AMBER Archive (2006) - Aug 2006 By Author

Starting: Tue Aug 01 2006 - 00:33:38 CDT
Ending: Thu Aug 31 2006 - 23:38:02 CDT

• a a
  • AMBER: Tutorial 2 - Section 4: Summary.density and summary.temp (Tue Aug 29 2006 - 05:15:07 CDT)
  • AMBER: Can I run RED/RESP for Platinum Complexes? (Thu Aug 24 2006 - 04:50:42 CDT)
  • AMBER: (no subject) (Tue Aug 15 2006 - 05:13:49 CDT)
  • RE: AMBER: RE: AMBER Tutorial 2 section 6, rmsd calculation: rmsd for residues number? (Tue Aug 15 2006 - 00:48:49 CDT)
  • AMBER: AMBER Tutorial 2 section 6, rmsd calculation: rmsd for residues number? (Mon Aug 14 2006 - 06:25:31 CDT)
  • Re: AMBER: PO2 in a DNA fragement, not a type in xleap? What canI do next? (Sun Aug 13 2006 - 23:29:59 CDT)
  • Re: AMBER: Phosphated Tyrosine, not a type (xleap)? (Thu Aug 10 2006 - 21:38:47 CDT)
  • Re: AMBER: PO2 in a DNA fragement, not a type in xleap? What can I do next? (Thu Aug 10 2006 - 21:39:54 CDT)
  • AMBER: PO2 in a DNA fragement, not a type in xleap? What can I do next? (Thu Aug 10 2006 - 04:26:01 CDT)
  • AMBER: Phosphated Tyrosine, not a type (xleap)? (Thu Aug 10 2006 - 04:22:27 CDT)
• Abhilash
  • AMBER: how to do a molecular dynamic study on a trimer (Fri Aug 11 2006 - 10:05:44 CDT)
• Adrian Roitberg
  • Re: AMBER: Temperature fluctuation with Langevin Temperature control (Sun Aug 27 2006 - 16:07:07 CDT)
  • Re: AMBER: Where can I find the SMD parameter file (or simple turtorial) in AMBER9 (Fri Aug 11 2006 - 15:23:10 CDT)
  • Re: AMBER: Re: Confusion re AMBER SMD output (Tue Aug 01 2006 - 06:07:03 CDT)
• Akshay Patny
  • RE: AMBER: GAFF parameters: DPPC Bilayer (Wed Aug 09 2006 - 16:08:00 CDT)
  • AMBER: GAFF parameters: DPPC Bilayer (Tue Aug 08 2006 - 14:53:49 CDT)
• Amarda Shehu
  • Re: ***SPAM*** Re: AMBER: problem imposing arbitrary peptide bonds through leap (Mon Aug 14 2006 - 11:56:31 CDT)
  • AMBER: problem imposing arbitrary peptide bonds through leap (Mon Aug 14 2006 - 11:27:24 CDT)
• Amber admin
  • Re: AMBER: increase force constants (Thu Aug 24 2006 - 19:15:24 CDT)
  • RE: AMBER: compiling parallel amber 9 in linux (Thu Aug 24 2006 - 19:10:57 CDT)
  • AMBER: compiling parallel amber 9 in linux (Wed Aug 23 2006 - 14:00:08 CDT)
• Andrea Bortolato
  • AMBER: TI vlimit exceeded (Thu Aug 24 2006 - 08:42:21 CDT)
• Andreas Svrcek-Seiler
  • Re: AMBER: building AMBER9 with gfortran/cygwin (Fri Aug 25 2006 - 05:39:08 CDT)
  • Re: AMBER: Maximum system size in simulated annealing (Thu Aug 03 2006 - 04:23:13 CDT)
• anna.schrey_at_gmx.de
  • AMBER: problems with ptraj (Thu Aug 03 2006 - 09:49:39 CDT)
• Arvind Marathe
  • AMBER: regarding diffusion command output (Tue Aug 01 2006 - 05:45:21 CDT)
• Atro Tossavainen
  • Re: AMBER: nmode memory problem (Fri Aug 25 2006 - 05:10:50 CDT)
• Austin B. Yongye
  • AMBER: REMD: Hybrid topology file (Wed Aug 30 2006 - 09:30:34 CDT)
• AYTUG TUNCEL
  • AMBER: nmode: number of atoms limitation (Mon Aug 28 2006 - 18:15:04 CDT)
  • AMBER: mm_pbsa calculation allocation error (Mon Aug 21 2006 - 08:15:31 CDT)
  • AMBER: input conversion error mm_pbsa (Tue Aug 15 2006 - 17:23:28 CDT)
  • AMBER: brookhaven to amber pdb format (Wed Aug 02 2006 - 04:08:50 CDT)
  • AMBER: pdb error (Tue Aug 01 2006 - 14:36:39 CDT)
• backy
  • Re: AMBER: DIELC? (Sat Aug 19 2006 - 03:04:14 CDT)
  • AMBER: DIELC? (Sat Aug 12 2006 - 07:16:47 CDT)
  • AMBER: Could mm_pbsa decompose energy only for the receptor ? (Fri Aug 11 2006 - 09:10:52 CDT)
  • Re: AMBER: Energy differecnes as using igb=1 and igb=0 (Thu Aug 10 2006 - 01:47:37 CDT)
  • AMBER: Energy differecnes as using igb=1 and igb=0 (Wed Aug 09 2006 - 09:46:56 CDT)
• bala
  • AMBER: parallel pmemd with intel 9 fc (Sat Aug 12 2006 - 10:56:15 CDT)
• Bill Ross
  • Re: AMBER: 1-4 interaction in AMBER8 (Wed Aug 30 2006 - 16:17:10 CDT)
  • Re: AMBER: 1-4 interaction in AMBER8 (Wed Aug 30 2006 - 16:05:27 CDT)
  • Re: AMBER: how to limit the simulation space (Mon Aug 28 2006 - 20:04:39 CDT)
  • Re: AMBER: Periodic boundary condition (PBC) (Mon Aug 28 2006 - 18:21:57 CDT)
  • Re: AMBER: How to create a modified NA in leap (Sat Aug 26 2006 - 19:21:41 CDT)
  • Re: AMBER: How to create a modified NA in leap (Fri Aug 25 2006 - 16:52:40 CDT)
  • Re: AMBER: Carnal: Internal error: stream file name 2 out of range (Wed Aug 23 2006 - 16:16:16 CDT)
  • Re: AMBER: holding a pair of residues fixed during minimization (Wed Aug 23 2006 - 15:45:13 CDT)
  • Re: AMBER: amber naming conventions for structure files (Tue Aug 22 2006 - 17:00:10 CDT)
  • Re: AMBER: Execution time discrepancies (Thu Aug 17 2006 - 20:24:13 CDT)
  • Re: AMBER: help with leap (Wed Aug 16 2006 - 19:51:56 CDT)
• Biswa Ranjan Meher
  • AMBER: TI-FEP for ILE--->VAL. (Thu Aug 03 2006 - 00:26:22 CDT)
• Björn C-G. Karlsson
  • AMBER: Calculate interaction energy between small organic molecules (Thu Aug 24 2006 - 01:17:56 CDT)
  • AMBER: Calculate interaction energy between small organic molecules (Mon Aug 21 2006 - 01:37:24 CDT)
• Brent Krueger
  • Re: AMBER: DOTA-Lanthanide complexes in Amber (Wed Aug 16 2006 - 15:08:57 CDT)
• Carlos Simmerling
  • Re: AMBER: reference of ff99 (Thu Aug 31 2006 - 11:18:09 CDT)
  • Re: AMBER: 1-4 interaction in AMBER8 (Wed Aug 30 2006 - 16:23:26 CDT)
  • Re: AMBER: 1-4 interaction in AMBER8 (Wed Aug 30 2006 - 16:15:23 CDT)
  • Re: AMBER: 1-4 interaction in AMBER8 (Wed Aug 30 2006 - 14:22:13 CDT)
  • Re: AMBER: REMD: Hybrid topology file (Wed Aug 30 2006 - 09:48:20 CDT)
  • Re: AMBER: Periodic boundary condition (PBC) (Mon Aug 28 2006 - 15:40:05 CDT)
  • Re: AMBER: TI, mutation (Mon Aug 28 2006 - 07:18:56 CDT)
  • Re: AMBER: missing values in md.out (Fri Aug 25 2006 - 07:53:26 CDT)
  • Re: AMBER: missing values in md.out (Thu Aug 24 2006 - 11:24:28 CDT)
  • Re: AMBER: problem relating all atom structure prediction and folding simulations on AMBER8 (Wed Aug 23 2006 - 07:18:03 CDT)
  • Re: AMBER: problem relating all atom structure prediction and folding simulations on AMBER8 (Mon Aug 21 2006 - 09:19:10 CDT)
  • AMBER: Re: Simulated annealing (Thu Aug 10 2006 - 06:40:24 CDT)
  • Re: AMBER: Energy differecnes as using igb=1 and igb=0 (Thu Aug 10 2006 - 05:09:23 CDT)
  • Re: AMBER: Energy differecnes as using igb=1 and igb=0 (Wed Aug 09 2006 - 10:01:27 CDT)
  • Re: AMBER: Format of mdcrd files (Wed Aug 09 2006 - 09:24:35 CDT)
  • Re: AMBER: cutting the box after "solvatebox" (Tue Aug 08 2006 - 07:43:47 CDT)
  • Re: AMBER: Problem with restarting MD simulation (Tue Aug 08 2006 - 06:08:27 CDT)
  • Re: AMBER: SURFTEN in GB (mm_pbsa calculations) (Thu Aug 03 2006 - 14:38:59 CDT)
  • Re: AMBER: Need to know meaning of numbers in parm99.dat file to be able to write frcmod file for dummy atoms (Thu Aug 03 2006 - 10:33:34 CDT)
  • AMBER: ff03 and ff99SB force fields (Thu Aug 03 2006 - 05:59:11 CDT)
  • Re: AMBER: Maximum system size in simulated annealing (Thu Aug 03 2006 - 05:26:58 CDT)
  • Re: AMBER: Ignoring every other frame in a .crd trajectory in Ptraj (Tue Aug 01 2006 - 13:13:07 CDT)
  • Re: AMBER: How to set Bondi Radii using xleap (Tue Aug 01 2006 - 12:43:04 CDT)
• Cenk Andac
  • Re: AMBER: nmode: number of atoms limitation (Wed Aug 30 2006 - 08:01:58 CDT)
• Changge Ji
  • Re: Re: AMBER: nmode: number of atoms limitation (Tue Aug 29 2006 - 01:33:27 CDT)
• Cheng Luo, Ph.D.
  • AMBER: Where can I find the SMD parameter file (or simple turtorial) in AMBER9 (Fri Aug 11 2006 - 15:41:32 CDT)
• Chris Moth
  • AMBER: Missing LES reference in Amber 9 manual (Tue Aug 29 2006 - 13:43:12 CDT)
• Christophe Guilbert
  • AMBER: antechamber charge calculation very sensitive to conformations ? (Wed Aug 23 2006 - 20:59:08 CDT)
• Chunhu Tan
  • AMBER: ´ð¸´: AMBER: pmf input files (Thu Aug 17 2006 - 11:36:30 CDT)
• Claire Zerafa
  • Fw: AMBER: HBOND ANALYSIS (Sat Aug 05 2006 - 14:45:10 CDT)
  • AMBER: HBOND ANALYSIS (Fri Aug 04 2006 - 09:35:50 CDT)
• Come On
  • AMBER: to do tutorial 4 using tleap (Fri Aug 04 2006 - 11:50:53 CDT)
• cristian obiol
  • AMBER: counterions and particle-mesh-ewald (Tue Aug 29 2006 - 03:06:20 CDT)
• darden
  • Re: AMBER: counterions and particle-mesh-ewald (Wed Aug 30 2006 - 17:59:32 CDT)
• David A. Case
  • Re: AMBER: reference of ff99 (Thu Aug 31 2006 - 11:43:50 CDT)
  • Re: AMBER: counterions and particle-mesh-ewald (Wed Aug 30 2006 - 15:14:40 CDT)
  • Re: AMBER: Missing LES reference in Amber 9 manual (Wed Aug 30 2006 - 11:03:34 CDT)
  • Re: AMBER: (Tue Aug 29 2006 - 10:09:23 CDT)
  • Re: AMBER: nmode: number of atoms limitation (Tue Aug 29 2006 - 00:55:53 CDT)
  • Re: AMBER: Periodic boundary condition (PBC) (Mon Aug 28 2006 - 19:17:42 CDT)
  • Re: AMBER: preparing ligand/rna structure for MD (Mon Aug 28 2006 - 19:11:34 CDT)
  • Re: AMBER: Temperature fluctuation with Langevin Temperature control (Mon Aug 28 2006 - 12:32:08 CDT)
  • Re: AMBER: Error in compliling AMBER 9 on Fedora 5 linux machine (Sun Aug 27 2006 - 11:03:54 CDT)
  • Re: AMBER: TI vlimit exceeded (Sat Aug 26 2006 - 12:38:58 CDT)
  • Re: AMBER: building AMBER9 with gfortran/cygwin (Fri Aug 25 2006 - 11:39:40 CDT)
  • Re: AMBER: building AMBER9 with gfortran/cygwin (Fri Aug 25 2006 - 10:41:49 CDT)
  • Re: AMBER: Installation amber 9 on IBM SP4 (Fri Aug 25 2006 - 10:03:10 CDT)
  • Re: AMBER: increase force constants (Thu Aug 24 2006 - 17:56:33 CDT)
  • Re: AMBER: how to use AddPdbAtomMap (Thu Aug 24 2006 - 17:47:50 CDT)
  • Re: AMBER: Backbone & Sidechain atoms: Definition (Thu Aug 24 2006 - 10:15:44 CDT)
  • Re: AMBER: 0 steps the same as 1 step? (Wed Aug 23 2006 - 20:14:53 CDT)
  • Re: AMBER: holding a pair of residues fixed during minimization (Wed Aug 23 2006 - 15:05:25 CDT)
  • Re: AMBER: compiling parallel amber 9 in linux (Wed Aug 23 2006 - 15:01:35 CDT)
  • Re: AMBER: Calculate interaction energy between small organic molecules (Tue Aug 22 2006 - 01:14:15 CDT)
  • Re: AMBER: GBSA EGB = NaN (Mon Aug 21 2006 - 13:21:10 CDT)
  • Re: AMBER: GBSA EGB = NaN (Mon Aug 21 2006 - 12:10:24 CDT)
  • Re: AMBER: The PB GB energy from mm_pbsa will be positive on high charged system (Fri Aug 18 2006 - 13:35:04 CDT)
  • Re: AMBER: The PB GB energy from mm_pbsa will be positive on high charged system (Fri Aug 18 2006 - 12:50:32 CDT)
  • Re: AMBER: generate "template" frcmod from standard residues? (Thu Aug 17 2006 - 13:01:45 CDT)
  • Re: AMBER: generate "template" frcmod from standard residues? (Thu Aug 17 2006 - 11:04:22 CDT)
  • Re: AMBER: reading ff file into XLeap (Wed Aug 16 2006 - 12:21:47 CDT)
  • Re: AMBER: DOTA-Lanthanide complexes in Amber (Wed Aug 16 2006 - 11:59:22 CDT)
  • Re: AMBER: MM_PBSA : Question about Stability? (Wed Aug 16 2006 - 11:24:48 CDT)
  • Re: AMBER: MMPBSA: positive energies during nmode (Wed Aug 16 2006 - 11:10:29 CDT)
  • Re: AMBER: TI tutorial (Tue Aug 15 2006 - 18:34:58 CDT)
  • Re: AMBER: antechamber failure on FMN (Tue Aug 15 2006 - 18:14:41 CDT)
  • Re: AMBER: (Another) Question about using antechamber with G03 (Tue Aug 15 2006 - 18:09:56 CDT)
  • Re: AMBER: input conversion error mm_pbsa (Tue Aug 15 2006 - 17:47:19 CDT)
  • Re: AMBER: Question about using antechamber with G03 (Tue Aug 15 2006 - 16:15:26 CDT)
  • Re: AMBER: amber9 Test Failer (Tue Aug 15 2006 - 10:05:54 CDT)
  • Re: AMBER: Problem with sander in Linux (Mon Aug 14 2006 - 11:49:53 CDT)
  • Re: AMBER: klambda (Mon Aug 14 2006 - 11:48:30 CDT)
  • Re: AMBER: problem imposing arbitrary peptide bonds through leap (Mon Aug 14 2006 - 11:45:48 CDT)
  • Re: AMBER: how to do a molecular dynamic study on a trimer (Sun Aug 13 2006 - 11:37:03 CDT)
  • Re: AMBER: Problem: Flag "SOLVENT_POINTERS" not found in PARM file (Sun Aug 13 2006 - 11:49:27 CDT)
  • Re: AMBER: DIELC? (Sun Aug 13 2006 - 11:43:58 CDT)
  • Re: AMBER: Middlebury College Cluster and Amber 8 (Fri Aug 11 2006 - 13:30:46 CDT)
  • Re: AMBER: how to do a molecular dynamic study on a trimer (Fri Aug 11 2006 - 11:05:12 CDT)
  • Re: AMBER: Leap adds hydrogens but cannot resolve their type. (Thu Aug 10 2006 - 15:15:16 CDT)
  • Re: AMBER: Phosphated Tyrosine, not a type (xleap)? (Thu Aug 10 2006 - 11:07:09 CDT)
  • Re: AMBER: build box info for acetonitrile in the simulation with periodic boundary condition (Wed Aug 09 2006 - 15:45:42 CDT)
  • Re: AMBER: how to reassign charges (Wed Aug 09 2006 - 15:43:07 CDT)
  • Re: AMBER: Amber Installation Help (Tue Aug 08 2006 - 10:25:49 CDT)
  • Re: AMBER: Info regarding reduced cysteines (Mon Aug 07 2006 - 10:02:57 CDT)
  • Re: AMBER: question on chargning free energy in solvent vs vacuum (Fri Aug 04 2006 - 11:18:53 CDT)
  • Re: AMBER: problems with ptraj (Thu Aug 03 2006 - 11:46:19 CDT)
  • Re: AMBER: TI-FEP for ILE--->VAL. (Thu Aug 03 2006 - 11:43:44 CDT)
  • Re: AMBER: about Silica's polarizability (Thu Aug 03 2006 - 11:16:40 CDT)
  • Re: AMBER: brookhaven to amber pdb format (Wed Aug 02 2006 - 09:48:23 CDT)
  • Re: AMBER: any work-around for 80 character mask string limit? (Tue Aug 01 2006 - 16:37:36 CDT)
  • Re: AMBER: GB tutorials and disulphide bonds (Tue Aug 01 2006 - 12:14:20 CDT)
  • Re: AMBER: Using a trajectory and some PDB files as input for PCA (Tue Aug 01 2006 - 12:10:29 CDT)
  • Re: AMBER: How to set Bondi Radii using xleap (Tue Aug 01 2006 - 12:17:38 CDT)
• David LeBard
  • Re: AMBER: Calculate interaction energy between small organic molecules (Thu Aug 24 2006 - 16:01:16 CDT)
• David Mobley
  • Re: AMBER: antechamber charge calculation very sensitive to conformations ? (Fri Aug 25 2006 - 10:08:44 CDT)
  • Re: AMBER: Calculate interaction energy between small organic molecules (Thu Aug 24 2006 - 15:07:57 CDT)
  • Re: AMBER: Calculate interaction energy between small organic molecules (Mon Aug 21 2006 - 09:20:42 CDT)
  • AMBER: Re: antechamber failure on FMN (Fri Aug 18 2006 - 13:46:58 CDT)
  • Re: AMBER: generate "template" frcmod from standard residues? (Fri Aug 18 2006 - 11:13:08 CDT)
  • Re: AMBER: generate "template" frcmod from standard residues? (Wed Aug 16 2006 - 16:51:47 CDT)
  • Re: AMBER: antechamber failure on FMN (Tue Aug 15 2006 - 13:16:47 CDT)
  • AMBER: antechamber failure on FMN (Tue Aug 15 2006 - 13:04:42 CDT)
  • Re: AMBER: how to reassign charges (Wed Aug 09 2006 - 15:03:10 CDT)
  • AMBER: antechamber bond typing questions (Mon Aug 07 2006 - 15:14:42 CDT)
• Don.Bashford_at_stjude.org
  • Re: AMBER: How to set Bondi Radii using xleap. . (Tue Aug 01 2006 - 12:23:51 CDT)
• Eric Hu
  • AMBER: how to limit the simulation space (Mon Aug 28 2006 - 19:55:11 CDT)
  • Re: AMBER: transition state (Mon Aug 21 2006 - 19:06:22 CDT)
  • Re: AMBER: build box info for acetonitrile in the simulation with periodic boundary condition (Wed Aug 09 2006 - 16:30:04 CDT)
  • Re: AMBER: transition state (Wed Aug 09 2006 - 14:05:14 CDT)
  • AMBER: build box info for acetonitrile in the simulation with periodic boundary condition (Wed Aug 09 2006 - 13:06:30 CDT)
• eric.henon_at_univ-reims.fr
  • Re: AMBER: TI, mutation (Tue Aug 29 2006 - 03:43:04 CDT)
  • AMBER: TI, mutation (Mon Aug 28 2006 - 07:39:48 CDT)
• Evan Kelly
  • AMBER: Please DISREGARD previous message (restraint=0.0000) (Thu Aug 03 2006 - 12:57:46 CDT)
  • AMBER: restraint=0.0000 during minimization? (Thu Aug 03 2006 - 12:48:17 CDT)
• Fabian Boes
  • Re: AMBER: amber 9 intel 9.1 ia64 (Tue Aug 15 2006 - 08:59:39 CDT)
• Fabián Alejandro Rodríguez
  • Re: AMBER: from traj to crd (Tue Aug 01 2006 - 10:41:22 CDT)
  • Re: AMBER: Xmgr in Windows (Tue Aug 01 2006 - 06:39:19 CDT)
• Feng X Zhou
  • AMBER: Advice on linux cluster sought (Mon Aug 14 2006 - 13:34:16 CDT)
• Florian Haberl
  • Re: AMBER: Xmgr in Windows (Tue Aug 01 2006 - 07:11:44 CDT)
• Franck_Vendeix_at_ncsu.edu
  • Re: AMBER: help with leap (Thu Aug 17 2006 - 09:46:07 CDT)
• FyD
  • Re: AMBER: Details about Gaussian basis set for Cobalt complex (Mon Aug 21 2006 - 07:28:49 CDT)
  • Re: AMBER: PO2 in a DNA fragement, not a type in xleap? What can I do next? (Sat Aug 12 2006 - 14:09:29 CDT)
  • Re: AMBER: neutral N-terminal amino-acid parameters for ff03 (Sat Aug 05 2006 - 03:16:23 CDT)
• Glass, Kevin A
  • AMBER: Execution time discrepancies (Thu Aug 17 2006 - 19:18:20 CDT)
  • AMBER: (Mon Aug 07 2006 - 15:09:02 CDT)
• Gloria T. Anderle
  • AMBER: Residue connection points on prep.in (Fri Aug 04 2006 - 11:10:53 CDT)
• Gobind Bisht
  • AMBER: Error in compliling AMBER 9 on Fedora 5 linux machine (Sun Aug 27 2006 - 00:24:12 CDT)
  • Re: AMBER: how to do a molecular dynamic study on a trimer (Sat Aug 12 2006 - 12:05:29 CDT)
  • AMBER: Format of mdcrd files (Wed Aug 09 2006 - 08:56:18 CDT)
  • AMBER: Problem with restarting MD simulation (Tue Aug 08 2006 - 00:02:56 CDT)
• Gobind Singh Bisht
  • AMBER: Temperature fluctuation with Langevin Temperature control (Sun Aug 27 2006 - 14:06:49 CDT)
• Guanglei Cui
  • Re: AMBER: zero entry in LENNARD_JONES_ACOEF of prmtop files (Fri Aug 11 2006 - 08:57:46 CDT)
  • Re: AMBER: cutting the box after "solvatebox" (Tue Aug 08 2006 - 09:38:06 CDT)
  • Re: AMBER: Distance between two regions (Tue Aug 01 2006 - 10:35:54 CDT)
  • Re: AMBER: from traj to crd (Tue Aug 01 2006 - 10:30:59 CDT)
• Guillaume Bollot
  • AMBER: MM_PBSA : Question about Stability? (Wed Aug 16 2006 - 02:00:15 CDT)
• Gustavo Seabra
  • Re: AMBER: Question about using antechamber with G03 (Wed Aug 16 2006 - 08:49:42 CDT)
  • AMBER: (Another) Question about using antechamber with G03 (Tue Aug 15 2006 - 12:51:16 CDT)
  • AMBER: Question about using antechamber with G03 (Tue Aug 15 2006 - 10:58:40 CDT)
• Ilyas Yildirim
  • Re: AMBER: minimization with my own charges (Thu Aug 31 2006 - 22:37:18 CDT)
  • Re: AMBER: minimization with my own charges (Thu Aug 31 2006 - 18:47:54 CDT)
  • Re: AMBER: minimization with my own charges (Thu Aug 31 2006 - 17:50:26 CDT)
  • Re: AMBER: minimization with my own charges (Thu Aug 31 2006 - 17:12:24 CDT)
  • Re: AMBER: how to use AddPdbAtomMap (Thu Aug 24 2006 - 15:27:41 CDT)
  • Re: AMBER: GBSA EGB = NaN (Mon Aug 21 2006 - 11:14:54 CDT)
  • Re: AMBER: cutting the box after "solvatebox" (Thu Aug 17 2006 - 14:28:55 CDT)
  • Re: AMBER: klambda (Mon Aug 14 2006 - 12:31:24 CDT)
  • Re: AMBER: TI-FEP for ILE--->VAL. (Thu Aug 03 2006 - 01:15:10 CDT)
  • Re: AMBER: brookhaven to amber pdb format (Wed Aug 02 2006 - 13:55:38 CDT)
  • Re: AMBER: pdb error (Tue Aug 01 2006 - 14:23:30 CDT)
  • AMBER: How to set Bondi Radii using xleap (Tue Aug 01 2006 - 00:40:15 CDT)
  • Re: AMBER: Xmgr in Windows (Tue Aug 01 2006 - 00:33:38 CDT)
• Isherwood, James
  • AMBER: Nature of QM scanning protocol for parameter development (Fri Aug 11 2006 - 11:17:01 CDT)
• Jardas sucuriba
  • RE: AMBER: RDF output (Wed Aug 30 2006 - 16:31:08 CDT)
  • AMBER: RDF output (Tue Aug 29 2006 - 09:48:29 CDT)
  • AMBER: waters closest to specific residues (Sat Aug 26 2006 - 10:39:35 CDT)
  • Re: AMBER: missing values in md.out (Fri Aug 25 2006 - 07:36:45 CDT)
  • AMBER: missing values in md.out (Thu Aug 24 2006 - 11:15:40 CDT)
  • AMBER: ptraj script (Fri Aug 18 2006 - 15:08:31 CDT)
• Jianhui
  • Re: AMBER: 1-4 interaction in AMBER8 (Wed Aug 30 2006 - 14:48:28 CDT)
  • AMBER: 1-4 interaction in AMBER8 (Wed Aug 30 2006 - 14:08:09 CDT)
  • AMBER: Problem: Flag "SOLVENT_POINTERS" not found in PARM file (Fri Aug 11 2006 - 13:50:54 CDT)
• Jianyin Shao
  • Re: AMBER: mm_pbsa_statistical.pl (Wed Aug 30 2006 - 12:52:56 CDT)
• Jing Huang
  • AMBER: zero entry in LENNARD_JONES_ACOEF of prmtop files (Fri Aug 11 2006 - 08:35:12 CDT)
• John Chuang²øÂ`»·¦Ñ®v
  • Re: AMBER: transition state (Mon Aug 14 2006 - 17:20:20 CDT)
  • AMBER: transition state (Mon Aug 07 2006 - 11:06:50 CDT)
• Joseph Nachman
  • AMBER: ptraj: nofit option for rmsd (Tue Aug 08 2006 - 10:27:41 CDT)
• JunJun Liu
  • AMBER: parameter for Cd2+? (Fri Aug 04 2006 - 10:50:46 CDT)
• Junmei Wang
  • RE: AMBER: antechamber charge calculation very sensitive to conformations ? (Thu Aug 24 2006 - 21:51:07 CDT)
  • AMBER: RE: antechamber failure on FMN (Thu Aug 17 2006 - 18:14:47 CDT)
  • RE: AMBER: antechamber error -> metals (Wed Aug 16 2006 - 21:29:46 CDT)
  • AMBER: RE: antechamber bond typing questions (Mon Aug 07 2006 - 20:43:05 CDT)
• Juraj Kotulic Bunta
  • AMBER: Maximum system size in simulated annealing (Wed Aug 02 2006 - 21:03:11 CDT)
• Jyh-Shyong Ho
  • Re: AMBER: Installation amber 9 on IBM SP4 (Fri Aug 25 2006 - 21:11:21 CDT)
  • AMBER: building AMBER9 with gfortran/cygwin (Thu Aug 24 2006 - 21:30:02 CDT)
• Kateryna Miroshnychenko
  • AMBER: RE: AMBER Tutorial 2 section 6, rmsd calculation: rmsd for residues number? (Mon Aug 14 2006 - 08:19:46 CDT)
• kawamura_hiro_at_riken.jp
  • AMBER: amber9 Test Failer (Tue Aug 15 2006 - 07:21:49 CDT)
• Kirk Hevener
  • AMBER: Amber Installation Help (Mon Aug 07 2006 - 07:43:25 CDT)
• Knut Langsestmo
  • Re: AMBER: nmode memory problem (Thu Aug 24 2006 - 11:17:04 CDT)
• Lauren O'Neil
  • AMBER: pmf input files (Wed Aug 16 2006 - 12:20:45 CDT)
• Lubans, Peter S
  • AMBER: Middlebury College Cluster and Amber 8 (Fri Aug 11 2006 - 11:55:19 CDT)
• Lwin, ThuZar
  • AMBER: how to reassign charges (Wed Aug 09 2006 - 13:16:01 CDT)
  • RE: AMBER: question on chargning free energy in solvent vs vacuum. . (Fri Aug 04 2006 - 14:02:10 CDT)
  • AMBER: how to take care of toluene system neutrality (Fri Aug 04 2006 - 13:31:53 CDT)
  • AMBER: how to take care of toluene system neutrality (Fri Aug 04 2006 - 13:27:39 CDT)
  • AMBER: question on chargning free energy in solvent vs vacuum (Thu Aug 03 2006 - 12:08:07 CDT)
  • AMBER: Need to know meaning of numbers in parm99.dat file to be able to write frcmod file for dummy atoms (Thu Aug 03 2006 - 10:14:28 CDT)
• Mahalakshmi Sahasranaman
  • AMBER: increase force constants (Thu Aug 24 2006 - 08:45:28 CDT)
• Marcelo Puiatti
  • AMBER: Heme parameters (Wed Aug 09 2006 - 17:58:35 CDT)
• Mark Williamson
  • Re: AMBER: Format of mdcrd files (Wed Aug 09 2006 - 09:32:06 CDT)
• Markus Kaukonen
  • AMBER: ptraj dumpq feature/bug (Thu Aug 24 2006 - 03:31:51 CDT)
• mernst_at_tricity.wsu.edu
  • Re: AMBER: generate "template" frcmod from standard residues? (Thu Aug 17 2006 - 12:06:07 CDT)
  • AMBER: generate "template" frcmod from standard residues? (Wed Aug 16 2006 - 13:41:02 CDT)
• Miguel Ferreira
  • AMBER: atomifluct (Fri Aug 25 2006 - 06:09:03 CDT)
• Mingfeng Yang
  • AMBER: TI tutorial (Tue Aug 15 2006 - 17:22:10 CDT)
  • Re: AMBER: Modify charges to increase/decrease hydrogen bond interaction (Mon Aug 14 2006 - 14:06:56 CDT)
  • AMBER: Modify charges to increase/decrease hydrogen bond interaction (Mon Aug 14 2006 - 13:25:19 CDT)
• Myunggi Yi
  • Re: AMBER: minimization with my own charges (Thu Aug 31 2006 - 20:16:49 CDT)
  • Re: AMBER: minimization with my own charges (Thu Aug 31 2006 - 18:13:29 CDT)
  • Re: AMBER: minimization with my own charges (Thu Aug 31 2006 - 17:22:08 CDT)
  • AMBER: minimization with my own charges (Thu Aug 31 2006 - 17:01:24 CDT)
  • Re: AMBER: reference of ff99 (Thu Aug 31 2006 - 11:26:09 CDT)
  • Re: AMBER: reference of ff99 (Thu Aug 31 2006 - 11:21:59 CDT)
  • AMBER: reference of ff99 (Thu Aug 31 2006 - 10:59:51 CDT)
  • Re: AMBER: Installation amber 9 on IBM SP4 (Fri Aug 25 2006 - 21:41:46 CDT)
  • Re: AMBER: Installation amber 9 on IBM SP4 (Fri Aug 25 2006 - 20:20:47 CDT)
  • Re: AMBER: Installation amber 9 on IBM SP4 (Thu Aug 24 2006 - 22:20:12 CDT)
  • Re: AMBER: Installation amber 9 on IBM SP4 (Thu Aug 24 2006 - 22:09:29 CDT)
  • Re: AMBER: Installation amber 9 on IBM SP4 (Thu Aug 24 2006 - 21:59:09 CDT)
  • Re: AMBER: Installation amber 9 on IBM SP4 (Thu Aug 24 2006 - 21:48:07 CDT)
  • Re: AMBER: Installation amber 9 on IBM SP4 (Thu Aug 24 2006 - 21:39:43 CDT)
  • Re: AMBER: Installation amber 9 on IBM SP4 (Thu Aug 24 2006 - 20:29:58 CDT)
  • Re: AMBER: Installation amber 9 on IBM SP4 (Thu Aug 24 2006 - 14:00:04 CDT)
  • AMBER: Installation amber 9 on IBM SP4 (Thu Aug 24 2006 - 11:05:50 CDT)
• Navnit Kumar Mishra
  • Re: AMBER: (no subject) (Tue Aug 15 2006 - 07:51:49 CDT)
• Nitin Bhardwaj
  • Re: AMBER: GAFF parameters: DPPC Bilayer (Tue Aug 08 2006 - 14:58:59 CDT)
• opitz_at_che.udel.edu
  • Re: AMBER: DOTA-Lanthanide complexes in Amber (Wed Aug 16 2006 - 12:27:23 CDT)
  • AMBER: DOTA-Lanthanide complexes in Amber (Tue Aug 15 2006 - 12:48:23 CDT)
• Paul R Brenner
  • Re: AMBER: Leap adds hydrogens but cannot resolve their type. (Tue Aug 15 2006 - 10:39:08 CDT)
  • AMBER: Leap adds hydrogens but cannot resolve their type. (Thu Aug 10 2006 - 14:23:55 CDT)
• Petr Jerabek
  • AMBER: reading ff file into XLeap (Wed Aug 16 2006 - 11:21:00 CDT)
• Petr Kulhanek
  • AMBER: AMBER8 - RDF bug (Fri Aug 11 2006 - 11:00:57 CDT)
• Piotr Cieplak
  • Re: AMBER: impose command in leap problem (Mon Aug 14 2006 - 15:44:02 CDT)
  • AMBER: impose command in leap problem (Fri Aug 11 2006 - 19:56:40 CDT)
• pkb bioinfo
  • Re: AMBER: mm_pbsa.pl fails to start in linux cluster (Wed Aug 02 2006 - 08:58:48 CDT)
  • AMBER: mm_pbsa.pl fails to start in linux cluster (Wed Aug 02 2006 - 07:07:22 CDT)
• Pradipta Bandyopadhyay
  • Re: AMBER: TI, mutation (Mon Aug 28 2006 - 07:46:43 CDT)
• Prashanth Athri
  • AMBER: amidine group/ gaff parameters (Fri Aug 18 2006 - 14:00:17 CDT)
• priya priya
  • RE: AMBER: problem relating all atom structure prediction and folding simulations on AMBER8 (Tue Aug 22 2006 - 23:16:42 CDT)
  • AMBER: problem relating all atom structure prediction and folding simulations on AMBER8 (Mon Aug 21 2006 - 02:46:29 CDT)
• Qingning Shu
  • Re: Re: AMBER: (Tue Aug 29 2006 - 11:26:34 CDT)
  • AMBER: (Tue Aug 29 2006 - 08:01:58 CDT)
• Rafi Ahmad
  • AMBER: Info regarding reduced cysteines (Mon Aug 07 2006 - 09:06:40 CDT)
• Rahaman, Asif
  • RE: AMBER: Periodic boundary condition (PBC) > Problem now with ptraj (Thu Aug 31 2006 - 17:29:25 CDT)
  • RE: AMBER: Periodic boundary condition (PBC) > Problem now with ptraj (Thu Aug 31 2006 - 16:34:50 CDT)
  • RE: AMBER: Periodic boundary condition (PBC) > Problem now with ptraj (Thu Aug 31 2006 - 15:24:43 CDT)
  • AMBER: Periodic boundary condition (PBC) (Mon Aug 28 2006 - 15:24:19 CDT)
• Ray Luo
  • Re: AMBER: mm_pbsa calculation allocation error (Mon Aug 21 2006 - 11:37:14 CDT)
  • Re: AMBER: ff03 and ff99SB force fields (Thu Aug 03 2006 - 07:21:03 CDT)
• Robert Duke
  • Re: AMBER: parallel pmemd with intel 9 fc (Sat Aug 12 2006 - 13:58:59 CDT)
  • Re: AMBER: Middlebury College Cluster and Amber 8 (Fri Aug 11 2006 - 12:33:13 CDT)
  • AMBER: Bugfixes available for pmemd iwrap problem (Wed Aug 02 2006 - 12:05:32 CDT)
• Ross Walker
  • RE: AMBER: Tutorial 2 - Section 4: Summary.density and summary.temp (Wed Aug 30 2006 - 21:04:36 CDT)
  • RE: AMBER: Installation amber 9 on IBM SP4 (Fri Aug 25 2006 - 11:16:13 CDT)
  • RE: AMBER: Installation amber 9 on IBM SP4 (Thu Aug 24 2006 - 17:08:03 CDT)
  • RE: AMBER: nmode memory problem (Thu Aug 24 2006 - 12:57:12 CDT)
  • RE: AMBER: Installation amber 9 on IBM SP4 (Thu Aug 24 2006 - 12:23:02 CDT)
  • RE: AMBER: compiling parallel amber 9 in linux (Wed Aug 23 2006 - 14:54:39 CDT)
  • RE: AMBER: problem relating all atom structure prediction and folding simulations on AMBER8 (Mon Aug 21 2006 - 10:48:00 CDT)
  • RE: AMBER: GBSA EGB = NaN (Fri Aug 18 2006 - 17:11:52 CDT)
  • RE: AMBER: Execution time discrepancies (Thu Aug 17 2006 - 22:00:29 CDT)
  • RE: AMBER: GBSA EGB = NaN (Thu Aug 17 2006 - 21:57:29 CDT)
  • RE: AMBER: identical high energies (Thu Aug 17 2006 - 21:52:38 CDT)
• S. Jamal Rahi
  • AMBER: 0 steps the same as 1 step? (Wed Aug 23 2006 - 16:25:44 CDT)
• S.Sundar Raman
  • Re: AMBER: Details about Gaussian basis set for Cobalt complex (Sat Aug 26 2006 - 05:51:04 CDT)
  • AMBER: Details about Gaussian basis set for Cobalt complex (Sun Aug 20 2006 - 09:07:57 CDT)
• sangeeta
  • AMBER: H-bonds of peptide with water (Fri Aug 04 2006 - 08:20:13 CDT)
• Scott Brozell
  • Re: AMBER: Installation amber 9 on IBM SP4 (Fri Aug 25 2006 - 01:45:09 CDT)
  • Re: AMBER: Installation amber 9 on IBM SP4 (Fri Aug 25 2006 - 01:28:35 CDT)
  • Re: AMBER: Installation amber 9 on IBM SP4 (Thu Aug 24 2006 - 21:58:20 CDT)
  • Re: AMBER: Installation amber 9 on IBM SP4; bugfix 12 (Thu Aug 24 2006 - 21:57:03 CDT)
  • Re: AMBER: Installation amber 9 on IBM SP4 (Thu Aug 24 2006 - 20:50:31 CDT)
  • Re: AMBER: antechamber error -> metals (Sun Aug 13 2006 - 16:58:14 CDT)
  • Re: AMBER: impose command in leap problem (Fri Aug 11 2006 - 20:57:21 CDT)
  • Re: AMBER: Amber Installation Help; link woes (Tue Aug 08 2006 - 14:36:32 CDT)
  • Re: AMBER: (Mon Aug 07 2006 - 19:37:19 CDT)
• Scott Pendley
  • Re: AMBER: Ptraj selecting specific atoms in specific residues (Wed Aug 16 2006 - 12:19:31 CDT)
  • Re: AMBER: H-bonds of peptide with water (Mon Aug 07 2006 - 14:56:04 CDT)
• Seth Lilavivat
  • AMBER: holding a pair of residues fixed during minimization (Tue Aug 22 2006 - 22:22:06 CDT)
• sethl_at_gatech.edu
  • AMBER: preparing ligand/rna structure for MD (Mon Aug 28 2006 - 13:45:17 CDT)
  • Re: AMBER: How to create a modified NA in leap (Sat Aug 26 2006 - 15:13:10 CDT)
  • AMBER: How to create a modified NA in leap (Fri Aug 25 2006 - 15:20:35 CDT)
  • AMBER: how to use AddPdbAtomMap (Thu Aug 24 2006 - 15:03:59 CDT)
  • AMBER: amber naming conventions for structure files (Tue Aug 22 2006 - 16:36:56 CDT)
  • AMBER: help with leap (Wed Aug 16 2006 - 18:24:42 CDT)
• Shawn yy
  • AMBER: ptraj quasiharmonic analysis question (Fri Aug 11 2006 - 09:45:21 CDT)
• Shuting Wei
  • AMBER: Carnal: Internal error: stream file name 2 out of range (Wed Aug 23 2006 - 15:43:31 CDT)
  • AMBER: SURFTEN in GB (mm_pbsa calculations) (Thu Aug 03 2006 - 14:18:10 CDT)
• Steve Seibold
  • AMBER: checkmask (Wed Aug 16 2006 - 13:14:29 CDT)
  • RE: AMBER: Ptraj selecting specific atoms in specific residues (Wed Aug 16 2006 - 12:50:16 CDT)
  • AMBER: Ptraj selecting specific atoms in specific residues (Wed Aug 16 2006 - 12:05:16 CDT)
• Suxin Zheng
  • Re: AMBER: The PB GB energy from mm_pbsa will be positive on high charged system (Fri Aug 18 2006 - 13:23:17 CDT)
  • AMBER: The PB GB energy from mm_pbsa will be positive on high charged system (Wed Aug 16 2006 - 13:23:44 CDT)
• Tanya Johannsen
  • AMBER: identical high energies (Thu Aug 17 2006 - 21:22:40 CDT)
  • AMBER: any work-around for 80 character mask string limit? (Tue Aug 01 2006 - 15:12:22 CDT)
• Thomas Cheatham
  • RE: AMBER: Periodic boundary condition (PBC) > Problem now with ptraj (Thu Aug 31 2006 - 23:38:02 CDT)
  • Re: AMBER: minimization with my own charges (Thu Aug 31 2006 - 23:07:40 CDT)
  • RE: AMBER: Periodic boundary condition (PBC) > Problem now with ptraj (Thu Aug 31 2006 - 16:50:33 CDT)
  • RE: AMBER: Periodic boundary condition (PBC) > Problem now with ptraj (Thu Aug 31 2006 - 15:49:42 CDT)
  • Re: AMBER: RDF output (Wed Aug 30 2006 - 17:18:29 CDT)
  • Re: AMBER: Details about Gaussian basis set for Cobalt complex (Fri Aug 25 2006 - 13:21:07 CDT)
  • Re: AMBER: ptraj dumpq feature/bug (Thu Aug 24 2006 - 15:16:23 CDT)
  • Re: AMBER: identical high energies (Thu Aug 17 2006 - 21:57:23 CDT)
  • Re: AMBER: Ptraj selecting specific atoms in specific residues (Wed Aug 16 2006 - 12:32:24 CDT)
  • Re: AMBER: Modify charges to increase/decrease hydrogen bond interaction (Mon Aug 14 2006 - 13:42:52 CDT)
  • Re: AMBER: source code (Mon Aug 14 2006 - 13:31:08 CDT)
  • Re: AMBER: HBOND ANALYSIS (Thu Aug 10 2006 - 18:57:34 CDT)
  • Re: AMBER: PO2 in a DNA fragement, not a type in xleap? What can I do next? (Thu Aug 10 2006 - 17:18:00 CDT)
  • Re: AMBER: problems with ptraj (Thu Aug 10 2006 - 14:25:18 CDT)
• Tim Robinson
  • AMBER: amber 9 intel 9.1 ia64 (Tue Aug 15 2006 - 08:45:16 CDT)
• Vitor Manuel Sousa F?x
  • AMBER: klambda (Mon Aug 14 2006 - 05:45:10 CDT)
• Vlad Cojocaru
  • Re: AMBER: PCA: can't complete projection (Tue Aug 08 2006 - 09:56:49 CDT)
  • Re: AMBER: cutting the box after "solvatebox" (Tue Aug 08 2006 - 07:52:39 CDT)
  • AMBER: cutting the box after "solvatebox" (Tue Aug 08 2006 - 07:12:37 CDT)
  • Re: AMBER: ff03 and ff99SB force fields (Fri Aug 04 2006 - 03:17:59 CDT)
  • Re: AMBER: PhosphoThreonine Parms for use with ff03 (Thu Aug 03 2006 - 05:07:48 CDT)
  • AMBER: neutral N-terminal amino-acid parameters for ff03 (Wed Aug 02 2006 - 09:21:31 CDT)
• Weihua Li
  • Re: AMBER: Heme parameters (Wed Aug 09 2006 - 21:44:15 CDT)
• William Lianhu Wei
  • AMBER: GBSA EGB = NaN (Thu Aug 17 2006 - 21:30:50 CDT)
• William Wei
  • AMBER: Question about free energy with mm_pbsa (Thu Aug 31 2006 - 13:50:11 CDT)
  • Re: AMBER: mm_pbsa_statistical.pl (Wed Aug 30 2006 - 16:11:51 CDT)
  • AMBER: mm_pbsa_statistical.pl (Tue Aug 29 2006 - 16:02:32 CDT)
  • Re: AMBER: nmode memory problem (Thu Aug 24 2006 - 16:05:55 CDT)
  • Re: AMBER: nmode memory problem (Thu Aug 24 2006 - 12:04:59 CDT)
  • AMBER: nmode memory problem (Thu Aug 24 2006 - 10:29:13 CDT)
  • Re: AMBER: GBSA EGB = NaN (Mon Aug 21 2006 - 13:00:21 CDT)
  • Re: AMBER: GBSA EGB = NaN (Mon Aug 21 2006 - 11:37:47 CDT)
  • Re: AMBER: GBSA EGB = NaN (Mon Aug 21 2006 - 11:04:36 CDT)
  • Re: AMBER: GBSA EGB = NaN (Mon Aug 21 2006 - 11:04:26 CDT)
  • Re: AMBER: GBSA EGB = NaN (Fri Aug 18 2006 - 10:12:10 CDT)
• Wimal
  • AMBER: Problem with sander in Linux (Mon Aug 14 2006 - 03:14:00 CDT)
• Xiaojian Deng
  • Re: AMBER: Ignoring every other frame in a .crd trajectory in Ptraj (Tue Aug 01 2006 - 13:02:22 CDT)
  • AMBER: Ignoring every other frame in a .crd trajectory in Ptraj (Tue Aug 01 2006 - 12:55:31 CDT)
• Yannick Bomble
  • AMBER: source code (Mon Aug 14 2006 - 13:09:31 CDT)
• Yong Duan
  • RE: AMBER: how to reassign charges (Wed Aug 09 2006 - 16:26:10 CDT)
  • RE: AMBER: GAFF parameters: DPPC Bilayer (Tue Aug 08 2006 - 15:42:50 CDT)
  • RE: AMBER: ff03 and ff99SB force fields (Fri Aug 04 2006 - 06:58:51 CDT)
  • RE: AMBER: ff03 and ff99SB force fields (Thu Aug 03 2006 - 14:29:51 CDT)
• yxiong99
  • AMBER: about Silica's polarizability (Thu Aug 03 2006 - 10:20:19 CDT)
  • AMBER: where can I find the force field paramete r for Silica (Wed Aug 02 2006 - 14:53:33 CDT)
• Zu Thur Yew
  • Re: AMBER: Backbone & Sidechain atoms: Definition (Thu Aug 24 2006 - 12:32:14 CDT)
  • AMBER: Backbone & Sidechain atoms: Definition (Thu Aug 24 2006 - 08:13:14 CDT)
  • AMBER: MMPBSA: positive energies during nmode (Wed Aug 16 2006 - 09:15:11 CDT)
  • Re: AMBER: PCA: can't complete projection (Tue Aug 08 2006 - 11:42:04 CDT)
  • AMBER: PCA: can't complete projection (Tue Aug 08 2006 - 09:17:31 CDT)

Last message date: Sat Dec 30 2006 - 07:20:23 CST
Archived on: Wed Feb 21 2007 - 22:44:16 CST