Amber Archive Dec 2005: by date

Wednesday, 30 November 2005
- AMBER: Fluorine in MM-PBSA (AMBER8) yuann.bioinfo.ndhu.edu.tw
- Re: AMBER: Fluorine in MM-PBSA (AMBER8) sychen
- Re: AMBER: MM-PBSA: plot the "Ggas+Gsol" vs time Holger Gohlke
Thursday, 1 December 2005
- AMBER: Creating an Ester with Antechamber/Gaff John O'Mahony
- AMBER: regarding ambpdb S.Sundar Raman
- Re: AMBER: regarding ambpdb Ilyas Yildirim
- Re: AMBER: regarding ambpdb S.Sundar Raman
- Re: AMBER: regarding ambpdb Carlos Simmerling
- Re: AMBER: Residual Dipolar Refinement David A. Case
- AMBER: MD without a thermostat Vlad Cojocaru
- AMBER: no thermostat versus very weak thermostat Vlad Cojocaru
- AMBER: Some explanations of MM_PBSA .DECOMP OUTPUT file? Peng Tao
- AMBER: Mg2+ issues of using MM-PB/GBSA mingche Pan
- Re: AMBER: Mg2+ issues of using MM-PB/GBSA Carlos Simmerling
- Re: AMBER: MD without a thermostat David A. Case
- AMBER: Radial Distribution functions by ptraj Priti Hansia
- Re: AMBER: Mg2+ issues of using MM-PB/GBSA David A. Case
- AMBER: Position restraints and Models Steve Seibold
- AMBER: Questions about MM-PBSA in Amber8 zgleo
- Re: AMBER: Mg2+ issues of using MM-PB/GBSA Thomas Cheatham
Friday, 2 December 2005
- AMBER: Problem in running AMBER 7 in solaris ! Pradipta Bandyopadhyay
- Re: AMBER: Problem in running AMBER 7 in solaris ! Atro Tossavainen
- AMBER: Problem with sander test suites in solaris ! Pradipta Bandyopadhyay
- Re: AMBER: Mg2+ issues of using MM-PB/GBSA mingche Pan
- AMBER: ptraj crash error Simon Whitehead
- Re: AMBER: Mg2+ issues of using MM-PB/GBSA mingche Pan
- Re: AMBER: ptraj crash error David E. Konerding
- AMBER: rotational motion in periodic simulation Douali, Latifa
- Re: AMBER: Mg2+ issues of using MM-PB/GBSA mingche Pan
- AMBER: Replica-Exchange MD from AMBER8! Peng Tao
- Re: AMBER: Replica-Exchange MD from AMBER8! Carlos Simmerling
- AMBER: ERROR in readParm: ...failed to find BONDS_WITHOUT_HYDROGEN Rhoad, Jonathan S.
- Re: AMBER: rotational motion in periodic simulation David A. Case
- Re: AMBER: Using OPLS atom types David A. Case
- Re: AMBER: Creating an Ester with Antechamber/Gaff David A. Case
- AMBER: parmchk bug fix David A. Case
- AMBER: parmchk bug fix, with attachment David A. Case
Saturday, 3 December 2005
- AMBER: Alignment tensor and Interia tensor RadhaKumari Yadav
- Re: AMBER: Replica-Exchange MD from AMBER8! Peng Tao
- Re: AMBER: Using OPLS atom types Bill Ross
- Re: AMBER: Alignment tensor and Interia tensor David A. Case
- Re: AMBER: Replica-Exchange MD from AMBER8! Peng Tao
- Re: AMBER: Replica-Exchange MD from AMBER8! Carlos Simmerling
Sunday, 4 December 2005
- AMBER: The error during calculating PB with pbsa zhli_2000.126.com
- Re: AMBER: The error during calculating PB with pbsa Ray Luo
Monday, 5 December 2005
- AMBER: RMSD Calculations Kara Di Giorgio
- Re: AMBER: RMSD Calculations Carlos Simmerling
- Re: AMBER: RMSD Calculations Kara Wald
- Re: AMBER: RMSD Calculations Carlos Simmerling
- Re: AMBER: RMSD Calculations kkirschn.hamilton.edu
- AMBER: RESP: Question Carlos Jaime
- Re: AMBER: RESP: Question Piotr Cieplak
- Re: AMBER: Mg2+ issues of using MM-PB/GBSA. . Don.Bashford.stjude.org
- Re: AMBER: RESP: Question FyD
- Re: AMBER: RMSD Calculations Thomas Cheatham
Tuesday, 6 December 2005
- Re[2]: AMBER: What does a crash mean while running a md simulation? sychen
- Re: AMBER: RESP: Question FyD
- AMBER: 6-thioguanine E.A.Moore
- AMBER: MM_PBSA parameters Nelson Fonseca
- RE: Re[2]: AMBER: What does a crash mean while running a md simulation? Ross Walker
Wednesday, 7 December 2005
- AMBER: hi Germán Sciaini
- AMBER: about resp JAVIER PEREZ
- Re:AMBER: about resp Kateryna Miroshnychenko
- AMBER: Relax in tLEaP ? FyD
- AMBER: AMBER vs QM: base pairing and stacking Jiri Sponer
- AMBER: Clustering - MMTSB Toolkit kclust kkirschn.hamilton.edu
- Re: AMBER: hi David A. Case
- Re: AMBER: Relax in tLEaP ? David A. Case
- Re: AMBER: Clustering - MMTSB Toolkit kclust Adrian Roitberg
- AMBER: Adding/recognizing calcium atoms Nitin Bhardwaj
- Re: AMBER: Adding/recognizing calcium atoms Bill Ross
Thursday, 8 December 2005
- AMBER: error about using ambmask zhli_2000.126.com
- Re: AMBER: error about using ambmask Viktor Hornak
Friday, 9 December 2005
- AMBER: Question on makeing up of missing atoms Benjamin Juhl
- Re: AMBER: Question on makeing up of missing atoms Carlos Simmerling
Monday, 12 December 2005
- AMBER: reading frcmod torsional parameters ivan.mmb.pcb.ub.es
- Re: AMBER: reading frcmod torsional parameters David A. Case
- AMBER: question about mmpbsa cui wei
- Re: AMBER: question about mmpbsa Ray Luo
Tuesday, 13 December 2005
- Re: AMBER: reading frcmod torsional parameters ivan.mmb.pcb.ub.es
- Re: AMBER: question about mmpbsa cui wei
Wednesday, 14 December 2005
- AMBER: How to add water to calculate MMPBSA Kitiyaporn Wittayanarakul
- Re: AMBER: How to add water to calculate MMPBSA David A. Case
- AMBER: E of amber calculations YoungJin Cho
- AMBER: nmode error: GNORM is greater than the requested maximum zhli_2000.126.com
- AMBER: error with compiling amber8 with lam on intel pc clusters Ye Mei
- AMBER: about antechamber(amber8) linfu
- Re: AMBER: error with compiling amber8 with lam on intel pc clusters Xuebin Qiao
Thursday, 15 December 2005
- AMBER: aniso and iso Yam
- Re: AMBER: E of amber calculations Carlos Simmerling
- AMBER: parameters for fluorine atom Morena Spreafico
- Re: AMBER: about antechamber(amber8) Carlos Simmerling
- Re: AMBER: parameters for fluorine atom Carlos Simmerling
- AMBER: Build for single precision David Caliga
- RE: AMBER: about antechamber(amber8) Junmei Wang
- RE: AMBER: error with compiling amber8 with lam on intel pc clusters Ross Walker
- Re: AMBER: Build for single precision Robert Duke
- RE: AMBER: E of amber calculations Ross Walker
- Re: AMBER: aniso and iso David A. Case
- RE: AMBER: Build for single precision Ross Walker
- Re: AMBER: How to add water to calculate MMPBSA. . Don.Bashford.stjude.org
- Re: AMBER: question about mmpbsa Ray Luo
- Re: AMBER: How to add water to calculate MMPBSA. . Thomas Cheatham
- AMBER: parallel AMBER on cluster Kateryna Miroshnychenko
- Re: AMBER: parallel AMBER on cluster Robert Duke
- RE: AMBER: parallel AMBER on cluster Ross Walker
- Re: AMBER: parallel AMBER on cluster Carlos Simmerling
- AMBER: | ERROR: Could not read coords from rst file Jiapu.Zhang.csiro.au
- Re: AMBER: | ERROR: Could not read coords from rst file Robert Duke
Friday, 16 December 2005
- AMBER: installation on a dual core Barbault Florent
- Re: AMBER: installation on a dual core Nelson Fonseca
- Re: AMBER: nmode error: GNORM is greater than the requested maximum David A. Case
- AMBER: About Salt concentration Varsha Goyal
- Re: AMBER: About Salt concentration Jiri Sponer
- Re: AMBER: About Salt concentration Varsha Goyal
Saturday, 17 December 2005
- AMBER: distance restraints Ed Pate
- Re: AMBER: distance restraints Carlos Simmerling
- AMBER: | ERROR: Could not read coords from *.rst Jiapu.Zhang.csiro.au
Sunday, 18 December 2005
- AMBER: No exchange among replicas in REMD! Peng Tao
- AMBER: No exchange among replicas in REMD! Peng Tao
- Re: AMBER: No exchange among replicas in REMD! Carlos Simmerling
- Re: AMBER: No exchange among replicas in REMD! Carlos Simmerling
- Re: AMBER: No exchange among replicas in REMD! Adrian E. Roitberg
- Re: AMBER: No exchange among replicas in REMD! Peng Tao
- Re: AMBER: No exchange among replicas in REMD! Carlos Simmerling
- Re: AMBER: No exchange among replicas in REMD! Carlos Simmerling
Monday, 19 December 2005
- Re: AMBER: aniso and iso Yam
- AMBER: a quistion about compile cui wei
- Re: AMBER: aniso and iso Carlos Simmerling
- AMBER: MD problems (SHAKE) blakrose.gazeta.pl
- AMBER: Atoms restrain Angelo Pugliese
- Re: AMBER: No exchange among replicas in REMD! Peng Tao
- AMBER: compiling leap with Xeon EM64 (suse linux 9.2) HL Eastwood
- AMBER: re: leap compilation problems xeon EM64 processor HL Eastwood
- Re: AMBER: Atoms restrain David A. Case
- Re: AMBER: a quistion about compile David A. Case
- Re: AMBER: No exchange among replicas in REMD! Carlos Simmerling
- Re: AMBER: a quistion about compile Wei Zhang
- Re: AMBER: No exchange among replicas in REMD! Peng Tao
- AMBER: MD problems/shake blakrose.gazeta.pl
- Re: AMBER: MD problems/shake Thomas E. Cheatham, III
- Re: AMBER: MD problems/shake Bill Ross
- Re: AMBER: MD problems/shake blakrose.gazeta.pl
- AMBER: rdc multiple tensors dmcelh.uchicago.edu
- Re: AMBER: MD problems/shake Bill Ross
- Re: AMBER: MD problems/shake blakrose.gazeta.pl
- Re: AMBER: MD problems/shake Thomas E. Cheatham, III
- Re: AMBER: MD problems/shake blakrose.gazeta.pl
- Re: AMBER: MD problems/shake Bill Ross
- Re: AMBER: MD problems/shake Bill Ross
- Re: AMBER: MD problems/shake blakrose.gazeta.pl
- Re: AMBER: MD problems/shake blakrose.gazeta.pl
- AMBER: Ligand problem bybaker.itsa.ucsf.edu
- Re: AMBER: a quistion about compile cui wei
- Re: AMBER: Ligand problem blakrose.gazeta.pl
- Re: AMBER: a quistion about compile cui wei
- Re: AMBER: Ligand problem Suxin Zheng
Tuesday, 20 December 2005
- Re: AMBER: a quistion about compile snowyowls
- AMBER: Sander.LES questions Bing Liu
- Re: AMBER: Sander.LES questions Carlos Simmerling
- AMBER: rmsd Anthony Cruz
- Re: AMBER: a quistion about compile Wei Zhang
- Re: AMBER: a quistion about compile David A. Case
- Fwd: AMBER: rdc multiple tensors dmcelh.uchicago.edu
- AMBER: Re: Ligand problem bybaker.itsa.ucsf.edu
- Re: AMBER: MD problems/shake Thomas E. Cheatham, III
- Re: AMBER: MD problems/shake-many thanks blakrose.gazeta.pl
- Re: AMBER: MD problems/shake blakrose.gazeta.pl
- Re: AMBER: Re: Ligand problem Ilyas Yildirim
- AMBER: some questions about nmode zhli_2000.126.com
Wednesday, 21 December 2005
- Re: AMBER: a quistion about compile snowyowls
- AMBER: No skew or curtosis when zero variance in moment Ye Mei
- Re: AMBER: a quistion about compile David A. Case
- RE: AMBER: About Salt concentration David Cowburn
- AMBER: lib-4324 : UNRECOVERABLE library error lv haiting
- Re: AMBER: lib-4324 : UNRECOVERABLE library error Thomas Cheatham
- Re: AMBER: lib-4324 : UNRECOVERABLE library error lv haiting
- Re: AMBER: antechamber problem bybaker.itsa.ucsf.edu
- AMBER: Amber crashes at simulation in the NVT ensemble with the periodic box equiilbrated in the NPT ensemble. Sergey Krishtal
Thursday, 22 December 2005
- AMBER: Merry Xmas Angelo Pugliese
- Re: AMBER: No skew or curtosis when zero variance in moment David A. Case
- AMBER: increase the limit of restraintmask Sichun Yang
- Re: AMBER: Amber crashes at simulation in the NVT ensemble with the periodic box equiilbrated in the NPT ensemble. David A. Case
- RE: AMBER: does the result of H bond is consistent with the ?Eele of MM_PBSA? Yong Duan
- RE: AMBER: the averaged structure VS the specific snapshot Yong Duan
- AMBER: does the result of H bond is consistent with the ∆Eele of MM_PBSA? haixiao jin
Friday, 23 December 2005
- Re: AMBER: a quistion about compile snowyowls
- Re: AMBER: does the result of H bond is consistent with the ?Eele of MM_PBSA? cristian obiol
- AMBER: ERROR in readParm: ...failed to find ANGLES_INC_HYDROGEN Priti Hansia
Thursday, 22 December 2005
- AMBER: the averaged structure VS the specific snapshot haixiao jin
Friday, 23 December 2005
- AMBER: ambpdb TER problems Sam
- AMBER: To post or mail to the list (subscribers only) ping jiang
- AMBER: (no subject) ping jiang
- Re: AMBER: (no subject) Thomas Cheatham
- Re: AMBER: (no subject) David A. Case
- Re: AMBER: ambpdb TER problems David A. Case
- Re: AMBER: (no subject) ping jiang
Monday, 26 December 2005
- AMBER: problem with improper torsions in parmchk Kateryna Miroshnychenko
- Re: AMBER: ambpdb TER problems samuel.arey.epfl.ch
- AMBER: building amino acid based surfactants? Eugene Billiot
- Re: AMBER: ambpdb TER problems Bill Ross
- Re: AMBER: building amino acid based surfactants? David A. Case
- Re: AMBER: ambpdb TER problems David A. Case
Tuesday, 27 December 2005
- Re: AMBER: ERROR in readParm: ...failed to find ANGLES_INC_HYDROGEN David A. Case
- Re: AMBER: ambpdb TER problems Sam
- Re: AMBER: ERROR in readParm: ...failed to find ANGLES_INC_HYDROGEN Priti Hansia
- AMBER: distance restraint simulation Ed Pate
- Re: AMBER: ERROR in readParm: ...failed to find ANGLES_INC_HYDROGEN David A. Case
- AMBER: problem with ssh and xleap A D
- Re: AMBER: distance restraint simulation David A. Case
- Re: AMBER: ambpdb TER problems David A. Case
- AMBER: problem of calculate the charge ping jiang
- AMBER: problem of calculate the charge2 ping jiang
Wednesday, 28 December 2005
- Re: AMBER: ERROR in readParm: ...failed to find ANGLES_INC_HYDROGEN Priti Hansia
- Re: AMBER: ambpdb TER problems Sam
- Re: AMBER: problem with ssh and xleap Scott Brozell
- AMBER: Question about partial charge for ligand molecules Woojin Lee
- AMBER: non bond over flow S.Sundar Raman
Thursday, 29 December 2005
- RE: AMBER: non bond over flow Ross Walker
- AMBER:how to deal with metal ion? snowyowls
Friday, 30 December 2005
- Re: AMBER:how to deal with metal ion? samuel.arey.epfl.ch
- Re: AMBER:how to deal with metal ion? samuel.arey.epfl.ch
- Re: AMBER:how to deal with metal ion? Tim Meyer
- Re: AMBER:how to deal with metal ion? Tim Meyer
- Re: AMBER: problem of calculate the charge David A. Case
- Re: AMBER: ambpdb TER problems David A. Case
- Re: AMBER: problem of calculate the charge ping jiang
- Re: AMBER: antechamber problem Ilyas Yildirim
- Re: AMBER: problem with ssh and xleap A D
Saturday, 31 December 2005
- AMBER: Installation of AMBER8 on a PC with a Pentium EE type CPU Cenk Andac

Last message date: Wed Jan 04 2006 - 18:17:07 PST
Archived on: Fri Nov 22 2024 - 05:53:27 PST

Amber Archive Dec 2005 by date