Amber Archive Dec 2002 by date

170 messages: Starting Sun Dec 01 2002 - 13:57:13 PST, Ending Tue Dec 31 2002 - 13:51:31 PST
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Sunday, 1 December 2002
- RE: solvateOct Kristina Furse
Monday, 2 December 2002
- carnal amber 7.0 Vlad Cojocaru
- combinig two trajectory files. Yongjun Jiang
- Re: combinig two trajectory files. Carlos Simmerling
- Re: combinig two trajectory files. Pascal Bonnet
- Re: solvateOct David A. Case
- err in specifying disulphide bridge using xleap! A.Madhumalar
- LEAP - Introducing dummy atoms Miguel de Federico
- Re: err in specifying disulphide bridge using xleap! David A. Case
- penalty function in NMR refinement Mahadevan Seetharaman
- Re: err in specifying disulphide bridge using xleap! James W. Caldwell
- Re: LEAP - Introducing dummy atoms James W. Caldwell
Tuesday, 3 December 2002
- Biphasic box (fwd) amber_at_heimdal.compchem.ucsf.edu
- test mail Jim Caldwell
- freeware for RNA modeling on Linux (fwd) amber_at_heimdal.compchem.ucsf.edu
- Re: CCL:freeware for RNA modeling on Linux (fwd) amber_at_heimdal.compchem.ucsf.edu
- Constraints in Amber (fwd) amber_at_heimdal.compchem.ucsf.edu
- gB vs. explicit (fwd) amber_at_heimdal.compchem.ucsf.edu
- Amber Trajectories + VMD (fwd) amber_at_heimdal.compchem.ucsf.edu
- Energy decomposition with ANAL (fwd) amber_at_heimdal.compchem.ucsf.edu
- Reflector problems amber_at_heimdal.compchem.ucsf.edu
- Re: Biphasic box David A. Case
- Re: freeware for RNA modeling on Linux (fwd) David A. Case
- Re: Biphasic box (fwd) James W. Caldwell
- Re: Constraints in Amber David A. Case
- RE: Amber Trajectories + VMD (fwd) Nicholson, James D Mr ARO
- Re: corrupted trajectory Shixiang Yan
- increasing the number of processors Ioana Cozmuta
- increasing the number of processors (fwd) Ioana Cozmuta
- Re: corrupted trajectory CUI, Guanglei
Wednesday, 4 December 2002
- Re: Biphasic box Gemma Kinsella
- Re: gB vs. explicit David A. Case
- Re: Energy decomposition with ANAL (fwd) David A. Case
- restrained MD Vlad Cojocaru
- DIANA like files Vlad Cojocaru
- Amber 7 bugfix 27 !! urgent William Wei
- Re: Amber 7 bugfix 27 !! urgent Holger Gohlke
- MDaemon Warning - Virus Found postmaster_at_bydnet.com.pl
Thursday, 5 December 2002
- bug fixes Filip Lankas
- not compiled with -DHAS_10_12!! William Wei
- Re: bug fixes David A. Case
- Re: not compiled with -DHAS_10_12!! Sarah Tschampel
- Re: not compiled with -DHAS_10_12!! Carlos Simmerling
- md failure: deep energetics problem eric hu
- About counterions Andrei Leit�o
- Re: Cap-atom-pointer in GIBBS James W. Caldwell
- Re: About counterions David A. Case
- Cap-atom-pointer in GIBBS Jose Ramon Blas
- Re: md failure: deep energetics problem David A. Case
- ptraj rmsd calculation Thomas Steinbrecher
- Overwrite files Joffre Heredia
- Re: Overwrite files Long Hai
- Re: Overwrite files Scott Brozell
- RE: Overwrite files Yong Duan
Friday, 6 December 2002
- timings? Arvid Soederhaell
- positional restraints Vlad Cojocaru
- Re: timings? David A. Case
- Re: positional restraints David A. Case
- Re: Energy decomposition with ANAL Numan Oezguen
- Re: Energy decomposition with ANAL Natasja Brooijmans
- default GB radii Robert G. Endres
- Re: default GB radii David A. Case
- carnal Ioana Cozmuta
- Re: carnal Bill Ross
Saturday, 7 December 2002
- Re: default GB radii Andreas Svrcek-Seiler
- (no subject) Jennifer Hawkings
- CHARMm NPT input files Mahadevan Seetharaman
Monday, 9 December 2002
- NMR restrains Marcela Madrid
- running sander_classic for amber6 using different version of mpi Asif Rahaman
- difference in energy in amber6 and amber7 Prabal Maiti
Tuesday, 10 December 2002
- Question to perturbation charge meiselba
- Re: FEP/Gibbs question Lepsa
- dual H-bonding of bridging waters - CARNAL Michael Ford
- bad protein structure eric hu
Wednesday, 11 December 2002
- Re: difference in energy in amber6 and amber7 David A. Case
- Fw: Charges derivation question! Lepsa
- Re: CCL:Amber7 and partial charges David Case
- MM-PBSA: .crg file for Delphi Thomas Steinbrecher
- Re: MM-PBSA: .crg file for Delphi Holger Gohlke
- Question on 2 stage RESP fit Ambarish Nag
Thursday, 12 December 2002
- Fw: Fw: Charges derivation question! Lepsa
- Re: Question on 2 stage RESP fit M. L. Dodson
- Business Cooperation (Inheritance Claim) Mr. Daniel Osondu
- Amber 7 MM-PBSA for Amber 6 trajectories Qing Zhang
- ambpdb Vlad Cojocaru
- Re: ambpdb Holger Gohlke
Friday, 13 December 2002
- Business Cooperation (Inheritance Claim) Mr. Daniel Osondu
- GIBBS - end-of-file during read Miguel de Federico
- plotting electrostatic potential surface Ioana Cozmuta
- Re: ambpdb David A. Case
Saturday, 14 December 2002
- solvating a protein with large cavity Tom Bishop
- Re: solvating a protein with large cavity M. L. Dodson
- FEP/Gibbs question to valine alanine tutorial meiselba
- Re: Amber 7 MM-PBSA for Amber 6 trajectories David A. Case
- a question about force field in AMBER jzhou
- Re: a question about force field in AMBER sychen
Monday, 16 December 2002
- disulfide bond link between two chains pu xuemei
- Fw: Valine to alanine Gibbs tutorial Lepsa
- Re: disulfide bond link between two chains Natasja Brooijmans
- Re: Energy decomposition with ANAL Numan Oezguen
- Re: a question about force field in AMBER David A. Case
- Re: freeware for RNA modeling on Linux (fwd) Joerg-Gerald Siebers
- sander (CAP) chokes on efc (Itanium2/Linux) Tadashi Takemori
Tuesday, 17 December 2002
- RST file for nonstandard residue vannajan_at_chiangmai.ac.th
- GIBBS - Routine TORCON (internal constraints) failed Miguel de Federico
- Re: freeware for RNA modeling on Linux (fwd) James W. Caldwell
- Chains, LEaP and ambpdb Luis Gracia
- Re: Chains, LEaP and ambpdb Ioana Cozmuta
- Re: Chains, LEaP and ambpdb David A. Case
- Re: Chains, LEaP and ambpdb Luis Gracia
- RE: sander (CAP) chokes on efc (Itanium2/Linux) Karen Haskell
- water box, Ioana Cozmuta
- solvatebox Luis Gracia
- Re: Chains, LEaP and ambpdb David A. Case
- amber trajectory Ioana Cozmuta
- message during minimization Ioana Cozmuta
- Studying in Australia John Pritchard
Wednesday, 18 December 2002
- Re: sander (CAP) chokes on efc (Itanium2/Linux) Tadashi Takemori
- Re: Resp Multiconformational charge fitting! Pascal Bonnet
- Re: water box, Carlos Simmerling
- SUMMARY: solvating a protein with large cavity Tom Bishop
- MPI_BCAST error Nathan A. Baker
- Re: solvatebox Luis Gracia
- Re: message during minimization darden
- Re: water box, darden
- off-to-mol2 Anke Eisenmann
- mm_pbsa error message! William Wei
- Re: mm_pbsa error message! Michael Ford
- Re: off-to-mol2 David A. Case
- About heating... Andrei Leit�o
- antechamber Carsten Detering
- Re: About heating... David A. Case
- Re: SUMMARY: solvating a protein with large cavity Richard Henchman
- roar-cp problems M. L. Dodson
- Re: MPI_BCAST error Scott Brozell
- antechamber Carsten Detering
- Re: message during minimization Ioana Cozmuta
- atomicfluct in ptraj Kristina Furse
- Re: water box, Ioana Cozmuta
- Re: water box, David A. Case
- Re: message during minimization darden
- Re: water box, darden
- Re: SUMMARY: solvating a protein with large cavity Ioana Cozmuta
- Re: MPI_BCAST error Nathan A. Baker
- water/nonTIP3P Ioana Cozmuta
- Re: message during minimization Ioana Cozmuta
- Re: water/nonTIP3P Ioana Cozmuta
Thursday, 19 December 2002
- ntwv saves v(t) or v(t+dt/2) ? hagop demirdjian
- Re: message during minimization David A. Case
- Re: ntwv saves v(t) or v(t+dt/2) ? David A. Case
- Re: atomicfluct in ptraj David A. Case
- chirality.c failure - diagnosis, but no cure... Michael Ford
- RE: atomicfluct in ptraj Kristina Furse
- RESTARTED DUE TO LINMIN FAILURE William Wei
- Nmode Pratul Agarwal
- Re: RESTARTED DUE TO LINMIN FAILURE Natasja Brooijmans
- Re: Nmode James Caldwell
- Re: chirality.c failure - diagnosis, but no cure... Michael Ford
Friday, 20 December 2002
- selection of residues Ioana Cozmuta
Sunday, 22 December 2002
- cap option Ioana Cozmuta
- beginners question dynamic group
Thursday, 26 December 2002
- targeted MD sample eric hu
Friday, 27 December 2002
- Molecular dynamic protocol... Andrei Leit�o
- Re: Molecular dynamic protocol... David A. Case
Saturday, 28 December 2002
- cannot deal with large trajectory? yuann
Sunday, 29 December 2002
- Trajectory file converted in pdb file Yongjun Jiang
Monday, 30 December 2002
- Sander rfree error kxg2248_at_njit.edu
- Re: Sander rfree error James Caldwell
- Re: cannot deal with large trajectory? yuann
Tuesday, 31 December 2002
- new on the Amber web pages... David A. Case

Last message date: Tue Dec 31 2002 - 13:51:31 PST
Archived on: Fri Nov 22 2024 - 05:53:16 PST