Amber Archive Nov 2003: by date

Monday, 3 November 2003
- AMBER: Freezing of water with TIP3P potential. Mahesh Chandran
- AMBER: question about input files for small molecule with fluorine aini.rwja.umdnj.edu
- Re: AMBER: question about input files for small molecule with fluorine Carlos Simmerling
- Re: AMBER: PMEMD 3.1 Release - High Scalability Update to PMEMD David E. Konerding
- AMBER: distrance restraints for alpha carbons Sheldon Holder
- Re: AMBER: PMEMD 3.1 Release - High Scalability Update to PMEMD Robert Duke
- Re: AMBER: distrance restraints for alpha carbons Sheldon Holder
Tuesday, 4 November 2003
- AMBER: Restart a simulation Frederico.Miranda.ibmb.uib.no
Monday, 3 November 2003
- Re: AMBER: distrance restraints for alpha carbons David A. Case
- Re: AMBER: make clean doesn't clean leap Karen Haskell
- AMBER: MD Equil Chenglong Li
- Re: AMBER: MD Equil David A. Case
- AMBER: make clean doesn't clean leap Karen Haskell
Tuesday, 4 November 2003
- AMBER: atomtypenumber Rajendra P. OJHA
- AMBER: RESP fitting limit? yuann
- RE: AMBER: make clean doesn't clean leap Ming Lei
- Re: AMBER: large file for carnal Bill Ross
- Re: AMBER: large file for carnal Bill Ross
Monday, 3 November 2003
- Re: AMBER: make clean doesn't clean leap David A. Case
Wednesday, 5 November 2003
- AMBER: How to estimate SD of the delta delta G between two mm_pbsa runs Zheng Suxin
- AMBER: absolute vs. relative binding free energy Qing Zhang
- Re: AMBER: absolute vs. relative binding free energy David A. Case
- AMBER: shake constraint on all bonds Jian Zhang, Dr
- RE: AMBER: shake constraint on all bonds Yong Duan
- Re: AMBER: How to estimate SD of the delta delta G between two mm_pbsa runs Holger Gohlke
Thursday, 6 November 2003
- AMBER: parmchk on MAC Kaushik Raha
- AMBER: handling non neutral systems hagop demirdjian
- AMBER: Restraints Steve Seibold
- Re: AMBER: Restraints David A. Case
- AMBER: Can use mm_pbsa_statistics.pl to calculate each snapshot's Delta Delta G, then give the SD Zheng Suxin
Friday, 7 November 2003
- Re: AMBER: Can use mm_pbsa_statistics.pl to calculate each snapshot's Delta Delta G, then give the SD Holger Gohlke
- AMBER: fix some area Helios Chen
- Re: AMBER: fix some area Carlos Simmerling
- AMBER: restrain Vlad Cojocaru
- Re: AMBER: restrain David A. Case
- RE: AMBER: infinitely long DNA (to Yong Duan) Endres, Robert G.
- Re: AMBER: infinitely long DNA (to Yong Duan) bishop
- RE: AMBER: infinitely long DNA (to Yong Duan) Yong Duan
Saturday, 8 November 2003
- AMBER: mpich problem Qiang Lu
- AMBER: mpich problem Qiang Lu
- Re: AMBER: mpich problem David E. Konerding
Sunday, 9 November 2003
- Re[2]: AMBER: mpich problem Qiang Lu
- Re[3]: AMBER: mpich problem Qiang Lu
- Re: AMBER: mpich problem Viktor Hornak
- RE: AMBER: mpich problem Yong Duan
- Re: AMBER: fix some area Helios Chen
- Re[2]: AMBER: mpich problem Qiang Lu
- Re[2]: AMBER: mpich problem Qiang Lu
- Re: AMBER: fix some area Carlos Simmerling
- AMBER: a problem with antechamber and leap Ye Mei
- Re: AMBER: a problem with antechamber and leap David A. Case
Monday, 10 November 2003
- Re: Re: AMBER: a problem with antechamber and leap Ye Mei
- AMBER: mgbjsb radii in GBSA Giulio Rastelli
- AMBER: AM1-BCC in Amber7 Joey Harriman
- Re: AMBER: AM1-BCC in Amber7 Ye Mei
- Re: AMBER: AM1-BCC in Amber7 Joey Harriman
- Re: AMBER: mgbjsb radii in GBSA David A. Case
- Re: AMBER: AM1-BCC in Amber7 David A. Case
- Re: AMBER: mgbjsb radii in GBSA Giulio Rastelli
- AMBER: change force constants Obdulia Rabal
- AMBER: Re: AM1-BCC in Amber7 Rhonda Torres
- Re[2]: AMBER: mpich problem Qiang Lu
- Re: AMBER: change force constants David A. Case
Tuesday, 11 November 2003
- AMBER: restraints and reordering water Vlad Cojocaru
- AMBER: Protein Rotation Frederico.Miranda.ibmb.uib.no
- Re: AMBER: Protein Rotation Carlos Simmerling
- Re: AMBER: Protein Rotation Frederico.Miranda.ibmb.uib.no
- Re: AMBER: Protein Rotation Carlos Simmerling
- Re: AMBER: Protein Rotation Bill Ross
- Re: AMBER: RMSd per residue Bill Ross
- Re: AMBER: Protein Rotation Bill Ross
- Re: AMBER: restraints and reordering water David A. Case
- AMBER: GB/SA Yichen Cao
Wednesday, 12 November 2003
- Re: AMBER: GB/SA Chris Moth
Tuesday, 11 November 2003
- Re: AMBER: GB/SA Holger Gohlke
- Re: AMBER: AM1-BCC in Amber7 Junmei Wang
- Re: AMBER: mgbjsb radii in GBSA Junmei Wang
- Re: Re: AMBER: a problem with antechamber and leap Junmei Wang
- Re: Re: AMBER: a problem with antechamber and leap Junmei Wang
- Re: Re: AMBER: a problem with antechamber and leap David A. Case
- AMBER: Separation of a Water molecules nabe
- Re: AMBER: Separation of a Water molecules Carlos Simmerling
- Re: AMBER: Separation of a Water molecules Thomas E. Cheatham, III
Wednesday, 12 November 2003
- Re: AMBER: Separation of a Water molecules nabe
- Re: Re: Re: AMBER: a problem with antechamber and leap Ye Mei
- Re: AMBER: Correction [Separation of a Water molecules] nabe
- Re: AMBER: Separation of a Water molecules Carlos Simmerling
- AMBER: antechamber mopac7 parameters Joey Harriman
- AMBER: average coordinates Frederico.Miranda.ibmb.uib.no
- Re: AMBER: average coordinates Bill Ross
- Re: AMBER: average coordinates Bill Ross
- AMBER: about some of the cards in Sander 7 Pingna Xu
- Re: AMBER: about some of the cards in Sander 7 Rhonda Torres
- Re: AMBER: about some of the cards in Sander 7 Vlad Cojocaru
- Re: Re: AMBER: a problem with antechamber and leap Junmei Wang
- Re: Re: Re: AMBER: a problem with antechamber and leap Junmei Wang
- Re: AMBER: Separation of a Water molecules nabe
- Re: AMBER: Separation of a Water molecules Thomas E. Cheatham, III
- Re: AMBER: Separation of a Water molecules Dr. Yong Duan
- Re: Re: Re: Re: AMBER: a problem with antechamber and leap Ye Mei
Thursday, 13 November 2003
- AMBER: atmtypenumbers for halogens Thomas.Fox.bc.boehringer-ingelheim.com
- AMBER: ndfmin in belly runs John
- AMBER: RNA and Protein questions (also some general questions) a b
- Re: AMBER: RNA and Protein questions (also some general questions) Balvinder Singh
- AMBER: GIBBS - PMF problem: Lambda has not changed Jiri Matousek
- Re: AMBER: Separation of a Water molecules Carlos Simmerling
- Re: AMBER: RNA and Protein questions (also some general questions) Dr. Yong Duan
- Re: AMBER: GIBBS - PMF problem: Lambda has not changed David Smith
- Re: AMBER: ndfmin in belly runs David A. Case
- AMBER: high temperature, 498K, unfolding simulations james tomomi macdonald
- AMBER: Nmode Problem Yuqin Cai
- Re: AMBER: RNA and Protein questions (also some general questions) FyD
- Re: AMBER: high temperature, 498K, unfolding simulations Andreas Svrcek-Seiler
- Re: AMBER: GIBBS - PMF problem: Lambda has not changed Jiri Matousek
- Re: AMBER: RNA and Protein questions (also some general questions) Piotr Cieplak
- Re: AMBER: Nmode Problem Holger Gohlke
- AMBER: water prep file needed Youyi Peng
- AMBER: Any correct way to image a molecule ? Teletchéa Stéphane
- Re: AMBER: water prep file needed David A. Case
- Re: AMBER: Any correct way to image a molecule ? Thomas E. Cheatham, III
- Re: AMBER: Any correct way to image a molecule ? Teletchéa Stéphane
- Re: AMBER: Any correct way to image a molecule ? Carlos Simmerling
Friday, 14 November 2003
- Re: AMBER: atmtypenumbers for halogens Giulio Rastelli
- Re: AMBER: Any correct way to image a molecule ? Teletchéa Stéphane
- Re: AMBER: Any correct way to image a molecule ? Carlos Simmerling
- Re: AMBER: GIBBS - PMF problem: Lambda has not changed David Smith
- AMBER: Problems restarting with sander raist.mmb.pcb.ub.es
- AMBER: rotation removal in sander GB Mu Yuguang (Dr)
- Re: AMBER: Problems restarting with sander David A. Case
- Re: AMBER: rotation removal in sander GB David A. Case
- Re: AMBER: Problems restarting with sander raist.mmb.pcb.ub.es
- AMBER: update of BOX dim. Endres, Robert G.
- RE: AMBER: update of BOX dim. Endres, Robert G.
Saturday, 15 November 2003
- AMBER: sander lastist Frederico.Miranda.ibmb.uib.no
- Re: AMBER: mgbjsb radii in GBSA Giulio Rastelli
- Re: AMBER: sander lastist David A. Case
- Re: AMBER: mgbjsb radii in GBSA David A. Case
- AMBER: Diffusion constant franck
- Re: AMBER: Diffusion constant David A. Case
Sunday, 16 November 2003
- AMBER: a problem with memory size Ye Mei
- AMBER: MM_pbsa Rajendra P. OJHA
- AMBER: dual processor Rajendra P. OJHA
- AMBER: Pressure during MD João Barroso
- Re: AMBER: a problem with memory size David A. Case
- Re: AMBER: Pressure during MD David A. Case
Monday, 17 November 2003
- Re: AMBER: Pressure during MD João Barroso
- AMBER: Restarting MD amber7 raist.mmb.pcb.ub.es
Sunday, 16 November 2003
- Re: AMBER: Restarting MD amber7 Carlos Simmerling
Monday, 17 November 2003
- AMBER: RESP charge Youyi Peng
- AMBER: ptraj and charmm files Endres, Robert G.
- Re: AMBER: ptraj and charmm files Thomas E. Cheatham, III
- AMBER: Lone pairs and resp Perdita Barran
- AMBER: Lone pairs and resp Perdita Barran
- AMBER: antechamber test failure Meg McCarrick
- Re: AMBER: RESP charge FyD
- AMBER: amber on mac cluster yu275197.yorku.ca
- Re: AMBER: Lone pairs and resp FyD
- Re: AMBER: Pressure during MD David A. Case
- Re: AMBER: antechamber test failure David A. Case
Tuesday, 18 November 2003
- AMBER: Compiling AMBER7 on Suse Herbert Georg
- AMBER: Zinc parameters Annette Höglund
- Re: AMBER: Compiling AMBER7 on Suse Andreas Svrcek-Seiler
- AMBER: Problem with MPI_Finalize Thomas.Fox.bc.boehringer-ingelheim.com
- Re: AMBER: Problem with MPI_Finalize Robert Duke
- AW: AMBER: Problem with MPI_Finalize Thomas.Fox.bc.boehringer-ingelheim.com
- RE: AMBER: antechamber test failure Meg McCarrick
- Re: AMBER: Problem with MPI_Finalize Bill Ross
- Re: AMBER: Compiling AMBER7 on Suse Bill Ross
- AMBER: molsuf failure with too many intersecting cusps Lee, Matthew
- RE: AMBER: Zinc parameters Ross Walker
- Re: AMBER: antechamber test failure David A. Case
Wednesday, 19 November 2003
- AMBER: Cutress %cmass error Jory Zmuda
- AMBER: MM_PB/GB/SA Chenglong Li
- Re: AMBER: Cutress %cmass error Bill Ross
Thursday, 20 November 2003
- Re: AMBER: MM_PB/GB/SA Holger Gohlke
- [Fwd: AMBER: MM_PB/GB/SA] Chenglong Li
Friday, 21 November 2003
- AMBER: missing of VdW Parameters for N3 Nikolai Smolin
- Re: AMBER: missing of VdW Parameters for N3 David A. Case
- Re: AMBER: missing of VdW Parameters for N3 Piotr Cieplak
- AMBER: Why I get the same TSTRA for different strucutures from Nmode calculation? Yuqin Cai
- AMBER: Compaq Tru64 Unix Herbert de Castro Georg
- Re: AMBER: Compaq Tru64 Unix David A. Case
- Re: AMBER: Why I get the same TSTRA for different strucutures from Nmode calculation? David A. Case
Saturday, 22 November 2003
- AMBER: mm_pbsa and antechamber Rajendra P. OJHA
- AMBER: structure refinement using CNS vs. AMBER a b
Monday, 24 November 2003
- AMBER: Fluorine in GBSA aini.UMDNJ.EDU
- AMBER: protein MD - problem RAJA SWAMINATHAN
- Re: AMBER: protein MD - problem Carlos Simmerling
- Re: AMBER: protein MD - problem David A. Case
- AMBER: water mediated contacts Vlad Cojocaru
- AMBER: Re: AMBER water mediated contacts Rhonda Torres
- Re: AMBER: mm_pbsa and antechamber Holger Gohlke
- AMBER: torsion problems of dummy atoms Difei Wang
- Re: AMBER: torsion problems of dummy atoms Bill Ross
- AMBER: saveamberparm Atchara Wijitkosoom
- Re: AMBER: saveamberparm Bill Ross
- Re: AMBER: saveamberparm David A. Case
Tuesday, 25 November 2003
- AMBER: charge fitting Itziar Maestre Asenjo
- Re: AMBER: charge fitting FyD
- AMBER: 1 fs timestep for GB? Peter VARNAI
- Re: AMBER: charge fitting Piotr Cieplak
- Re: AMBER: 1 fs timestep for GB? Andreas Svrcek-Seiler
- RE: AMBER: image question Rhonda Torres
- AMBER: image question Li Ying
- Re: AMBER: 1 fs timestep for GB? Alexey Onufriev
- Re: AMBER: Fluorine in GBSA Alexey Onufriev
- AMBER: intermolecular force Dave S Walker
- AMBER: gaff errors? Difei Wang
Wednesday, 26 November 2003
- AMBER: compiling amber using gcc on SGI Unix machines Wayne Dawson
- Re: AMBER: gaff errors? David A. Case
- AMBER: restart MD program Do Anh Tuan
- Re: AMBER: restart MD program Carlos Simmerling
- AMBER: restarted MD and ptraj Frederico.Miranda.ibmb.uib.no
Thursday, 27 November 2003
- Re: AMBER: charge fitting Itziar Maestre Asenjo
Friday, 28 November 2003
- AMBER: Nmode problem Wu Yingliang
- Re: AMBER: Nmode problem Holger Gohlke
- Re: AMBER: charge fitting FyD
Saturday, 29 November 2003
- AMBER: Hello Rajendra P. OJHA
- AMBER: Pseudouridine force field parameters Peter Gannett
- Re: AMBER: Pseudouridine force field parameters David A. Case
- AMBER: Re: Nmode problem Wu Yingliang
Sunday, 30 November 2003
- AMBER: Re: Nmode problem Holger Gohlke
- Re: AMBER: Pseudouridine force field parameters Pascal Auffinger
- Re: AMBER: Pseudouridine force field parameters Peter Gannett

Last message date: Wed Jan 14 2004 - 15:53:02 PST
Archived on: Fri Dec 20 2024 - 05:53:21 PST

Amber Archive Nov 2003 by date