Amber Archive Dec 2006 by thread
336 messages
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Starting
Sun Dec 03 2006 - 06:07:40 PST,
Ending
Sun Dec 31 2006 - 06:07:50 PST
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AMBER: MM-PBSA problem
vanessa wai
(Thu Nov 30 2006 - 17:27:06 PST)
AMBER: How to keep an hydrogen bond during an implicit MD calculation?
a a
(Fri Dec 01 2006 - 02:35:31 PST)
Re: AMBER: How to keep an hydrogen bond during an implicit MD calculation?
j j
(Fri Dec 01 2006 - 02:59:59 PST)
Re: AMBER: MM-PBSA problem
Varsha Goyal
(Fri Dec 01 2006 - 13:35:27 PST)
Re: AMBER: MM-PBSA problem
vanessa wai
(Sat Dec 02 2006 - 01:11:18 PST)
RE: AMBER: MM-PBSA problem
Ray Luo
(Fri Dec 01 2006 - 13:51:52 PST)
Re: AMBER: MM-PBSA problem
vanessa wai
(Sat Dec 02 2006 - 01:08:15 PST)
RE: AMBER: MM-PBSA problem
Ray Luo
(Sat Dec 02 2006 - 07:55:46 PST)
Re: AMBER: MM-PBSA problem
vanessa wai
(Sun Dec 03 2006 - 17:52:25 PST)
RE: AMBER: MM-PBSA problem
Ray Luo
(Tue Dec 05 2006 - 11:16:32 PST)
Re: AMBER: MM-PBSA problem
vanessa wai
(Tue Dec 05 2006 - 17:33:35 PST)
Re: AMBER: How to apply a force to some atom in a residues?
a a
(Fri Dec 01 2006 - 02:26:51 PST)
AMBER: Ions analysis with hbond, How can I specify an input for hbond to probe ions interactions?
j j
(Fri Dec 01 2006 - 02:51:06 PST)
Re: AMBER: Ions analysis with hbond, How can I specify an input for hbond to probe ions interactions?
Thomas Cheatham
(Fri Dec 01 2006 - 09:53:50 PST)
Re: AMBER: Ions analysis with hbond, How can I specify an input for hbond to probe ions interactions?
j j
(Fri Dec 01 2006 - 12:28:24 PST)
Re: AMBER: Ions analysis with hbond, How can I specify an input for hbond to probe ions interactions?
Thomas Cheatham
(Fri Dec 01 2006 - 14:01:35 PST)
Re: AMBER: Ions analysis with hbond, How can I specify an input for hbond to probe ions interactions?
j j
(Mon Dec 04 2006 - 04:56:54 PST)
AMBER: about the std of computational alanine scanning
tongli
(Fri Dec 01 2006 - 03:50:11 PST)
AMBER: question on protein folding simulation
Noriaki Okimoto
(Fri Dec 01 2006 - 04:01:27 PST)
RE: AMBER: question on protein folding simulation
Yong Duan
(Fri Dec 01 2006 - 10:32:58 PST)
Re: AMBER: question on protein folding simulation
Noriaki Okimoto
(Sun Dec 03 2006 - 18:43:11 PST)
Re: AMBER: question on protein folding simulation
Carlos Simmerling
(Mon Dec 04 2006 - 04:32:16 PST)
Re: AMBER: question on protein folding simulation
Gustavo Seabra
(Mon Dec 04 2006 - 10:31:54 PST)
Re: AMBER: question on protein folding simulation
Fenghui Fan
(Fri Dec 01 2006 - 11:56:06 PST)
Re: AMBER: question on protein folding simulation
Noriaki Okimoto
(Sun Dec 03 2006 - 18:51:17 PST)
Re: AMBER: question on protein folding simulation
Fenghui Fan
(Mon Dec 04 2006 - 16:47:32 PST)
RE: AMBER: question on protein folding simulation
Yong Duan
(Tue Dec 05 2006 - 11:57:45 PST)
Re: AMBER: question on protein folding simulation
Noriaki Okimoto
(Thu Dec 07 2006 - 04:25:51 PST)
AMBER: sander error about fortran
Shuting Wei
(Fri Dec 01 2006 - 07:58:25 PST)
Re: AMBER: sander error about fortran
Scott Brozell
(Fri Dec 01 2006 - 23:10:03 PST)
Re: AMBER: sander error about fortran
Shuting Wei
(Mon Dec 04 2006 - 09:02:52 PST)
Re: AMBER: sander error about fortran
Scott Brozell
(Mon Dec 04 2006 - 13:26:52 PST)
AMBER: H-bond analysis (Ptraj) input file
Esther Brugger
(Fri Dec 01 2006 - 08:22:44 PST)
Re: AMBER: H-bond analysis (Ptraj) input file
Thomas Cheatham
(Fri Dec 01 2006 - 09:56:57 PST)
Re: AMBER: amber9 parralel compiling
Nikola Trbovic
(Fri Dec 01 2006 - 08:46:33 PST)
Re: AMBER: amber9 parralel compiling
Scott Brozell
(Fri Dec 01 2006 - 11:40:54 PST)
Re: AMBER: H-bond analysis (Ptraj)
Thomas Cheatham
(Fri Dec 01 2006 - 10:00:05 PST)
Re: AMBER: H-bond analysis (Ptraj)
Esther Brugger
(Fri Dec 01 2006 - 11:01:25 PST)
AMBER: dihedral calculation problem
Esther Brugger
(Fri Dec 01 2006 - 13:39:23 PST)
AMBER: Making sure that Amber jobs use Infiniband?
Michael John Hanby
(Fri Dec 01 2006 - 14:13:05 PST)
Re: AMBER: Making sure that Amber jobs use Infiniband?
David A. Case
(Fri Dec 01 2006 - 16:24:44 PST)
AMBER: LogP
Cenk Andac
(Sat Dec 02 2006 - 02:44:06 PST)
AMBER: problem at the start of heating up (using extra-point)
Rachel
(Sat Dec 02 2006 - 07:29:09 PST)
Re: AMBER: problem at the start of heating up (using extra-point)
Cenk Andac
(Sat Dec 02 2006 - 09:32:50 PST)
Re: AMBER: problem at the start of heating up (using extra-point)
David A. Case
(Sun Dec 03 2006 - 14:04:25 PST)
AMBER: LEaP not recognising Phosphate group in TYR
bertrand russell
(Sat Dec 02 2006 - 08:41:23 PST)
Re: AMBER: LEaP not recognising Phosphate group in TYR
David A. Case
(Sat Dec 02 2006 - 09:52:44 PST)
AMBER: MD with restraint (nmropt=1)
a a
(Tue Dec 05 2006 - 00:11:38 PST)
Re: AMBER: MD with restraint (nmropt=1)
David A. Case
(Tue Dec 05 2006 - 13:24:37 PST)
Re: AMBER: MD with restraint (nmropt=1)
a a
(Tue Dec 05 2006 - 22:11:59 PST)
Re: AMBER: MD with restraint (nmropt=1)
David A. Case
(Wed Dec 06 2006 - 07:59:43 PST)
Re: AMBER: MD with restraint (nmropt=1)
a a
(Wed Dec 06 2006 - 20:48:32 PST)
Re: AMBER: MD with restraint (nmropt=1)
Thomas Cheatham
(Wed Dec 06 2006 - 21:14:56 PST)
Re: AMBER: LEaP not recognising Phosphate group in TYR
bertrand russell
(Thu Dec 07 2006 - 02:39:46 PST)
Re: AMBER: LEaP not recognising Phosphate group in TYR
David A. Case
(Thu Dec 07 2006 - 09:06:17 PST)
AMBER: Problem with specifying NOSHAKEMASK
Gobind Singh Bisht
(Sun Dec 03 2006 - 02:42:01 PST)
Re: AMBER: Problem with specifying NOSHAKEMASK
Carlos Simmerling
(Sun Dec 03 2006 - 05:48:56 PST)
Re: AMBER: Problem with specifying NOSHAKEMASK
Gobind Singh Bisht
(Sun Dec 03 2006 - 07:26:27 PST)
Re: AMBER: Problem with specifying NOSHAKEMASK
David A. Case
(Sun Dec 03 2006 - 14:06:10 PST)
Re: AMBER: Problem with specifying NOSHAKEMASK
Gobind Singh Bisht
(Sun Dec 03 2006 - 19:11:57 PST)
Re: AMBER: Problem with specifying NOSHAKEMASK
David A. Case
(Mon Dec 04 2006 - 08:33:02 PST)
Re: AMBER: Problem with specifying NOSHAKEMASK
Gobind Singh Bisht
(Mon Dec 04 2006 - 20:26:16 PST)
AMBER: bugfix
mahdi fathi
(Sun Dec 03 2006 - 07:17:42 PST)
Re: AMBER: bugfix
Ye Mei
(Sun Dec 03 2006 - 07:38:40 PST)
AMBER: About the creation of 1-4 pairs in AMBER program
J. Zhang
(Sun Dec 03 2006 - 18:17:02 PST)
AMBER: The VDW correctioin
J. Zhang
(Sun Dec 03 2006 - 18:29:28 PST)
AMBER: xleap problems
anna.schrey.gmx.de
(Mon Dec 04 2006 - 03:45:07 PST)
Re: AMBER: xleap problems
Cenk Andac
(Mon Dec 04 2006 - 07:46:34 PST)
Re: AMBER: xleap problems
David A. Case
(Mon Dec 04 2006 - 08:26:20 PST)
AMBER: how to include EXTRA POINTS in AMBER8
Rachel
(Mon Dec 04 2006 - 07:59:34 PST)
Re: AMBER: how to include EXTRA POINTS in AMBER8
David A. Case
(Mon Dec 04 2006 - 08:23:15 PST)
Re: AMBER: how to include EXTRA POINTS in AMBER8
Rachel
(Mon Dec 04 2006 - 09:03:11 PST)
Re: AMBER: how to include EXTRA POINTS in AMBER8
Rachel
(Mon Dec 04 2006 - 10:35:08 PST)
Re: AMBER: how to include EXTRA POINTS in AMBER8
David A. Case
(Wed Dec 06 2006 - 22:14:44 PST)
AMBER: DRMS setting for Nmode calculation
Shuting Wei
(Thu Dec 07 2006 - 12:46:54 PST)
AMBER: Is there anyway to recover the LISTOUT obtained after running a md with nmr restrictions
j j
(Mon Dec 04 2006 - 09:10:26 PST)
Re: AMBER: Is there anyway to recover the LISTOUT obtained after running a md with nmr restrictions
David A. Case
(Mon Dec 04 2006 - 09:45:11 PST)
Re: AMBER: Is there anyway to recover the LISTOUT obtained after running a md with nmr restrictions
j j
(Mon Dec 04 2006 - 14:28:14 PST)
Re: AMBER: phantom sander8 in dmesg
Lachele Foley (Lists)
(Mon Dec 04 2006 - 09:21:12 PST)
AMBER: ptraj vector corrplane bug
Myunggi Yi
(Mon Dec 04 2006 - 12:49:46 PST)
AMBER: Zn2+ and Ca2+ ions explicitly treated in MMPB/GB/SA
Piotr Cieplak
(Mon Dec 04 2006 - 16:20:02 PST)
AMBER: AMBER parallel run bombs
Rahaman, Asif
(Mon Dec 04 2006 - 16:29:53 PST)
Re: AMBER: AMBER parallel run bombs
Michael Crowley
(Mon Dec 04 2006 - 17:41:32 PST)
AMBER: A BUG report, "ptraj corrplane"
Myunggi Yi
(Tue Dec 05 2006 - 09:42:08 PST)
Re: AMBER: A BUG report, "ptraj corrplane"
Myunggi Yi
(Sun Dec 10 2006 - 17:32:22 PST)
AMBER: nonplanarity of NH2 groups
laura zanet
(Wed Dec 06 2006 - 07:48:33 PST)
Re: AMBER: nonplanarity of NH2 groups
FyD
(Thu Dec 07 2006 - 09:17:54 PST)
Re: AMBER: nonplanarity of NH2 groups
Jiri Sponer
(Thu Dec 07 2006 - 09:37:52 PST)
AMBER: perturbed and unperturbed charges
Rachel
(Wed Dec 06 2006 - 09:24:24 PST)
Re: AMBER: perturbed and unperturbed charges
David A. Case
(Wed Dec 06 2006 - 10:22:37 PST)
AMBER: parameter definitions
Ed Pate
(Wed Dec 06 2006 - 10:27:15 PST)
Re: AMBER: parameter definitions
David A. Case
(Wed Dec 06 2006 - 11:00:34 PST)
AMBER: setBox with buffer in leap
Steven Winfield
(Wed Dec 06 2006 - 11:05:22 PST)
AMBER: Amber9 failure to compile parallel on Rocks 4.2.1 system
Michael John Hanby
(Wed Dec 06 2006 - 13:26:11 PST)
RE: AMBER: Amber9 failure to compile parallel on Rocks 4.2.1 system
Ross Walker
(Wed Dec 06 2006 - 14:48:51 PST)
AMBER: Amber9 Parallel compiled with -lam, how to run test.parallel?
Michael John Hanby
(Sun Dec 10 2006 - 12:09:34 PST)
Re: AMBER: Amber9 Parallel compiled with -lam, how to run test.parallel?
David A. Case
(Sun Dec 10 2006 - 16:34:15 PST)
RE: AMBER: Amber9 Parallel compiled with -lam, how to run test.parallel?
Michael John Hanby
(Sun Dec 10 2006 - 19:31:57 PST)
AMBER: ibelly not work
JunJun Liu
(Wed Dec 06 2006 - 15:22:34 PST)
RE: AMBER: ibelly not work
Ross Walker
(Wed Dec 06 2006 - 16:07:45 PST)
RE: AMBER: ibelly not work
Andy Purkiss-Trew
(Thu Dec 07 2006 - 04:33:24 PST)
AMBER: setBox with buffer in leap
Steven Winfield
(Wed Dec 06 2006 - 16:43:58 PST)
Re: AMBER: setBox with buffer in leap
Scott Brozell
(Mon Dec 11 2006 - 21:08:38 PST)
Re: AMBER: setBox with buffer in leap
David A. Case
(Tue Dec 12 2006 - 08:30:25 PST)
AMBER: How could I simulate lipid membrane with AMBER9.0?
曹冉
(Wed Dec 06 2006 - 17:02:55 PST)
Re: AMBER: How could I simulate lipid membrane with AMBER9.0?
Fenghui Fan
(Wed Dec 06 2006 - 18:49:09 PST)
Re: AMBER: How could I simulate lipid membrane with AMBER9.0?
曹冉
(Thu Dec 07 2006 - 17:46:44 PST)
AMBER: What's going wrong when I use antechamber dealing with lipid molecular?
曹冉
(Wed Dec 06 2006 - 17:05:55 PST)
Re: AMBER: What's going wrong when I use antechamber dealing with lipid molecular?
Fenghui Fan
(Wed Dec 06 2006 - 18:51:41 PST)
AMBER: PMEMD scaling
Tiziano Tuccinardi
(Thu Dec 07 2006 - 00:46:49 PST)
Re: AMBER: PMEMD scaling
Robert Duke
(Thu Dec 07 2006 - 06:17:46 PST)
AMBER: Installing Amber 9 on Mac Pro
Burkhard Heil
(Thu Dec 07 2006 - 02:54:00 PST)
Re: AMBER: Installing Amber 9 on Mac Pro
Mathy Froeyen
(Thu Dec 07 2006 - 04:54:48 PST)
Re: AMBER: Installing Amber 9 on Mac Pro
Mengjuei Hsieh
(Mon Dec 11 2006 - 17:52:07 PST)
RE: AMBER: Problem about dummy atoms when running antechamber
Junmei Wang
(Thu Dec 07 2006 - 09:14:58 PST)
AMBER: MD with positional and NMR restraints
Mike Summers
(Thu Dec 07 2006 - 12:46:26 PST)
Re: AMBER: MD with positional and NMR restraints
David A. Case
(Thu Dec 07 2006 - 13:51:53 PST)
Re: AMBER: MD with positional and NMR restraints
Mike Summers
(Thu Dec 07 2006 - 15:34:07 PST)
Re: AMBER: MD with positional and NMR restraints
David A. Case
(Thu Dec 07 2006 - 15:54:33 PST)
AMBER: Simulating proteins with calcium ion
Qing Zhang
(Thu Dec 07 2006 - 16:15:42 PST)
Re: AMBER: Simulating proteins with calcium ion
Fenghui Fan
(Thu Dec 07 2006 - 17:56:02 PST)
Re: AMBER: Simulating proteins with calcium ion
Thomas Cheatham
(Thu Dec 07 2006 - 19:23:26 PST)
Re: AMBER: Simulating proteins with calcium ion
Qing Zhang
(Fri Dec 08 2006 - 16:31:02 PST)
Re: AMBER: Simulating proteins with calcium ion
Karen Callahan
(Tue Dec 12 2006 - 11:19:49 PST)
Re: AMBER: Simulating proteins with calcium ion
Bill Ross
(Tue Dec 12 2006 - 11:47:48 PST)
Re: AMBER: Simulating proteins with calcium ion
张勇
(Tue Dec 12 2006 - 16:25:03 PST)
Re: AMBER: Simulating proteins with calcium ion
Qing Zhang
(Fri Dec 22 2006 - 11:32:43 PST)
Re: AMBER: Simulating proteins with calcium ion
Bill Ross
(Fri Dec 22 2006 - 11:51:07 PST)
Re: AMBER: Simulating proteins with calcium ion
Qing Zhang
(Fri Dec 22 2006 - 12:22:53 PST)
Re: AMBER: Simulating proteins with calcium ion
Qing Zhang
(Fri Dec 22 2006 - 12:17:05 PST)
Re: AMBER: Simulating proteins with calcium ion
Bill Ross
(Fri Dec 22 2006 - 13:12:50 PST)
Re: AMBER: Simulating proteins with calcium ion
张勇
(Fri Dec 22 2006 - 17:02:57 PST)
Re: AMBER: Simulating proteins with calcium ion
Qing Zhang
(Fri Dec 22 2006 - 23:26:11 PST)
Re: AMBER: problem of the REMD with nmr constraints
wenfei Li
(Thu Dec 07 2006 - 16:55:04 PST)
AMBER: Error message in methane solvent system
Atsutoshi Okabe
(Thu Dec 07 2006 - 19:19:04 PST)
Re: AMBER: Error message in methane solvent system
David A. Case
(Fri Dec 08 2006 - 08:41:49 PST)
AMBER: atome type error
Steve Seibold
(Fri Dec 08 2006 - 07:08:35 PST)
RE: AMBER: atome type error
Ross Walker
(Fri Dec 08 2006 - 07:51:29 PST)
AMBER: Atom Type problem
Steve Seibold
(Fri Dec 08 2006 - 08:01:23 PST)
RE: AMBER: Atom Type problem
Ross Walker
(Fri Dec 08 2006 - 08:21:19 PST)
RE: AMBER: Atom Type problem
Steve Seibold
(Fri Dec 08 2006 - 10:09:05 PST)
AMBER: Atom Type problem
Steve Seibold
(Fri Dec 08 2006 - 08:04:29 PST)
AMBER: Compiling Amber 9 on SGI with gcc
Shin, John Y CONTRACTOR WRAIR-Wash DC
(Fri Dec 08 2006 - 10:46:32 PST)
Re: AMBER: Compiling Amber 9 on SGI with gcc
Scott Brozell
(Fri Dec 08 2006 - 19:29:15 PST)
Re: AMBER: Compiling Amber 9 on SGI with gcc
David A. Case
(Sat Dec 09 2006 - 08:55:20 PST)
AMBER: RDC refinement
Lee, Young-Tae
(Fri Dec 08 2006 - 12:50:42 PST)
Re: AMBER: RDC refinement
David A. Case
(Fri Dec 08 2006 - 15:52:11 PST)
AMBER: description of prep file
Piotr Cieplak
(Fri Dec 08 2006 - 14:28:29 PST)
Re: AMBER: description of prep file
David A. Case
(Fri Dec 08 2006 - 14:52:30 PST)
AMBER: dihedral angle problem
Esther Brugger
(Fri Dec 08 2006 - 14:53:32 PST)
Re: AMBER: dihedral angle problem
David A. Case
(Fri Dec 08 2006 - 15:47:39 PST)
Re: AMBER: dihedral angle problem
Esther Brugger
(Fri Dec 08 2006 - 17:00:48 PST)
Re: AMBER: dihedral angle problem
David A. Case
(Fri Dec 08 2006 - 18:10:36 PST)
AMBER: General Question about Abmer
Sanya Kryklia
(Mon Dec 11 2006 - 06:23:11 PST)
Re: AMBER: General Question about Abmer
M. L. Dodson
(Mon Dec 11 2006 - 06:34:45 PST)
AMBER: addition of subroutine in pmemd module
kakali sen
(Mon Dec 11 2006 - 10:52:37 PST)
AMBER: Atoms overlapping
Nitin Bhardwaj
(Mon Dec 11 2006 - 11:43:44 PST)
Re: AMBER: Atoms overlapping
David A. Case
(Mon Dec 11 2006 - 12:08:58 PST)
Re: AMBER: Atoms overlapping
Nitin Bhardwaj
(Mon Dec 11 2006 - 12:48:53 PST)
Re: AMBER: Atoms overlapping
Thomas Steinbrecher
(Mon Dec 11 2006 - 14:11:47 PST)
AMBER: Building Parameters
Steve Seibold
(Mon Dec 11 2006 - 13:29:15 PST)
AMBER: Coodinates not being unique
Nitin Bhardwaj
(Mon Dec 11 2006 - 16:50:41 PST)
AMBER: QM/MD energy conservation
Evan Kelly
(Mon Dec 11 2006 - 19:17:59 PST)
Re: AMBER: QM/MD energy conservation
Gustavo Seabra
(Tue Dec 12 2006 - 06:02:39 PST)
AMBER: LEaP problem
bertrand russell
(Mon Dec 11 2006 - 21:10:48 PST)
Re: AMBER: LEaP problem
Bill Ross
(Mon Dec 11 2006 - 22:24:33 PST)
Re: AMBER: LEaP problem
Fenghui Fan
(Mon Dec 11 2006 - 22:32:06 PST)
AMBER: ERROR: The PDB file is not in the working directory
saurabh agrawal
(Tue Dec 12 2006 - 03:39:39 PST)
Re: AMBER: ERROR: The PDB file is not in the working directory
FyD
(Tue Dec 12 2006 - 04:57:56 PST)
Re: AMBER: ERROR: The PDB file is not in the working directory
saurabh agrawal
(Wed Dec 13 2006 - 23:18:33 PST)
Re: AMBER: ERROR: The PDB file is not in the working directory
saurabh agrawal
(Thu Dec 14 2006 - 03:38:05 PST)
Re: AMBER: ERROR: The PDB file is not in the working directory
FyD
(Fri Dec 15 2006 - 00:21:21 PST)
AMBER: RDF problem
Esther Brugger
(Tue Dec 12 2006 - 11:45:14 PST)
Re: AMBER: How to run QM/MM simulation of DNA duplex bound with platinum moietes
Chengwen Chen
(Tue Dec 12 2006 - 23:01:03 PST)
AMBER: floating point assist faults on IA64 PMEMD 9
Jarrod Smith
(Wed Dec 13 2006 - 10:42:06 PST)
Re: AMBER: floating point assist faults on IA64 PMEMD 9
Robert Duke
(Wed Dec 13 2006 - 12:22:23 PST)
Re: AMBER: floating point assist faults on IA64 PMEMD 9
Jarrod Smith
(Wed Dec 13 2006 - 13:54:18 PST)
Re: AMBER: floating point assist faults on IA64 PMEMD 9
Jarrod Smith
(Wed Dec 13 2006 - 14:13:29 PST)
Re: AMBER: floating point assist faults on IA64 PMEMD 9
Robert Duke
(Wed Dec 13 2006 - 14:41:52 PST)
Re: AMBER: floating point assist faults on IA64 PMEMD 9
Jarrod Smith
(Wed Dec 13 2006 - 15:32:36 PST)
AMBER: Unit 5 Error on OPEN: md.in
Rachel
(Wed Dec 13 2006 - 11:55:58 PST)
Re: AMBER: Unit 5 Error on OPEN: md.in
Rachel
(Sat Dec 16 2006 - 10:01:12 PST)
Re: AMBER: Unit 5 Error on OPEN: md.in
Chris Moth
(Sat Dec 16 2006 - 10:25:03 PST)
Re: AMBER: Unit 5 Error on OPEN: md.in
Chris Moth
(Sat Dec 16 2006 - 10:27:17 PST)
AMBER: amber 9 installation problem
Ed Pate
(Wed Dec 13 2006 - 16:34:19 PST)
AMBER: coordinate out of bounds
Miguel Ferreira
(Wed Dec 13 2006 - 17:09:57 PST)
Re: AMBER: coordinate out of bounds
j j
(Thu Dec 14 2006 - 02:21:50 PST)
AMBER: ISTRNG or SALT in MM_PBSA
Qizhi Cui
(Wed Dec 13 2006 - 19:23:48 PST)
AMBER: Free energy perturbation in SANDER
Yumi Nukusina
(Thu Dec 14 2006 - 00:59:36 PST)
Re: AMBER: Free energy perturbation in SANDER
Sergey Samsonov
(Thu Dec 14 2006 - 01:38:46 PST)
AMBER: Free energy perturbation in SANDER
Chris Moth
(Thu Dec 14 2006 - 06:21:11 PST)
Re: AMBER: RESP charges of iron-porphyrin system
Shin Tokumoto
(Thu Dec 14 2006 - 01:31:13 PST)
AMBER: parallel computation time vs serial computation time
Cenk Andac
(Thu Dec 14 2006 - 03:17:28 PST)
Re: AMBER: parallel computation time vs serial computation time
Robert Duke
(Thu Dec 14 2006 - 06:16:22 PST)
AMBER: sander: cannot execute binary file
Kailee
(Thu Dec 14 2006 - 07:53:50 PST)
RE: AMBER: sander: cannot execute binary file
Michael John Hanby
(Thu Dec 14 2006 - 13:52:23 PST)
RE: AMBER: sander: cannot execute binary file
Ross Walker
(Thu Dec 14 2006 - 15:15:46 PST)
Re: AMBER: sander: cannot execute binary file
Kailee
(Fri Dec 15 2006 - 09:25:21 PST)
Re: AMBER: sander: cannot execute binary file
David A. Case
(Fri Dec 15 2006 - 09:48:49 PST)
Re: AMBER: sander: cannot execute binary file
Kailee
(Mon Dec 18 2006 - 08:41:11 PST)
Re: AMBER: sander: cannot execute binary file
Kailee
(Mon Dec 18 2006 - 09:06:36 PST)
RE: AMBER: sander: cannot execute binary file
Ross Walker
(Mon Dec 18 2006 - 11:52:05 PST)
Re: AMBER: sander: cannot execute binary file
Kailee
(Tue Dec 19 2006 - 08:13:48 PST)
AMBER: Test Message Please Ignore
Ross Walker
(Thu Dec 14 2006 - 13:01:07 PST)
AMBER: Test Message Please Ignore.
Ross Walker
(Thu Dec 14 2006 - 13:01:07 PST)
AMBER: Can't compile PMEMD
Michael John Hanby
(Thu Dec 14 2006 - 13:47:15 PST)
Re: AMBER: Can't compile PMEMD
Robert Duke
(Thu Dec 14 2006 - 14:12:12 PST)
RE: AMBER: Can't compile PMEMD
Michael John Hanby
(Thu Dec 14 2006 - 15:13:47 PST)
Re: AMBER: Can't compile PMEMD
Robert Duke
(Thu Dec 14 2006 - 15:42:02 PST)
AMBER: rdparm
venditti2.unisi.it
(Fri Dec 15 2006 - 08:08:17 PST)
Re: AMBER: rdparm
Thomas Cheatham
(Sat Dec 16 2006 - 19:43:55 PST)
Re: AMBER: rdparm
Tim Meyer
(Tue Dec 19 2006 - 07:22:45 PST)
AMBER: AMBER - leap - problems with impose command
Piotr Cieplak
(Fri Dec 15 2006 - 10:18:06 PST)
Re: AMBER: AMBER - leap - problems with impose command
FyD
(Fri Dec 15 2006 - 22:22:36 PST)
Re: AMBER: AMBER - leap - problems with impose command
Piotr Cieplak
(Fri Dec 15 2006 - 23:04:05 PST)
Re: AMBER: AMBER - leap - problems with impose command
Ilyas Yildirim
(Sat Dec 16 2006 - 03:17:22 PST)
Re: AMBER: AMBER - leap - problems with impose command
Piotr Cieplak
(Sat Dec 16 2006 - 23:20:28 PST)
Re: AMBER: AMBER - leap - problems with impose command
Ilyas Yildirim
(Sun Dec 17 2006 - 00:45:13 PST)
AMBER: Is there a way to simulate a box of pure water with amber
Li Su
(Fri Dec 15 2006 - 10:28:12 PST)
RE: AMBER: Is there a way to simulate a box of pure water with amber
Ross Walker
(Fri Dec 15 2006 - 10:52:53 PST)
Re: AMBER: Is there a way to simulate a box of pure water with amber
Sergey Samsonov
(Sun Dec 17 2006 - 23:43:27 PST)
Re: AMBER: Is there a way to simulate a box of pure water with amber
Bill Ross
(Fri Dec 15 2006 - 11:06:49 PST)
AMBER: Solvating a bilayer
Matthew Tessier
(Fri Dec 15 2006 - 11:32:25 PST)
AMBER: Error in sysdepend.c?
Shin, John Y CONTRACTOR WRAIR-Wash DC
(Fri Dec 15 2006 - 11:44:50 PST)
Re: AMBER: Error in sysdepend.c?
David A. Case
(Fri Dec 15 2006 - 15:24:00 PST)
RE: AMBER: Error in sysdepend.c?
Shin, John Y CONTRACTOR WRAIR-Wash DC
(Mon Dec 18 2006 - 12:27:24 PST)
RE: AMBER: Error in sysdepend.c?
Scott Brozell
(Tue Dec 19 2006 - 11:19:38 PST)
RE: AMBER: Error in sysdepend.c?
Shin, John Y CONTRACTOR WRAIR-Wash DC
(Tue Dec 19 2006 - 13:29:12 PST)
AMBER: Volume of ucell too big
Atsutoshi Okabe
(Sat Dec 16 2006 - 00:41:43 PST)
Re: AMBER: Volume of ucell too big
Nicolas Lux Fawzi
(Sat Dec 16 2006 - 10:37:31 PST)
AMBER: How to make a movie with .crd files in VMD?
bertrand russell
(Sat Dec 16 2006 - 02:03:53 PST)
Re: AMBER: How to make a movie with .crd files in VMD?
Carlos Simmerling
(Sat Dec 16 2006 - 05:22:04 PST)
Re: AMBER: How to make a movie with .crd files in VMD?
bertrand russell
(Sat Dec 16 2006 - 09:35:16 PST)
Re: AMBER: How to make a movie with .crd files in VMD?
Chris Moth
(Sat Dec 16 2006 - 10:35:13 PST)
Re: AMBER: How to make a movie with .crd files in VMD?
Carlos Simmerling
(Sat Dec 16 2006 - 10:54:37 PST)
Re: AMBER: How to make a movie with .crd files in VMD?
Nicolas Lux Fawzi
(Sat Dec 16 2006 - 10:32:35 PST)
AMBER: Amber 9 Leap install error
A Box
(Sun Dec 17 2006 - 20:06:52 PST)
Re: AMBER: Amber 9 Leap install error
David A. Case
(Sun Dec 17 2006 - 21:54:56 PST)
AMBER: (no subject)
lily ferreira
(Mon Dec 18 2006 - 00:14:44 PST)
AMBER: Parallelization method
Jordi Camps
(Tue Dec 19 2006 - 10:19:40 PST)
Re: AMBER: Parallelization method
Robert Duke
(Tue Dec 19 2006 - 10:29:09 PST)
Re: AMBER: Parallelization method
Scott Brozell
(Tue Dec 19 2006 - 10:58:07 PST)
AMBER: MM-PBSA
Shozeb Haider
(Mon Dec 18 2006 - 09:57:17 PST)
Re: AMBER: MM-PBSA
Angelo
(Mon Dec 18 2006 - 08:30:00 PST)
AMBER: RESP charge fitting for HFIP
Mingfeng Yang
(Mon Dec 18 2006 - 18:44:19 PST)
Re: AMBER: RESP charge fitting for HFIP
Raviprasad Aduri
(Mon Dec 18 2006 - 19:46:05 PST)
Re: AMBER: RESP charge fitting for HFIP
Mingfeng Yang
(Mon Dec 18 2006 - 23:17:24 PST)
Re: AMBER: RESP charge fitting for HFIP
FyD
(Tue Dec 19 2006 - 23:21:42 PST)
Re: AMBER: RESP charge fitting for HFIP
Mingfeng Yang
(Wed Dec 20 2006 - 10:31:53 PST)
Re: AMBER: RESP charge fitting for HFIP
FyD
(Mon Dec 18 2006 - 23:44:05 PST)
AMBER: sander ntc=2 ntf=1
Nicolas Lux Fawzi
(Mon Dec 18 2006 - 19:10:42 PST)
Re: AMBER: sander ntc=2 ntf=1
Carlos Simmerling
(Tue Dec 19 2006 - 03:39:38 PST)
AMBER: Frozen at Minimization
Steve Seibold
(Tue Dec 19 2006 - 06:18:21 PST)
Re: AMBER: Frozen at Minimization
Chris Moth
(Tue Dec 19 2006 - 07:01:16 PST)
AMBER: Renumber residues in LEAP
Akshay Patny
(Tue Dec 19 2006 - 13:55:57 PST)
Re: AMBER: Renumber residues in LEAP
David A. Case
(Mon Dec 25 2006 - 14:11:34 PST)
AMBER: charge problem in MM-PBSA
linfu
(Tue Dec 19 2006 - 17:53:52 PST)
AMBER: mixing GAFF and CHARMM
Ravinder Abrol
(Tue Dec 19 2006 - 23:09:08 PST)
Re:AMBER: mixing GAFF and CHARMM
曹冉
(Wed Dec 20 2006 - 09:12:05 PST)
Re: AMBER: mixing GAFF and CHARMM
Ravinder Abrol
(Wed Dec 20 2006 - 09:38:23 PST)
RE: AMBER: mixing GAFF and CHARMM
Akshay Patny
(Wed Dec 20 2006 - 09:46:45 PST)
Re: AMBER: mixing GAFF and CHARMM
Christophe Guilbert
(Wed Dec 20 2006 - 11:51:18 PST)
Re: AMBER: mixing GAFF and CHARMM
Ravinder Abrol
(Wed Dec 20 2006 - 16:58:36 PST)
AMBER: Installation help - SGI Altix 350
bertrand russell
(Wed Dec 20 2006 - 02:47:03 PST)
Re: AMBER: Installation help - SGI Altix 350
Gustavo Seabra
(Wed Dec 20 2006 - 07:31:01 PST)
RE: AMBER: Installation help - SGI Altix 350
Ross Walker
(Wed Dec 20 2006 - 08:38:16 PST)
Re: AMBER: Installation help - SGI Altix 350
bertrand russell
(Wed Dec 20 2006 - 20:13:03 PST)
RE: AMBER: Installation help - SGI Altix 350
Ross Walker
(Wed Dec 20 2006 - 20:36:10 PST)
Re: AMBER: Installation help - SGI Altix 350
bertrand russell
(Wed Dec 20 2006 - 21:09:48 PST)
RE: AMBER: Installation help - SGI Altix 350
Ross Walker
(Wed Dec 20 2006 - 21:30:53 PST)
Re: AMBER: Installation help - SGI Altix 350
bertrand russell
(Thu Dec 21 2006 - 21:51:48 PST)
Re: AMBER: Installation help - SGI Altix 350
Gustavo Seabra
(Fri Dec 22 2006 - 17:42:03 PST)
Re: AMBER: Installation help - SGI Altix 350
bertrand russell
(Tue Dec 26 2006 - 00:25:10 PST)
Re: AMBER: Installation help - SGI Altix 350
David A. Case
(Tue Dec 26 2006 - 13:45:54 PST)
AMBER: Amber9 - openmpi?
bertrand russell
(Wed Dec 20 2006 - 03:22:37 PST)
Re: AMBER: Amber9 - openmpi?
Robert Duke
(Wed Dec 20 2006 - 05:23:10 PST)
AMBER: PMEMD and OpenMPI, anyone have config options?
Michael John Hanby
(Wed Dec 27 2006 - 12:04:50 PST)
Re: AMBER: Amber9 - openmpi?
Gustavo Seabra
(Wed Dec 20 2006 - 07:34:53 PST)
Re: AMBER: Amber9 - openmpi?
bertrand russell
(Wed Dec 20 2006 - 20:16:22 PST)
AMBER: MM_PBSA
lily ferreira
(Wed Dec 20 2006 - 05:42:20 PST)
AMBER: MM_PBSA
lily ferreira
(Wed Dec 20 2006 - 05:46:00 PST)
Re: AMBER: MM_PBSA
David A. Case
(Mon Dec 25 2006 - 14:15:26 PST)
AMBER: RED - help with installation / config
Seth Lilavivat
(Wed Dec 20 2006 - 07:18:49 PST)
Re: AMBER: RED - help with installation / config
FyD
(Thu Dec 21 2006 - 01:24:50 PST)
AMBER: Amber Input file from "qout", "resp.dat"
saurabh agrawal
(Thu Dec 21 2006 - 01:41:47 PST)
Re: AMBER: Amber Input file from "qout", "resp.dat"
FyD
(Thu Dec 21 2006 - 02:23:09 PST)
AMBER: RESP procedure for DMPC monomer
Akshay Patny
(Wed Dec 20 2006 - 08:04:00 PST)
Re: AMBER: RESP procedure for DMPC monomer
linfu
(Wed Dec 20 2006 - 16:54:43 PST)
AMBER: Replica exchange rate in REMD
Seongeun Yang
(Thu Dec 21 2006 - 03:42:59 PST)
AMBER: tetrolic acid
Russell Glavey
(Thu Dec 21 2006 - 04:29:35 PST)
AMBER: xleap, generating prep file
Seth Lilavivat
(Thu Dec 21 2006 - 08:49:56 PST)
AMBER: EXTRA_PTS: frtype 2 Should not be here
Kailee
(Thu Dec 21 2006 - 10:26:31 PST)
Re: AMBER: EXTRA_PTS: frtype 2 Should not be here
David A. Case
(Mon Dec 25 2006 - 14:32:11 PST)
AMBER: Sander--NMR refinement
Esther Brugger
(Thu Dec 21 2006 - 20:39:48 PST)
Re: AMBER: Sander--NMR refinement
David A. Case
(Tue Dec 26 2006 - 10:44:46 PST)
AMBER: Compiling Amber8 with Sun HPC ClusterTools 5 Software
Muhammad Naim Mohmad Rouyan
(Thu Dec 21 2006 - 23:40:32 PST)
Re: AMBER: Compiling Amber8 with Sun HPC ClusterTools 5 Software
David A. Case
(Sat Dec 23 2006 - 18:58:29 PST)
AMBER: Nucgen Problem
puneet kacker
(Fri Dec 22 2006 - 00:06:41 PST)
Re: AMBER: Nucgen Problem
Navnit Kumar Mishra
(Fri Dec 22 2006 - 01:55:26 PST)
Re: AMBER: Nucgen Problem
Bill Ross
(Fri Dec 22 2006 - 10:51:25 PST)
AMBER: Problem with LEaP
FyD
(Fri Dec 22 2006 - 11:42:13 PST)
AMBER: A problem with mm_pbsa
vic.mail.nankai.edu.cn
(Mon Dec 25 2006 - 17:41:41 PST)
AMBER: .crd file
bertrand russell
(Tue Dec 26 2006 - 01:16:53 PST)
Re: AMBER: .crd file
Fenghui Fan
(Tue Dec 26 2006 - 08:17:33 PST)
AMBER: bad connectivity
Seth Lilavivat
(Tue Dec 26 2006 - 09:24:17 PST)
Re: AMBER: bad connectivity
Fenghui Fan
(Tue Dec 26 2006 - 09:33:57 PST)
AMBER: bad connectivity - more detail
Seth Lilavivat
(Tue Dec 26 2006 - 10:02:27 PST)
Re: AMBER: bad connectivity - more detail
Fenghui Fan
(Tue Dec 26 2006 - 20:19:41 PST)
Re: AMBER: bad connectivity - more detail
Fenghui Fan
(Tue Dec 26 2006 - 22:25:41 PST)
Re: AMBER: bad connectivity - more detail
Seth Lilavivat
(Wed Dec 27 2006 - 08:26:14 PST)
Re: AMBER: bad connectivity - more detail
David A. Case
(Wed Dec 27 2006 - 08:52:41 PST)
Re: AMBER: bad connectivity - more detail
Seth Lilavivat
(Wed Dec 27 2006 - 09:44:29 PST)
Re: AMBER: bad connectivity - more detail
David A. Case
(Wed Dec 27 2006 - 10:31:58 PST)
Re: AMBER: bad connectivity - more detail
Seth Lilavivat
(Wed Dec 27 2006 - 11:42:42 PST)
Re: AMBER: bad connectivity - more detail
David A. Case
(Fri Dec 29 2006 - 00:15:16 PST)
AMBER: G5 OSX serial compile error
Kevin Kelliher
(Tue Dec 26 2006 - 13:18:56 PST)
Re: AMBER: G5 OSX serial compile error
Mathy Froeyen
(Thu Dec 28 2006 - 03:12:13 PST)
AMBER: Error compiling amber on parallel (MPICH)
Muhammad Naim Mohmad Rouyan
(Tue Dec 26 2006 - 22:35:47 PST)
Re: AMBER: Error compiling amber on parallel (MPICH)
David A. Case
(Wed Dec 27 2006 - 08:41:21 PST)
AMBER: recompiling bondtype.C
Seth Lilavivat
(Wed Dec 27 2006 - 08:49:32 PST)
Re: AMBER: recompiling bondtype.C
David A. Case
(Wed Dec 27 2006 - 10:30:10 PST)
AMBER: chirality.c line 121
Seth Lilavivat
(Wed Dec 27 2006 - 13:43:56 PST)
Re: AMBER: chirality.c line 121
David A. Case
(Wed Dec 27 2006 - 14:46:21 PST)
AMBER: PCA analysis
Jardas sucuriba
(Wed Dec 27 2006 - 21:04:41 PST)
AMBER: tree name generated by tleap is different from the input PREP parameter file
xiaoqin huang
(Thu Dec 28 2006 - 08:48:14 PST)
AMBER: problems trying to modify Amber8
Ed Pate
(Thu Dec 28 2006 - 14:41:33 PST)
AMBER: problems with Calcium ions treatment in GB run
Piotr Cieplak
(Thu Dec 28 2006 - 15:44:23 PST)
Re: AMBER: problems with Calcium ions treatment in GB run
David A. Case
(Thu Dec 28 2006 - 23:56:25 PST)
AMBER: tree name generated by tleap is different from the input PREP parameter file
xiaoqin huang
(Thu Dec 28 2006 - 16:53:39 PST)
AMBER: AMBER complile problem
Chengwen Chen
(Thu Dec 28 2006 - 23:41:21 PST)
Re: AMBER: AMBER complile problem
David A. Case
(Thu Dec 28 2006 - 23:51:49 PST)
AMBER: Simulated Annealing problem...
sai vikram
(Fri Dec 29 2006 - 02:33:50 PST)
Re: AMBER: Simulated Annealing problem...
David A. Case
(Fri Dec 29 2006 - 08:56:06 PST)
Re: AMBER: Simulated Annealing problem...
sai vikram
(Sat Dec 30 2006 - 05:12:53 PST)
Re: AMBER: tree name generated by tleap is different from the input PREP parameter file
Bill Ross
(Fri Dec 29 2006 - 19:00:26 PST)
AMBER: RE: protein simulation using AMBER
Ross Walker
(Fri Dec 29 2006 - 22:51:09 PST)
Last message date
:
Sun Dec 31 2006 - 06:07:50 PST
Archived on
: Fri Apr 26 2024 - 05:53:35 PDT
336 messages
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