 2009 - 21:53:09 PDT)
回复： 回复： [AMBER] antechamber
(Thu Jul 02 2009 - 17:53:06 PDT)
回复： [AMBER] antechamber
(Thu Jul 02 2009 - 17:45:41 PDT)
Last message date
:
Wed Aug 19 2009 - 19:59:29 PDT
Archived on
: Mon Dec 23 2024 - 05:53:49 PST
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