Amber Archive Aug 2006 By Thread
- Re: AMBER: Xmgr in Windows Ilyas Yildirim (Mon Jul 31 2006 - 22:33:38 PDT)
- Re: AMBER: Xmgr in Windows Fabi嫕 Alejandro Rodr璲uez (Tue Aug 01 2006 - 04:39:19 PDT)
- Re: AMBER: Xmgr in Windows Florian Haberl (Tue Aug 01 2006 - 05:11:44 PDT)
- AMBER: How to set Bondi Radii using xleap Ilyas Yildirim (Mon Jul 31 2006 - 22:40:15 PDT)
- Re: AMBER: How to set Bondi Radii using xleap David A. Case (Tue Aug 01 2006 - 10:17:38 PDT)
- Re: AMBER: How to set Bondi Radii using xleap Carlos Simmerling (Tue Aug 01 2006 - 10:43:04 PDT)
- Re: AMBER: How to set Bondi Radii using xleap. . Don.Bashford.stjude.org (Tue Aug 01 2006 - 10:23:51 PDT)
- Re: AMBER: How to set Bondi Radii using xleap David A. Case (Tue Aug 01 2006 - 10:17:38 PDT)
- AMBER: regarding diffusion command output Arvind Marathe (Tue Aug 01 2006 - 03:45:21 PDT)
- Re: AMBER: Re: Confusion re AMBER SMD output Adrian Roitberg (Tue Aug 01 2006 - 04:07:03 PDT)
- Re: AMBER: Distance between two regions Guanglei Cui (Tue Aug 01 2006 - 08:35:54 PDT)
- Re: AMBER: from traj to crd Guanglei Cui (Tue Aug 01 2006 - 08:30:59 PDT)
- Re: AMBER: from traj to crd Fabi嫕 Alejandro Rodr璲uez (Tue Aug 01 2006 - 08:41:22 PDT)
- Re: AMBER: GB tutorials and disulphide bonds David A. Case (Tue Aug 01 2006 - 10:14:20 PDT)
- Re: AMBER: Using a trajectory and some PDB files as input for PCA David A. Case (Tue Aug 01 2006 - 10:10:29 PDT)
- AMBER: Ignoring every other frame in a .crd trajectory in Ptraj Xiaojian Deng (Tue Aug 01 2006 - 10:55:31 PDT)
- Re: AMBER: Ignoring every other frame in a .crd trajectory in Ptraj Xiaojian Deng (Tue Aug 01 2006 - 11:02:22 PDT)
- Re: AMBER: Ignoring every other frame in a .crd trajectory in Ptraj Carlos Simmerling (Tue Aug 01 2006 - 11:13:07 PDT)
- AMBER: pdb error AYTUG TUNCEL (Tue Aug 01 2006 - 12:36:39 PDT)
- Re: AMBER: pdb error Ilyas Yildirim (Tue Aug 01 2006 - 12:23:30 PDT)
- AMBER: any work-around for 80 character mask string limit? Tanya Johannsen (Tue Aug 01 2006 - 13:12:22 PDT)
- Re: AMBER: any work-around for 80 character mask string limit? David A. Case (Tue Aug 01 2006 - 14:37:36 PDT)
- AMBER: brookhaven to amber pdb format AYTUG TUNCEL (Wed Aug 02 2006 - 02:08:50 PDT)
- Re: AMBER: brookhaven to amber pdb format David A. Case (Wed Aug 02 2006 - 07:48:23 PDT)
- Re: AMBER: brookhaven to amber pdb format Ilyas Yildirim (Wed Aug 02 2006 - 11:55:38 PDT)
- AMBER: mm_pbsa.pl fails to start in linux cluster pkb bioinfo (Wed Aug 02 2006 - 05:07:22 PDT)
- Re: AMBER: mm_pbsa.pl fails to start in linux cluster pkb bioinfo (Wed Aug 02 2006 - 06:58:48 PDT)
- AMBER: neutral N-terminal amino-acid parameters for ff03 Vlad Cojocaru (Wed Aug 02 2006 - 07:21:31 PDT)
- Re: AMBER: neutral N-terminal amino-acid parameters for ff03 FyD (Sat Aug 05 2006 - 01:16:23 PDT)
- AMBER: Bugfixes available for pmemd iwrap problem Robert Duke (Wed Aug 02 2006 - 10:05:32 PDT)
- AMBER: where can I find the force field paramete r for Silica yxiong99 (Wed Aug 02 2006 - 12:53:33 PDT)
- AMBER: Maximum system size in simulated annealing Juraj Kotulic Bunta (Wed Aug 02 2006 - 19:03:11 PDT)
- Re: AMBER: Maximum system size in simulated annealing Andreas Svrcek-Seiler (Thu Aug 03 2006 - 02:23:13 PDT)
- Re: AMBER: Maximum system size in simulated annealing Carlos Simmerling (Thu Aug 03 2006 - 03:26:58 PDT)
- AMBER: TI-FEP for ILE--->VAL. Biswa Ranjan Meher (Wed Aug 02 2006 - 22:26:22 PDT)
- Re: AMBER: TI-FEP for ILE--->VAL. Ilyas Yildirim (Wed Aug 02 2006 - 23:15:10 PDT)
- Re: AMBER: TI-FEP for ILE--->VAL. David A. Case (Thu Aug 03 2006 - 09:43:44 PDT)
- Re: AMBER: PhosphoThreonine Parms for use with ff03 Vlad Cojocaru (Thu Aug 03 2006 - 03:07:48 PDT)
- AMBER: ff03 and ff99SB force fields Carlos Simmerling (Thu Aug 03 2006 - 03:59:11 PDT)
- RE: AMBER: ff03 and ff99SB force fields Yong Duan (Thu Aug 03 2006 - 12:29:51 PDT)
- Re: AMBER: ff03 and ff99SB force fields Ray Luo (Thu Aug 03 2006 - 05:21:03 PDT)
- Re: AMBER: ff03 and ff99SB force fields Vlad Cojocaru (Fri Aug 04 2006 - 01:17:59 PDT)
- RE: AMBER: ff03 and ff99SB force fields Yong Duan (Fri Aug 04 2006 - 04:58:51 PDT)
- RE: AMBER: ff03 and ff99SB force fields Yong Duan (Thu Aug 03 2006 - 12:29:51 PDT)
- AMBER: ff03 and ff99SB force fields Carlos Simmerling (Thu Aug 03 2006 - 03:59:11 PDT)
- AMBER: problems with ptraj anna.schrey.gmx.de (Thu Aug 03 2006 - 07:49:39 PDT)
- Re: AMBER: problems with ptraj David A. Case (Thu Aug 03 2006 - 09:46:19 PDT)
- Re: AMBER: problems with ptraj Thomas Cheatham (Thu Aug 10 2006 - 12:25:18 PDT)
- AMBER: Need to know meaning of numbers in parm99.dat file to be able to write frcmod file for dummy atoms Lwin, ThuZar (Thu Aug 03 2006 - 08:14:28 PDT)
- Re: AMBER: Need to know meaning of numbers in parm99.dat file to be able to write frcmod file for dummy atoms Carlos Simmerling (Thu Aug 03 2006 - 08:33:34 PDT)
- AMBER: about Silica's polarizability yxiong99 (Thu Aug 03 2006 - 08:20:19 PDT)
- Re: AMBER: about Silica's polarizability David A. Case (Thu Aug 03 2006 - 09:16:40 PDT)
- AMBER: question on chargning free energy in solvent vs vacuum Lwin, ThuZar (Thu Aug 03 2006 - 10:08:07 PDT)
- Re: AMBER: question on chargning free energy in solvent vs vacuum David A. Case (Fri Aug 04 2006 - 09:18:53 PDT)
- AMBER: restraint=0.0000 during minimization? Evan Kelly (Thu Aug 03 2006 - 10:48:17 PDT)
- AMBER: Please DISREGARD previous message (restraint=0.0000) Evan Kelly (Thu Aug 03 2006 - 10:57:46 PDT)
- AMBER: SURFTEN in GB (mm_pbsa calculations) Shuting Wei (Thu Aug 03 2006 - 12:18:10 PDT)
- Re: AMBER: SURFTEN in GB (mm_pbsa calculations) Carlos Simmerling (Thu Aug 03 2006 - 12:38:59 PDT)
- AMBER: HBOND ANALYSIS Claire Zerafa (Fri Aug 04 2006 - 07:35:50 PDT)
- Fw: AMBER: HBOND ANALYSIS Claire Zerafa (Sat Aug 05 2006 - 12:45:10 PDT)
- Re: AMBER: HBOND ANALYSIS Thomas Cheatham (Thu Aug 10 2006 - 16:57:34 PDT)
- AMBER: klambda Vitor Manuel Sousa F?x (Mon Aug 14 2006 - 03:45:10 PDT)
- Re: AMBER: klambda David A. Case (Mon Aug 14 2006 - 09:48:30 PDT)
- Re: AMBER: klambda Ilyas Yildirim (Mon Aug 14 2006 - 10:31:24 PDT)
- AMBER: klambda Vitor Manuel Sousa F?x (Mon Aug 14 2006 - 03:45:10 PDT)
- AMBER: H-bonds of peptide with water sangeeta (Fri Aug 04 2006 - 06:20:13 PDT)
- Re: AMBER: H-bonds of peptide with water Scott Pendley (Mon Aug 07 2006 - 12:56:04 PDT)
- AMBER: Residue connection points on prep.in Gloria T. Anderle (Fri Aug 04 2006 - 09:10:53 PDT)
- AMBER: parameter for Cd2+? JunJun Liu (Fri Aug 04 2006 - 08:50:46 PDT)
- AMBER: to do tutorial 4 using tleap Come On (Fri Aug 04 2006 - 09:50:53 PDT)
- AMBER: how to take care of toluene system neutrality Lwin, ThuZar (Fri Aug 04 2006 - 11:27:39 PDT)
- AMBER: how to take care of toluene system neutrality Lwin, ThuZar (Fri Aug 04 2006 - 11:31:53 PDT)
- RE: AMBER: question on chargning free energy in solvent vs vacuum. . Lwin, ThuZar (Fri Aug 04 2006 - 12:02:10 PDT)
- AMBER: Amber Installation Help Kirk Hevener (Mon Aug 07 2006 - 05:43:25 PDT)
- Re: AMBER: Amber Installation Help David A. Case (Tue Aug 08 2006 - 08:25:49 PDT)
- Re: AMBER: Amber Installation Help; link woes Scott Brozell (Tue Aug 08 2006 - 12:36:32 PDT)
- Re: AMBER: Amber Installation Help David A. Case (Tue Aug 08 2006 - 08:25:49 PDT)
- AMBER: Info regarding reduced cysteines Rafi Ahmad (Mon Aug 07 2006 - 07:06:40 PDT)
- Re: AMBER: Info regarding reduced cysteines David A. Case (Mon Aug 07 2006 - 08:02:57 PDT)
- AMBER: transition state John Chuang莊曜遠老師 (Mon Aug 07 2006 - 09:06:50 PDT)
- Re: AMBER: transition state Eric Hu (Wed Aug 09 2006 - 12:05:14 PDT)
- Re: AMBER: transition state John Chuang莊曜遠老師 (Mon Aug 14 2006 - 15:20:20 PDT)
- Re: AMBER: transition state Eric Hu (Mon Aug 21 2006 - 17:06:22 PDT)
- Re: AMBER: transition state John Chuang莊曜遠老師 (Mon Aug 14 2006 - 15:20:20 PDT)
- Re: AMBER: transition state Eric Hu (Wed Aug 09 2006 - 12:05:14 PDT)
- AMBER: Glass, Kevin A (Mon Aug 07 2006 - 13:09:02 PDT)
- Re: AMBER: Scott Brozell (Mon Aug 07 2006 - 17:37:19 PDT)
- AMBER: antechamber bond typing questions David Mobley (Mon Aug 07 2006 - 13:14:42 PDT)
- AMBER: RE: antechamber bond typing questions Junmei Wang (Mon Aug 07 2006 - 18:43:05 PDT)
- AMBER: Problem with restarting MD simulation Gobind Bisht (Mon Aug 07 2006 - 22:02:56 PDT)
- Re: AMBER: Problem with restarting MD simulation Carlos Simmerling (Tue Aug 08 2006 - 04:08:27 PDT)
- AMBER: cutting the box after "solvatebox" Vlad Cojocaru (Tue Aug 08 2006 - 05:12:37 PDT)
- Re: AMBER: cutting the box after "solvatebox" Carlos Simmerling (Tue Aug 08 2006 - 05:43:47 PDT)
- Re: AMBER: cutting the box after "solvatebox" Vlad Cojocaru (Tue Aug 08 2006 - 05:52:39 PDT)
- Re: AMBER: cutting the box after "solvatebox" Guanglei Cui (Tue Aug 08 2006 - 07:38:06 PDT)
- Re: AMBER: cutting the box after "solvatebox" Ilyas Yildirim (Thu Aug 17 2006 - 12:28:55 PDT)
- Re: AMBER: cutting the box after "solvatebox" Carlos Simmerling (Tue Aug 08 2006 - 05:43:47 PDT)
- AMBER: PCA: can't complete projection Zu Thur Yew (Tue Aug 08 2006 - 07:17:31 PDT)
- Re: AMBER: PCA: can't complete projection Vlad Cojocaru (Tue Aug 08 2006 - 07:56:49 PDT)
- AMBER: ptraj: nofit option for rmsd Joseph Nachman (Tue Aug 08 2006 - 08:27:41 PDT)
- Re: AMBER: PCA: can't complete projection Zu Thur Yew (Tue Aug 08 2006 - 09:42:04 PDT)
- Re: AMBER: PCA: can't complete projection Vlad Cojocaru (Tue Aug 08 2006 - 07:56:49 PDT)
- AMBER: GAFF parameters: DPPC Bilayer Akshay Patny (Tue Aug 08 2006 - 12:53:49 PDT)
- Re: AMBER: GAFF parameters: DPPC Bilayer Nitin Bhardwaj (Tue Aug 08 2006 - 12:58:59 PDT)
- RE: AMBER: GAFF parameters: DPPC Bilayer Yong Duan (Tue Aug 08 2006 - 13:42:50 PDT)
- RE: AMBER: GAFF parameters: DPPC Bilayer Akshay Patny (Wed Aug 09 2006 - 14:08:00 PDT)
- RE: AMBER: GAFF parameters: DPPC Bilayer Yong Duan (Tue Aug 08 2006 - 13:42:50 PDT)
- Re: AMBER: GAFF parameters: DPPC Bilayer Nitin Bhardwaj (Tue Aug 08 2006 - 12:58:59 PDT)
- AMBER: Format of mdcrd files Gobind Bisht (Wed Aug 09 2006 - 06:56:18 PDT)
- Re: AMBER: Format of mdcrd files Carlos Simmerling (Wed Aug 09 2006 - 07:24:35 PDT)
- Re: AMBER: Format of mdcrd files Mark Williamson (Wed Aug 09 2006 - 07:32:06 PDT)
- AMBER: Energy differecnes as using igb=1 and igb=0 backy (Wed Aug 09 2006 - 07:46:56 PDT)
- Re: AMBER: Energy differecnes as using igb=1 and igb=0 Carlos Simmerling (Wed Aug 09 2006 - 08:01:27 PDT)
- Re: AMBER: Energy differecnes as using igb=1 and igb=0 backy (Wed Aug 09 2006 - 23:47:37 PDT)
- Re: AMBER: Energy differecnes as using igb=1 and igb=0 Carlos Simmerling (Thu Aug 10 2006 - 03:09:23 PDT)
- AMBER: Could mm_pbsa decompose energy only for the receptor ? backy (Fri Aug 11 2006 - 07:10:52 PDT)
- Re: AMBER: Energy differecnes as using igb=1 and igb=0 backy (Wed Aug 09 2006 - 23:47:37 PDT)
- Re: AMBER: Energy differecnes as using igb=1 and igb=0 Carlos Simmerling (Wed Aug 09 2006 - 08:01:27 PDT)
- AMBER: build box info for acetonitrile in the simulation with periodic boundary condition Eric Hu (Wed Aug 09 2006 - 11:06:30 PDT)
- Re: AMBER: build box info for acetonitrile in the simulation with periodic boundary condition David A. Case (Wed Aug 09 2006 - 13:45:42 PDT)
- Re: AMBER: build box info for acetonitrile in the simulation with periodic boundary condition Eric Hu (Wed Aug 09 2006 - 14:30:04 PDT)
- Re: AMBER: build box info for acetonitrile in the simulation with periodic boundary condition David A. Case (Wed Aug 09 2006 - 13:45:42 PDT)
- AMBER: how to reassign charges Lwin, ThuZar (Wed Aug 09 2006 - 11:16:01 PDT)
- Re: AMBER: how to reassign charges David Mobley (Wed Aug 09 2006 - 13:03:10 PDT)
- RE: AMBER: how to reassign charges Yong Duan (Wed Aug 09 2006 - 14:26:10 PDT)
- Re: AMBER: how to reassign charges David A. Case (Wed Aug 09 2006 - 13:43:07 PDT)
- AMBER: PO2 in a DNA fragement, not a type in xleap? What can I do next? a a (Thu Aug 10 2006 - 02:26:01 PDT)
- Re: AMBER: PO2 in a DNA fragement, not a type in xleap? What can I do next? Thomas Cheatham (Thu Aug 10 2006 - 15:18:00 PDT)
- Re: AMBER: PO2 in a DNA fragement, not a type in xleap? What can I do next? a a (Thu Aug 10 2006 - 19:39:54 PDT)
- Re: AMBER: PO2 in a DNA fragement, not a type in xleap? What can I do next? FyD (Sat Aug 12 2006 - 12:09:29 PDT)
- Re: AMBER: PO2 in a DNA fragement, not a type in xleap? What canI do next? a a (Sun Aug 13 2006 - 21:29:59 PDT)
- AMBER: Phosphated Tyrosine, not a type (xleap)? a a (Thu Aug 10 2006 - 02:22:27 PDT)
- Re: AMBER: Phosphated Tyrosine, not a type (xleap)? David A. Case (Thu Aug 10 2006 - 09:07:09 PDT)
- Re: AMBER: Phosphated Tyrosine, not a type (xleap)? a a (Thu Aug 10 2006 - 19:38:47 PDT)
- AMBER: PO2 in a DNA fragement, not a type in xleap? What can I do next? a a (Thu Aug 10 2006 - 02:26:01 PDT)
- Re: AMBER: how to reassign charges David Mobley (Wed Aug 09 2006 - 13:03:10 PDT)
- AMBER: Heme parameters Marcelo Puiatti (Wed Aug 09 2006 - 15:58:35 PDT)
- Re: AMBER: Heme parameters Weihua Li (Wed Aug 09 2006 - 19:44:15 PDT)
- AMBER: Re: Simulated annealing Carlos Simmerling (Thu Aug 10 2006 - 04:40:24 PDT)
- AMBER: Leap adds hydrogens but cannot resolve their type. Paul R Brenner (Thu Aug 10 2006 - 12:23:55 PDT)
- Re: AMBER: Leap adds hydrogens but cannot resolve their type. David A. Case (Thu Aug 10 2006 - 13:15:16 PDT)
- Re: AMBER: Leap adds hydrogens but cannot resolve their type. Paul R Brenner (Tue Aug 15 2006 - 08:39:08 PDT)
- Re: AMBER: Leap adds hydrogens but cannot resolve their type. David A. Case (Thu Aug 10 2006 - 13:15:16 PDT)
- AMBER: zero entry in LENNARD_JONES_ACOEF of prmtop files Jing Huang (Fri Aug 11 2006 - 06:35:12 PDT)
- Re: AMBER: zero entry in LENNARD_JONES_ACOEF of prmtop files Guanglei Cui (Fri Aug 11 2006 - 06:57:46 PDT)
- AMBER: ptraj quasiharmonic analysis question Shawn yy (Fri Aug 11 2006 - 07:45:21 PDT)
- AMBER: how to do a molecular dynamic study on a trimer Abhilash (Fri Aug 11 2006 - 08:05:44 PDT)
- Re: AMBER: how to do a molecular dynamic study on a trimer David A. Case (Fri Aug 11 2006 - 09:05:12 PDT)
- Re: AMBER: how to do a molecular dynamic study on a trimer Gobind Bisht (Sat Aug 12 2006 - 10:05:29 PDT)
- Re: AMBER: how to do a molecular dynamic study on a trimer David A. Case (Sun Aug 13 2006 - 09:37:03 PDT)
- AMBER: AMBER Tutorial 2 section 6, rmsd calculation: rmsd for residues number? a a (Mon Aug 14 2006 - 04:25:31 PDT)
- Re: AMBER: how to do a molecular dynamic study on a trimer Gobind Bisht (Sat Aug 12 2006 - 10:05:29 PDT)
- Re: AMBER: how to do a molecular dynamic study on a trimer David A. Case (Fri Aug 11 2006 - 09:05:12 PDT)
- AMBER: AMBER8 - RDF bug Petr Kulhanek (Fri Aug 11 2006 - 09:00:57 PDT)
- AMBER: Nature of QM scanning protocol for parameter development Isherwood, James (Fri Aug 11 2006 - 09:17:01 PDT)
- AMBER: Middlebury College Cluster and Amber 8 Lubans, Peter S (Fri Aug 11 2006 - 09:55:19 PDT)
- Re: AMBER: Middlebury College Cluster and Amber 8 Robert Duke (Fri Aug 11 2006 - 10:33:13 PDT)
- Re: AMBER: Middlebury College Cluster and Amber 8 David A. Case (Fri Aug 11 2006 - 11:30:46 PDT)
- AMBER: Problem: Flag "SOLVENT_POINTERS" not found in PARM file Jianhui (Fri Aug 11 2006 - 11:50:54 PDT)
- Re: AMBER: Problem: Flag "SOLVENT_POINTERS" not found in PARM file David A. Case (Sun Aug 13 2006 - 09:49:27 PDT)
- AMBER: Where can I find the SMD parameter file (or simple turtorial) in AMBER9 Cheng Luo, Ph.D. (Fri Aug 11 2006 - 13:41:32 PDT)
- Re: AMBER: Where can I find the SMD parameter file (or simple turtorial) in AMBER9 Adrian Roitberg (Fri Aug 11 2006 - 13:23:10 PDT)
- AMBER: impose command in leap problem Piotr Cieplak (Fri Aug 11 2006 - 17:56:40 PDT)
- Re: AMBER: impose command in leap problem Scott Brozell (Fri Aug 11 2006 - 18:57:21 PDT)
- Re: AMBER: impose command in leap problem Piotr Cieplak (Mon Aug 14 2006 - 13:44:02 PDT)
- Re: AMBER: impose command in leap problem Scott Brozell (Fri Aug 11 2006 - 18:57:21 PDT)
- AMBER: DIELC? backy (Sat Aug 12 2006 - 05:16:47 PDT)
- Re: AMBER: DIELC? David A. Case (Sun Aug 13 2006 - 09:43:58 PDT)
- Re: AMBER: DIELC? backy (Sat Aug 19 2006 - 01:04:14 PDT)
- Re: AMBER: DIELC? David A. Case (Sun Aug 13 2006 - 09:43:58 PDT)
- AMBER: parallel pmemd with intel 9 fc bala (Sat Aug 12 2006 - 08:56:15 PDT)
- Re: AMBER: parallel pmemd with intel 9 fc Robert Duke (Sat Aug 12 2006 - 11:58:59 PDT)
- Re: AMBER: antechamber error -> metals Scott Brozell (Sun Aug 13 2006 - 14:58:14 PDT)
- AMBER: Problem with sander in Linux Wimal (Mon Aug 14 2006 - 01:14:00 PDT)
- Re: AMBER: Problem with sander in Linux David A. Case (Mon Aug 14 2006 - 09:49:53 PDT)
- AMBER: RE: AMBER Tutorial 2 section 6, rmsd calculation: rmsd for residues number? Kateryna Miroshnychenko (Mon Aug 14 2006 - 06:19:46 PDT)
- RE: AMBER: RE: AMBER Tutorial 2 section 6, rmsd calculation: rmsd for residues number? a a (Mon Aug 14 2006 - 22:48:49 PDT)
- AMBER: (no subject) a a (Tue Aug 15 2006 - 03:13:49 PDT)
- Re: AMBER: (no subject) Navnit Kumar Mishra (Tue Aug 15 2006 - 05:51:49 PDT)
- AMBER: (no subject) a a (Tue Aug 15 2006 - 03:13:49 PDT)
- RE: AMBER: RE: AMBER Tutorial 2 section 6, rmsd calculation: rmsd for residues number? a a (Mon Aug 14 2006 - 22:48:49 PDT)
- AMBER: problem imposing arbitrary peptide bonds through leap Amarda Shehu (Mon Aug 14 2006 - 09:27:24 PDT)
- Re: AMBER: problem imposing arbitrary peptide bonds through leap David A. Case (Mon Aug 14 2006 - 09:45:48 PDT)
- Re: ***SPAM*** Re: AMBER: problem imposing arbitrary peptide bonds through leap Amarda Shehu (Mon Aug 14 2006 - 09:56:31 PDT)
- Re: AMBER: problem imposing arbitrary peptide bonds through leap David A. Case (Mon Aug 14 2006 - 09:45:48 PDT)
- AMBER: source code Yannick Bomble (Mon Aug 14 2006 - 11:09:31 PDT)
- Re: AMBER: source code Thomas Cheatham (Mon Aug 14 2006 - 11:31:08 PDT)
- AMBER: Modify charges to increase/decrease hydrogen bond interaction Mingfeng Yang (Mon Aug 14 2006 - 11:25:19 PDT)
- Re: AMBER: Modify charges to increase/decrease hydrogen bond interaction Thomas Cheatham (Mon Aug 14 2006 - 11:42:52 PDT)
- Re: AMBER: Modify charges to increase/decrease hydrogen bond interaction Mingfeng Yang (Mon Aug 14 2006 - 12:06:56 PDT)
- Re: AMBER: Modify charges to increase/decrease hydrogen bond interaction Thomas Cheatham (Mon Aug 14 2006 - 11:42:52 PDT)
- AMBER: Advice on linux cluster sought Feng X Zhou (Mon Aug 14 2006 - 11:34:16 PDT)
- AMBER: amber9 Test Failer kawamura_hiro.riken.jp (Tue Aug 15 2006 - 05:21:49 PDT)
- Re: AMBER: amber9 Test Failer David A. Case (Tue Aug 15 2006 - 08:05:54 PDT)
- AMBER: amber 9 intel 9.1 ia64 Tim Robinson (Tue Aug 15 2006 - 06:45:16 PDT)
- Re: AMBER: amber 9 intel 9.1 ia64 Fabian Boes (Tue Aug 15 2006 - 06:59:39 PDT)
- AMBER: Question about using antechamber with G03 Gustavo Seabra (Tue Aug 15 2006 - 08:58:40 PDT)
- Re: AMBER: Question about using antechamber with G03 David A. Case (Tue Aug 15 2006 - 14:15:26 PDT)
- Re: AMBER: Question about using antechamber with G03 Gustavo Seabra (Wed Aug 16 2006 - 06:49:42 PDT)
- Re: AMBER: Question about using antechamber with G03 David A. Case (Tue Aug 15 2006 - 14:15:26 PDT)
- AMBER: DOTA-Lanthanide complexes in Amber opitz.che.udel.edu (Tue Aug 15 2006 - 10:48:23 PDT)
- Re: AMBER: DOTA-Lanthanide complexes in Amber David A. Case (Wed Aug 16 2006 - 09:59:22 PDT)
- Re: AMBER: DOTA-Lanthanide complexes in Amber opitz.che.udel.edu (Wed Aug 16 2006 - 10:27:23 PDT)
- Re: AMBER: DOTA-Lanthanide complexes in Amber Brent Krueger (Wed Aug 16 2006 - 13:08:57 PDT)
- AMBER: (Another) Question about using antechamber with G03 Gustavo Seabra (Tue Aug 15 2006 - 10:51:16 PDT)
- Re: AMBER: (Another) Question about using antechamber with G03 David A. Case (Tue Aug 15 2006 - 16:09:56 PDT)
- AMBER: antechamber failure on FMN David Mobley (Tue Aug 15 2006 - 11:04:42 PDT)
- Re: AMBER: antechamber failure on FMN David Mobley (Tue Aug 15 2006 - 11:16:47 PDT)
- Re: AMBER: antechamber failure on FMN David A. Case (Tue Aug 15 2006 - 16:14:41 PDT)
- Re: AMBER: antechamber failure on FMN David Mobley (Tue Aug 15 2006 - 11:16:47 PDT)
- AMBER: input conversion error mm_pbsa AYTUG TUNCEL (Tue Aug 15 2006 - 15:23:28 PDT)
- Re: AMBER: input conversion error mm_pbsa David A. Case (Tue Aug 15 2006 - 15:47:19 PDT)
- AMBER: TI tutorial Mingfeng Yang (Tue Aug 15 2006 - 15:22:10 PDT)
- Re: AMBER: TI tutorial David A. Case (Tue Aug 15 2006 - 16:34:58 PDT)
- AMBER: MM_PBSA : Question about Stability? Guillaume Bollot (Wed Aug 16 2006 - 00:00:15 PDT)
- Re: AMBER: MM_PBSA : Question about Stability? David A. Case (Wed Aug 16 2006 - 09:24:48 PDT)
- AMBER: MMPBSA: positive energies during nmode Zu Thur Yew (Wed Aug 16 2006 - 07:15:11 PDT)
- Re: AMBER: MMPBSA: positive energies during nmode David A. Case (Wed Aug 16 2006 - 09:10:29 PDT)
- AMBER: reading ff file into XLeap Petr Jerabek (Wed Aug 16 2006 - 09:21:00 PDT)
- Re: AMBER: reading ff file into XLeap David A. Case (Wed Aug 16 2006 - 10:21:47 PDT)
- AMBER: Ptraj selecting specific atoms in specific residues Steve Seibold (Wed Aug 16 2006 - 10:05:16 PDT)
- Re: AMBER: Ptraj selecting specific atoms in specific residues Scott Pendley (Wed Aug 16 2006 - 10:19:31 PDT)
- RE: AMBER: Ptraj selecting specific atoms in specific residues Steve Seibold (Wed Aug 16 2006 - 10:50:16 PDT)
- Re: AMBER: Ptraj selecting specific atoms in specific residues Thomas Cheatham (Wed Aug 16 2006 - 10:32:24 PDT)
- Re: AMBER: Ptraj selecting specific atoms in specific residues Scott Pendley (Wed Aug 16 2006 - 10:19:31 PDT)
- AMBER: checkmask Steve Seibold (Wed Aug 16 2006 - 11:14:29 PDT)
- AMBER: The PB GB energy from mm_pbsa will be positive on high charged system Suxin Zheng (Wed Aug 16 2006 - 11:23:44 PDT)
- Re: AMBER: The PB GB energy from mm_pbsa will be positive on high charged system David A. Case (Fri Aug 18 2006 - 10:50:32 PDT)
- Re: AMBER: The PB GB energy from mm_pbsa will be positive on high charged system Suxin Zheng (Fri Aug 18 2006 - 11:23:17 PDT)
- Re: AMBER: The PB GB energy from mm_pbsa will be positive on high charged system David A. Case (Fri Aug 18 2006 - 11:35:04 PDT)
- Re: AMBER: The PB GB energy from mm_pbsa will be positive on high charged system Suxin Zheng (Fri Aug 18 2006 - 11:23:17 PDT)
- Re: AMBER: The PB GB energy from mm_pbsa will be positive on high charged system David A. Case (Fri Aug 18 2006 - 10:50:32 PDT)
- AMBER: pmf input files Lauren O'Neil (Wed Aug 16 2006 - 10:20:45 PDT)
- AMBER: 湘葩: AMBER: pmf input files Chunhu Tan (Thu Aug 17 2006 - 09:36:30 PDT)
- AMBER: generate "template" frcmod from standard residues? mernst.tricity.wsu.edu (Wed Aug 16 2006 - 11:41:02 PDT)
- Re: AMBER: generate "template" frcmod from standard residues? David Mobley (Wed Aug 16 2006 - 14:51:47 PDT)
- Re: AMBER: generate "template" frcmod from standard residues? David A. Case (Thu Aug 17 2006 - 09:04:22 PDT)
- Re: AMBER: generate "template" frcmod from standard residues? mernst.tricity.wsu.edu (Thu Aug 17 2006 - 10:06:07 PDT)
- Re: AMBER: generate "template" frcmod from standard residues? David A. Case (Thu Aug 17 2006 - 11:01:45 PDT)
- Re: AMBER: generate "template" frcmod from standard residues? David Mobley (Fri Aug 18 2006 - 09:13:08 PDT)
- Re: AMBER: generate "template" frcmod from standard residues? mernst.tricity.wsu.edu (Thu Aug 17 2006 - 10:06:07 PDT)
- AMBER: help with leap sethl.gatech.edu (Wed Aug 16 2006 - 16:24:42 PDT)
- Re: AMBER: help with leap Franck_Vendeix.ncsu.edu (Thu Aug 17 2006 - 07:46:07 PDT)
- Re: AMBER: help with leap Bill Ross (Wed Aug 16 2006 - 17:51:56 PDT)
- RE: AMBER: antechamber error -> metals Junmei Wang (Wed Aug 16 2006 - 19:29:46 PDT)
- AMBER: RE: antechamber failure on FMN Junmei Wang (Thu Aug 17 2006 - 16:14:47 PDT)
- AMBER: Re: antechamber failure on FMN David Mobley (Fri Aug 18 2006 - 11:46:58 PDT)
- AMBER: Execution time discrepancies Glass, Kevin A (Thu Aug 17 2006 - 17:18:20 PDT)
- RE: AMBER: Execution time discrepancies Ross Walker (Thu Aug 17 2006 - 20:00:29 PDT)
- Re: AMBER: Execution time discrepancies Bill Ross (Thu Aug 17 2006 - 18:24:13 PDT)
- AMBER: identical high energies Tanya Johannsen (Thu Aug 17 2006 - 19:22:40 PDT)
- RE: AMBER: identical high energies Ross Walker (Thu Aug 17 2006 - 19:52:38 PDT)
- Re: AMBER: identical high energies Thomas Cheatham (Thu Aug 17 2006 - 19:57:23 PDT)
- AMBER: GBSA EGB = NaN William Lianhu Wei (Thu Aug 17 2006 - 19:30:50 PDT)
- RE: AMBER: GBSA EGB = NaN Ross Walker (Thu Aug 17 2006 - 19:57:29 PDT)
- Re: AMBER: GBSA EGB = NaN William Wei (Fri Aug 18 2006 - 08:12:10 PDT)
- RE: AMBER: GBSA EGB = NaN Ross Walker (Fri Aug 18 2006 - 15:11:52 PDT)
- Re: AMBER: GBSA EGB = NaN William Wei (Mon Aug 21 2006 - 09:04:36 PDT)
- Re: AMBER: GBSA EGB = NaN William Wei (Mon Aug 21 2006 - 09:04:26 PDT)
- Re: AMBER: GBSA EGB = NaN Ilyas Yildirim (Mon Aug 21 2006 - 09:14:54 PDT)
- Re: AMBER: GBSA EGB = NaN William Wei (Mon Aug 21 2006 - 09:37:47 PDT)
- Re: AMBER: GBSA EGB = NaN David A. Case (Mon Aug 21 2006 - 10:10:24 PDT)
- Re: AMBER: GBSA EGB = NaN William Wei (Mon Aug 21 2006 - 11:00:21 PDT)
- Re: AMBER: GBSA EGB = NaN David A. Case (Mon Aug 21 2006 - 11:21:10 PDT)
- Re: AMBER: GBSA EGB = NaN William Wei (Fri Aug 18 2006 - 08:12:10 PDT)
- RE: AMBER: GBSA EGB = NaN Ross Walker (Thu Aug 17 2006 - 19:57:29 PDT)
- AMBER: amidine group/ gaff parameters Prashanth Athri (Fri Aug 18 2006 - 12:00:17 PDT)
- AMBER: ptraj script Jardas sucuriba (Fri Aug 18 2006 - 13:08:31 PDT)
- AMBER: missing values in md.out Jardas sucuriba (Thu Aug 24 2006 - 09:15:40 PDT)
- Re: AMBER: missing values in md.out Carlos Simmerling (Thu Aug 24 2006 - 09:24:28 PDT)
- Re: AMBER: missing values in md.out Jardas sucuriba (Fri Aug 25 2006 - 05:36:45 PDT)
- Re: AMBER: missing values in md.out Carlos Simmerling (Fri Aug 25 2006 - 05:53:26 PDT)
- Re: AMBER: missing values in md.out Carlos Simmerling (Thu Aug 24 2006 - 09:24:28 PDT)
- AMBER: missing values in md.out Jardas sucuriba (Thu Aug 24 2006 - 09:15:40 PDT)
- AMBER: Details about Gaussian basis set for Cobalt complex S.Sundar Raman (Sun Aug 20 2006 - 07:07:57 PDT)
- Re: AMBER: Details about Gaussian basis set for Cobalt complex FyD (Mon Aug 21 2006 - 05:28:49 PDT)
- Re: AMBER: Details about Gaussian basis set for Cobalt complex Thomas Cheatham (Fri Aug 25 2006 - 11:21:07 PDT)
- Re: AMBER: Details about Gaussian basis set for Cobalt complex S.Sundar Raman (Sat Aug 26 2006 - 03:51:04 PDT)
- AMBER: waters closest to specific residues Jardas sucuriba (Sat Aug 26 2006 - 08:39:35 PDT)
- AMBER: RDF output Jardas sucuriba (Tue Aug 29 2006 - 07:48:29 PDT)
- RE: AMBER: RDF output Jardas sucuriba (Wed Aug 30 2006 - 14:31:08 PDT)
- Re: AMBER: RDF output Thomas Cheatham (Wed Aug 30 2006 - 15:18:29 PDT)
- Re: AMBER: Details about Gaussian basis set for Cobalt complex S.Sundar Raman (Sat Aug 26 2006 - 03:51:04 PDT)
- AMBER: Calculate interaction energy between small organic molecules Bj顤n C-G. Karlsson (Sun Aug 20 2006 - 23:37:24 PDT)
- Re: AMBER: Calculate interaction energy between small organic molecules David Mobley (Mon Aug 21 2006 - 07:20:42 PDT)
- Re: AMBER: Calculate interaction energy between small organic molecules David A. Case (Mon Aug 21 2006 - 23:14:15 PDT)
- AMBER: problem relating all atom structure prediction and folding simulations on AMBER8 priya priya (Mon Aug 21 2006 - 00:46:29 PDT)
- Re: AMBER: problem relating all atom structure prediction and folding simulations on AMBER8 Carlos Simmerling (Mon Aug 21 2006 - 07:19:10 PDT)
- RE: AMBER: problem relating all atom structure prediction and folding simulations on AMBER8 Ross Walker (Mon Aug 21 2006 - 08:48:00 PDT)
- RE: AMBER: problem relating all atom structure prediction and folding simulations on AMBER8 priya priya (Tue Aug 22 2006 - 21:16:42 PDT)
- Re: AMBER: problem relating all atom structure prediction and folding simulations on AMBER8 Carlos Simmerling (Wed Aug 23 2006 - 05:18:03 PDT)
- AMBER: building AMBER9 with gfortran/cygwin Jyh-Shyong Ho (Thu Aug 24 2006 - 19:30:02 PDT)
- Re: AMBER: building AMBER9 with gfortran/cygwin Andreas Svrcek-Seiler (Fri Aug 25 2006 - 03:39:08 PDT)
- Re: AMBER: building AMBER9 with gfortran/cygwin David A. Case (Fri Aug 25 2006 - 09:39:40 PDT)
- Re: AMBER: building AMBER9 with gfortran/cygwin David A. Case (Fri Aug 25 2006 - 08:41:49 PDT)
- RE: AMBER: problem relating all atom structure prediction and folding simulations on AMBER8 priya priya (Tue Aug 22 2006 - 21:16:42 PDT)
- AMBER: mm_pbsa calculation allocation error AYTUG TUNCEL (Mon Aug 21 2006 - 06:15:31 PDT)
- Re: AMBER: mm_pbsa calculation allocation error Ray Luo (Mon Aug 21 2006 - 09:37:14 PDT)
- AMBER: amber naming conventions for structure files sethl.gatech.edu (Tue Aug 22 2006 - 14:36:56 PDT)
- Re: AMBER: amber naming conventions for structure files Bill Ross (Tue Aug 22 2006 - 15:00:10 PDT)
- AMBER: holding a pair of residues fixed during minimization Seth Lilavivat (Tue Aug 22 2006 - 20:22:06 PDT)
- Re: AMBER: holding a pair of residues fixed during minimization David A. Case (Wed Aug 23 2006 - 13:05:25 PDT)
- AMBER: Carnal: Internal error: stream file name 2 out of range Shuting Wei (Wed Aug 23 2006 - 13:43:31 PDT)
- Re: AMBER: holding a pair of residues fixed during minimization Bill Ross (Wed Aug 23 2006 - 13:45:13 PDT)
- Re: AMBER: holding a pair of residues fixed during minimization David A. Case (Wed Aug 23 2006 - 13:05:25 PDT)
- AMBER: compiling parallel amber 9 in linux Amber admin (Wed Aug 23 2006 - 12:00:08 PDT)
- RE: AMBER: compiling parallel amber 9 in linux Ross Walker (Wed Aug 23 2006 - 12:54:39 PDT)
- Re: AMBER: compiling parallel amber 9 in linux David A. Case (Wed Aug 23 2006 - 13:01:35 PDT)
- RE: AMBER: compiling parallel amber 9 in linux Amber admin (Thu Aug 24 2006 - 17:10:57 PDT)
- Re: AMBER: Carnal: Internal error: stream file name 2 out of range Bill Ross (Wed Aug 23 2006 - 14:16:16 PDT)
- AMBER: 0 steps the same as 1 step? S. Jamal Rahi (Wed Aug 23 2006 - 14:25:44 PDT)
- Re: AMBER: 0 steps the same as 1 step? David A. Case (Wed Aug 23 2006 - 18:14:53 PDT)
- AMBER: Can I run RED/RESP for Platinum Complexes? a a (Thu Aug 24 2006 - 02:50:42 PDT)
- AMBER: nmode memory problem William Wei (Thu Aug 24 2006 - 08:29:13 PDT)
- Re: AMBER: nmode memory problem Knut Langsestmo (Thu Aug 24 2006 - 09:17:04 PDT)
- Re: AMBER: nmode memory problem William Wei (Thu Aug 24 2006 - 10:04:59 PDT)
- RE: AMBER: nmode memory problem Ross Walker (Thu Aug 24 2006 - 10:57:12 PDT)
- Re: AMBER: nmode memory problem William Wei (Thu Aug 24 2006 - 14:05:55 PDT)
- Re: AMBER: nmode memory problem Atro Tossavainen (Fri Aug 25 2006 - 03:10:50 PDT)
- AMBER: Can I run RED/RESP for Platinum Complexes? a a (Thu Aug 24 2006 - 02:50:42 PDT)
- Re: AMBER: 0 steps the same as 1 step? David A. Case (Wed Aug 23 2006 - 18:14:53 PDT)
- AMBER: antechamber charge calculation very sensitive to conformations ? Christophe Guilbert (Wed Aug 23 2006 - 18:59:08 PDT)
- RE: AMBER: antechamber charge calculation very sensitive to conformations ? Junmei Wang (Thu Aug 24 2006 - 19:51:07 PDT)
- Re: AMBER: antechamber charge calculation very sensitive to conformations ? David Mobley (Fri Aug 25 2006 - 08:08:44 PDT)
- RE: AMBER: antechamber charge calculation very sensitive to conformations ? Junmei Wang (Thu Aug 24 2006 - 19:51:07 PDT)
- AMBER: Calculate interaction energy between small organic molecules Bj顤n C-G. Karlsson (Wed Aug 23 2006 - 23:17:56 PDT)
- Re: AMBER: Calculate interaction energy between small organic molecules David Mobley (Thu Aug 24 2006 - 13:07:57 PDT)
- Re: AMBER: Calculate interaction energy between small organic molecules David LeBard (Thu Aug 24 2006 - 14:01:16 PDT)
- Re: AMBER: Calculate interaction energy between small organic molecules David Mobley (Thu Aug 24 2006 - 13:07:57 PDT)
- AMBER: ptraj dumpq feature/bug Markus Kaukonen (Thu Aug 24 2006 - 01:31:51 PDT)
- Re: AMBER: ptraj dumpq feature/bug Thomas Cheatham (Thu Aug 24 2006 - 13:16:23 PDT)
- AMBER: Backbone & Sidechain atoms: Definition Zu Thur Yew (Thu Aug 24 2006 - 06:13:14 PDT)
- Re: AMBER: Backbone & Sidechain atoms: Definition David A. Case (Thu Aug 24 2006 - 08:15:44 PDT)
- Re: AMBER: Backbone & Sidechain atoms: Definition Zu Thur Yew (Thu Aug 24 2006 - 10:32:14 PDT)
- Re: AMBER: Backbone & Sidechain atoms: Definition David A. Case (Thu Aug 24 2006 - 08:15:44 PDT)
- AMBER: TI vlimit exceeded Andrea Bortolato (Thu Aug 24 2006 - 06:42:21 PDT)
- Re: AMBER: TI vlimit exceeded David A. Case (Sat Aug 26 2006 - 10:38:58 PDT)
- AMBER: increase force constants Mahalakshmi Sahasranaman (Thu Aug 24 2006 - 06:45:28 PDT)
- Re: AMBER: increase force constants David A. Case (Thu Aug 24 2006 - 15:56:33 PDT)
- Re: AMBER: increase force constants Amber admin (Thu Aug 24 2006 - 17:15:24 PDT)
- AMBER: Installation amber 9 on IBM SP4 Myunggi Yi (Thu Aug 24 2006 - 09:05:50 PDT)
- RE: AMBER: Installation amber 9 on IBM SP4 Ross Walker (Thu Aug 24 2006 - 10:23:02 PDT)
- Re: AMBER: Installation amber 9 on IBM SP4 Myunggi Yi (Thu Aug 24 2006 - 12:00:04 PDT)
- RE: AMBER: Installation amber 9 on IBM SP4 Ross Walker (Thu Aug 24 2006 - 15:08:03 PDT)
- Re: AMBER: Installation amber 9 on IBM SP4 Myunggi Yi (Thu Aug 24 2006 - 18:29:58 PDT)
- Re: AMBER: Installation amber 9 on IBM SP4 Scott Brozell (Thu Aug 24 2006 - 18:50:31 PDT)
- Re: AMBER: Installation amber 9 on IBM SP4 Myunggi Yi (Thu Aug 24 2006 - 19:39:43 PDT)
- Re: AMBER: Installation amber 9 on IBM SP4 Myunggi Yi (Thu Aug 24 2006 - 19:48:07 PDT)
- Re: AMBER: Installation amber 9 on IBM SP4 Myunggi Yi (Thu Aug 24 2006 - 19:59:09 PDT)
- Re: AMBER: Installation amber 9 on IBM SP4 Myunggi Yi (Thu Aug 24 2006 - 20:09:29 PDT)
- Re: AMBER: Installation amber 9 on IBM SP4 Myunggi Yi (Thu Aug 24 2006 - 20:20:12 PDT)
- Re: AMBER: Installation amber 9 on IBM SP4 Scott Brozell (Thu Aug 24 2006 - 23:28:35 PDT)
- Re: AMBER: Installation amber 9 on IBM SP4 Scott Brozell (Thu Aug 24 2006 - 23:45:09 PDT)
- Re: AMBER: Installation amber 9 on IBM SP4; bugfix 12 Scott Brozell (Thu Aug 24 2006 - 19:57:03 PDT)
- Re: AMBER: Installation amber 9 on IBM SP4 Scott Brozell (Thu Aug 24 2006 - 19:58:20 PDT)
- Re: AMBER: Installation amber 9 on IBM SP4 David A. Case (Fri Aug 25 2006 - 08:03:10 PDT)
- RE: AMBER: Installation amber 9 on IBM SP4 Ross Walker (Fri Aug 25 2006 - 09:16:13 PDT)
- Re: AMBER: Installation amber 9 on IBM SP4 Myunggi Yi (Fri Aug 25 2006 - 18:20:47 PDT)
- Re: AMBER: Installation amber 9 on IBM SP4 Jyh-Shyong Ho (Fri Aug 25 2006 - 19:11:21 PDT)
- Re: AMBER: Installation amber 9 on IBM SP4 Myunggi Yi (Fri Aug 25 2006 - 19:41:46 PDT)
- Re: AMBER: Installation amber 9 on IBM SP4 Myunggi Yi (Thu Aug 24 2006 - 12:00:04 PDT)
- RE: AMBER: Installation amber 9 on IBM SP4 Ross Walker (Thu Aug 24 2006 - 10:23:02 PDT)
- AMBER: how to use AddPdbAtomMap sethl.gatech.edu (Thu Aug 24 2006 - 13:03:59 PDT)
- Re: AMBER: how to use AddPdbAtomMap Ilyas Yildirim (Thu Aug 24 2006 - 13:27:41 PDT)
- Re: AMBER: how to use AddPdbAtomMap David A. Case (Thu Aug 24 2006 - 15:47:50 PDT)
- AMBER: atomifluct Miguel Ferreira (Fri Aug 25 2006 - 04:09:03 PDT)
- AMBER: How to create a modified NA in leap sethl.gatech.edu (Fri Aug 25 2006 - 13:20:35 PDT)
- Re: AMBER: How to create a modified NA in leap Bill Ross (Fri Aug 25 2006 - 14:52:40 PDT)
- Re: AMBER: How to create a modified NA in leap sethl.gatech.edu (Sat Aug 26 2006 - 13:13:10 PDT)
- Re: AMBER: How to create a modified NA in leap Bill Ross (Sat Aug 26 2006 - 17:21:41 PDT)
- AMBER: Error in compliling AMBER 9 on Fedora 5 linux machine Gobind Bisht (Sat Aug 26 2006 - 22:24:12 PDT)
- Re: AMBER: Error in compliling AMBER 9 on Fedora 5 linux machine David A. Case (Sun Aug 27 2006 - 09:03:54 PDT)
- AMBER: Temperature fluctuation with Langevin Temperature control Gobind Singh Bisht (Sun Aug 27 2006 - 12:06:49 PDT)
- Re: AMBER: Temperature fluctuation with Langevin Temperature control Adrian Roitberg (Sun Aug 27 2006 - 14:07:07 PDT)
- Re: AMBER: Temperature fluctuation with Langevin Temperature control David A. Case (Mon Aug 28 2006 - 10:32:08 PDT)
- AMBER: Tutorial 2 - Section 4: Summary.density and summary.temp a a (Tue Aug 29 2006 - 03:15:07 PDT)
- RE: AMBER: Tutorial 2 - Section 4: Summary.density and summary.temp Ross Walker (Wed Aug 30 2006 - 19:04:36 PDT)
- Re: AMBER: Temperature fluctuation with Langevin Temperature control David A. Case (Mon Aug 28 2006 - 10:32:08 PDT)
- Re: AMBER: Temperature fluctuation with Langevin Temperature control Adrian Roitberg (Sun Aug 27 2006 - 14:07:07 PDT)
- AMBER: TI, mutation eric.henon.univ-reims.fr (Mon Aug 28 2006 - 05:39:48 PDT)
- Re: AMBER: TI, mutation Carlos Simmerling (Mon Aug 28 2006 - 05:18:56 PDT)
- Re: AMBER: TI, mutation Pradipta Bandyopadhyay (Mon Aug 28 2006 - 05:46:43 PDT)
- Re: AMBER: TI, mutation eric.henon.univ-reims.fr (Tue Aug 29 2006 - 01:43:04 PDT)
- AMBER: preparing ligand/rna structure for MD sethl.gatech.edu (Mon Aug 28 2006 - 11:45:17 PDT)
- Re: AMBER: preparing ligand/rna structure for MD David A. Case (Mon Aug 28 2006 - 17:11:34 PDT)
- AMBER: Periodic boundary condition (PBC) Rahaman, Asif (Mon Aug 28 2006 - 13:24:19 PDT)
- Re: AMBER: Periodic boundary condition (PBC) Carlos Simmerling (Mon Aug 28 2006 - 13:40:05 PDT)
- RE: AMBER: Periodic boundary condition (PBC) > Problem now with ptraj Rahaman, Asif (Thu Aug 31 2006 - 13:24:43 PDT)
- RE: AMBER: Periodic boundary condition (PBC) > Problem now with ptraj Thomas Cheatham (Thu Aug 31 2006 - 13:49:42 PDT)
- RE: AMBER: Periodic boundary condition (PBC) > Problem now with ptraj Rahaman, Asif (Thu Aug 31 2006 - 14:34:50 PDT)
- RE: AMBER: Periodic boundary condition (PBC) > Problem now with ptraj Thomas Cheatham (Thu Aug 31 2006 - 14:50:33 PDT)
- RE: AMBER: Periodic boundary condition (PBC) > Problem now with ptraj Rahaman, Asif (Thu Aug 31 2006 - 15:29:25 PDT)
- RE: AMBER: Periodic boundary condition (PBC) > Problem now with ptraj Thomas Cheatham (Thu Aug 31 2006 - 21:38:02 PDT)
- RE: AMBER: Periodic boundary condition (PBC) > Problem now with ptraj Rahaman, Asif (Thu Aug 31 2006 - 13:24:43 PDT)
- Re: AMBER: Periodic boundary condition (PBC) Bill Ross (Mon Aug 28 2006 - 16:21:57 PDT)
- Re: AMBER: Periodic boundary condition (PBC) David A. Case (Mon Aug 28 2006 - 17:17:42 PDT)
- Re: AMBER: Periodic boundary condition (PBC) Carlos Simmerling (Mon Aug 28 2006 - 13:40:05 PDT)
- AMBER: nmode: number of atoms limitation AYTUG TUNCEL (Mon Aug 28 2006 - 16:15:04 PDT)
- Re: AMBER: nmode: number of atoms limitation David A. Case (Mon Aug 28 2006 - 22:55:53 PDT)
- Re: AMBER: nmode: number of atoms limitation Cenk Andac (Wed Aug 30 2006 - 06:01:58 PDT)
- Re: Re: AMBER: nmode: number of atoms limitation Changge Ji (Mon Aug 28 2006 - 23:33:27 PDT)
- AMBER: how to limit the simulation space Eric Hu (Mon Aug 28 2006 - 17:55:11 PDT)
- Re: AMBER: how to limit the simulation space Bill Ross (Mon Aug 28 2006 - 18:04:39 PDT)
- AMBER: counterions and particle-mesh-ewald cristian obiol (Tue Aug 29 2006 - 01:06:20 PDT)
- Re: AMBER: counterions and particle-mesh-ewald David A. Case (Wed Aug 30 2006 - 13:14:40 PDT)
- Re: AMBER: counterions and particle-mesh-ewald darden (Wed Aug 30 2006 - 15:59:32 PDT)
- Re: AMBER: counterions and particle-mesh-ewald David A. Case (Wed Aug 30 2006 - 13:14:40 PDT)
- AMBER: Qingning Shu (Tue Aug 29 2006 - 06:01:58 PDT)
- Re: AMBER: David A. Case (Tue Aug 29 2006 - 08:09:23 PDT)
- Re: Re: AMBER: Qingning Shu (Tue Aug 29 2006 - 09:26:34 PDT)
- AMBER: mm_pbsa_statistical.pl William Wei (Tue Aug 29 2006 - 14:02:32 PDT)
- Re: AMBER: mm_pbsa_statistical.pl Jianyin Shao (Wed Aug 30 2006 - 10:52:56 PDT)
- Re: AMBER: mm_pbsa_statistical.pl William Wei (Wed Aug 30 2006 - 14:11:51 PDT)
- AMBER: Missing LES reference in Amber 9 manual Chris Moth (Tue Aug 29 2006 - 11:43:12 PDT)
- Re: AMBER: Missing LES reference in Amber 9 manual David A. Case (Wed Aug 30 2006 - 09:03:34 PDT)
- Re: Re: AMBER: Qingning Shu (Tue Aug 29 2006 - 09:26:34 PDT)
- Re: AMBER: David A. Case (Tue Aug 29 2006 - 08:09:23 PDT)
- AMBER: REMD: Hybrid topology file Austin B. Yongye (Wed Aug 30 2006 - 07:30:34 PDT)
- Re: AMBER: REMD: Hybrid topology file Carlos Simmerling (Wed Aug 30 2006 - 07:48:20 PDT)
- AMBER: 1-4 interaction in AMBER8 Jianhui (Wed Aug 30 2006 - 12:08:09 PDT)
- Re: AMBER: 1-4 interaction in AMBER8 Carlos Simmerling (Wed Aug 30 2006 - 12:22:13 PDT)
- Re: AMBER: 1-4 interaction in AMBER8 Jianhui (Wed Aug 30 2006 - 12:48:28 PDT)
- Re: AMBER: 1-4 interaction in AMBER8 Carlos Simmerling (Wed Aug 30 2006 - 14:23:26 PDT)
- Re: AMBER: 1-4 interaction in AMBER8 Bill Ross (Wed Aug 30 2006 - 14:05:27 PDT)
- Re: AMBER: 1-4 interaction in AMBER8 Carlos Simmerling (Wed Aug 30 2006 - 14:15:23 PDT)
- Re: AMBER: 1-4 interaction in AMBER8 Bill Ross (Wed Aug 30 2006 - 14:17:10 PDT)
- AMBER: reference of ff99 Myunggi Yi (Thu Aug 31 2006 - 08:59:51 PDT)
- Re: AMBER: reference of ff99 Carlos Simmerling (Thu Aug 31 2006 - 09:18:09 PDT)
- Re: AMBER: reference of ff99 Myunggi Yi (Thu Aug 31 2006 - 09:21:59 PDT)
- Re: AMBER: reference of ff99 Myunggi Yi (Thu Aug 31 2006 - 09:26:09 PDT)
- Re: AMBER: reference of ff99 David A. Case (Thu Aug 31 2006 - 09:43:50 PDT)
- AMBER: Question about free energy with mm_pbsa William Wei (Thu Aug 31 2006 - 11:50:11 PDT)
- Re: AMBER: Question about free energy with mm_pbsa David A. Case (Thu Aug 31 2006 - 22:32:54 PDT)
- AMBER: Question about free energy with mm_pbsa William Wei (Thu Aug 31 2006 - 11:50:11 PDT)
- AMBER: minimization with my own charges Myunggi Yi (Thu Aug 31 2006 - 15:01:24 PDT)
- Re: AMBER: minimization with my own charges Ilyas Yildirim (Thu Aug 31 2006 - 15:12:24 PDT)
- Re: AMBER: minimization with my own charges Myunggi Yi (Thu Aug 31 2006 - 15:22:08 PDT)
- Re: AMBER: minimization with my own charges Ilyas Yildirim (Thu Aug 31 2006 - 15:50:26 PDT)
- Re: AMBER: minimization with my own charges Myunggi Yi (Thu Aug 31 2006 - 16:13:29 PDT)
- Re: AMBER: minimization with my own charges Ilyas Yildirim (Thu Aug 31 2006 - 16:47:54 PDT)
- Re: AMBER: minimization with my own charges Myunggi Yi (Thu Aug 31 2006 - 18:16:49 PDT)
- Re: AMBER: minimization with my own charges Ilyas Yildirim (Thu Aug 31 2006 - 20:37:18 PDT)
- Re: AMBER: minimization with my own charges Thomas Cheatham (Thu Aug 31 2006 - 21:07:40 PDT)
- Re: AMBER: minimization with my own charges Myunggi Yi (Thu Aug 31 2006 - 15:22:08 PDT)
- Re: AMBER: minimization with my own charges Ilyas Yildirim (Thu Aug 31 2006 - 15:12:24 PDT)
- Last message date: Sun Sep 03 2006 - 06:07:18 PDT
- Archived on: Mon Jan 05 2009 - 06:09:52 PST
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