Amber Archive Feb 2006: by date

Tuesday, 31 January 2006
- AMBER: Values of Spring Constants Sai Kumar Ramadugu
Wednesday, 1 February 2006
- AMBER: Gibbs PMF Calculation Atsutoshi Okabe
- Re: AMBER: Values of Spring Constants Carlos Simmerling
- Re: AMBER: Gibbs PMF Calculation Carlos Simmerling
- Re: AMBER: Values of Spring Constants Adrian Roitberg
- Re: AMBER: Values of Spring Constants Sai Kumar Ramadugu
- AMBER: prepi definitions Michael Mazanetz
- Re: AMBER: lifetimes David A. Case
- Re: AMBER: Values of Spring Constants David A. Case
- Re: AMBER: prepi definitions ivan.mmb.pcb.ub.es
- AMBER: protein ligand complex snoze pa
- Re: AMBER: protein ligand complex Carlos Simmerling
- Re: AMBER: protein ligand complex snoze pa
- Re: AMBER: protein ligand complex Carlos Simmerling
- Re: AMBER: protein ligand complex snoze pa
- Re: AMBER: Problem in compiling sander with MMTSB luckyang.gmail.com
- AMBER: Cannot successfully assign bond type for this molecule? snoze pa
- Re: AMBER: Cannot successfully assign bond type for this molecule? David Case
- AMBER: basic minimize question A D
- Re: AMBER: Cannot successfully assign bond type for this molecule? snoze pa
- RE: AMBER: basic minimize question Ross Walker
- Re: AMBER: basic minimize question A D
- Re: AMBER: Problem in compiling sander with MMTSB David A. Case
- Re: AMBER: basic minimize question David A. Case
- RE: AMBER: basic minimize question Ross Walker
- AMBER: Charges on atoms in protein :AMBER Varsha Goyal
- Re: AMBER: Problem in compiling sander with MMTSB luckyang.gmail.com
- RE: AMBER: Charges on atoms in protein :AMBER Ross Walker
- Re: AMBER: Values of Spring Constants Sai Kumar Ramadugu
Thursday, 2 February 2006
- Re: AMBER: Values of Spring Constants Carlos Simmerling
- AMBER: positional restraints & constant pressure Kateryna Miroshnychenko
- AMBER: lib file snoze pa
- RE: AMBER: Charges on atoms in protein :AMBER Bill Ross
- Re: AMBER: MM-PBSA David A. Case
- Re: AMBER: lib file Ilyas Yildirim
- RE: AMBER: Charges on atoms in protein :AMBER Varsha Goyal
- RE: AMBER: Charges on atoms in protein :AMBER Bill Ross
- AMBER: Amber8 parallel compilation problems on EM64T system HL Eastwood
- Re: AMBER: Charges on atoms in protein :AMBER Adrian Roitberg
- RE: AMBER: Charges on atoms in protein :AMBER Ilyas Yildirim
- Re: AMBER: lib file Ilyas Yildirim
- Re: AMBER: Amber8 parallel compilation problems on EM64T system David A. Case
- AMBER: parameter loading problem Lihua Wang
- AMBER: Amber8 parallel compilation problems on an OSCAR Cluster Aaron J. Greenwood
- AMBER: MD of oligomer sequences Atilio I Anzellotti/O/VCU
- Re: AMBER: Amber8 parallel compilation problems on an OSCAR Cluster David A. Case
- Re: AMBER: MD of oligomer sequences David A. Case
- AMBER: simulated annealing run--temp won't rise Kenley Barrett
- Re: AMBER: Values of Spring Constants Sai Kumar Ramadugu
- AMBER: Re: Force Decomposition for MTS in AMBER 8. David Case
- Re: AMBER: simulated annealing run--temp won't rise David Case
Friday, 3 February 2006
- AMBER: Gibbs PMF Calculation Atsutoshi Okabe
- Re: AMBER: Gibbs PMF Calculation Carlos Simmerling
- AMBER: MPICH-1.2.7 compilation problem ! Pradipta Bandyopadhyay
- Re: AMBER: Amber8 parallel compilation problems on an OSCAR Cluster Aaron J. Greenwood
- Re: AMBER: positional restraints & constant pressure David A. Case
- AMBER: AMBER 7 and cutoff's Toomas Kaevand
- Re: AMBER: AMBER 7 and cutoff's Carlos Simmerling
- Re: AMBER: lib file snoze pa
- AMBER: Rhoad, Jonathan S.
- AMBER: MMPBSA: magnitude of PB calculation sishi.tang.utoronto.ca
- Re: AMBER: David A. Case
- Re: AMBER: Values of Spring Constants David A. Case
- Re: AMBER: Problem in compiling sander with MMTSB David A. Case
Thursday, 2 February 2006
- Re: AMBER: MMPBSA: magnitude of PB calculation Ray Luo
Friday, 3 February 2006
- Re: AMBER: lib file Ilyas Yildirim
- Re: AMBER: Problem in compiling sander with MMTSB luckyang.gmail.com
Saturday, 4 February 2006
- AMBER: Paweł Gruszczyński
- AMBER: Strange minimization output problem andy ng
- AMBER: dihedral parameters richard dimelow
- Re: AMBER: Strange minimization output problem Ananda Rama Krishnan Selvaraj
- Re: AMBER: MMPBSA: magnitude of PB calculation sishi.tang.utoronto.ca
- Re: AMBER: dihedral parameters Carlos Simmerling
- Re: AMBER: David Mobley
- Re: AMBER: bugfix for impropers in parmchk David A. Case
- Re: AMBER: Strange minimization output problem David A. Case
- AMBER: What Viewer is best Brian Stupi
Sunday, 5 February 2006
- Re: AMBER: Strange minimization output problem Andreas Svrcek-Seiler
- AMBER: could amber calculte the binding free energy ofonly two small ligands (no big molecules) ? linfu
- Re: AMBER: What Viewer is best Vlad Cojocaru
Monday, 6 February 2006
- Re: AMBER: MMPBSA: magnitude of PB calculation Thomas Steinbrecher
- Re: AMBER: dihedral parameters richard dimelow
- AMBER: Hessian matrix Marie Brut
- Re: AMBER: dihedral parameters Carlos Simmerling
- Re: AMBER: MMPBSA: magnitude of PB calculation Natasja Brooijmans
- AMBER: helix content during my simulation julien
- Re: AMBER: helix content during my simulation Mingfeng Yang
- Re: AMBER: helix content during my simulation julien
- Re: AMBER: bugfix for impropers in parmchk Kateryna Miroshnychenko
- Re: AMBER: helix content during my simulation Mingfeng Yang
- AMBER: Parallel version of Amber: error message snoze pa
- Re: AMBER: Parallel version of Amber: error message Carlos Simmerling
- Re: AMBER: Parallel version of Amber: error message snoze pa
- Re: AMBER: Parallel version of Amber: error message David LeBard
- Re: AMBER: Parallel version of Amber: error message Lihua Wang
- Re: AMBER: Parallel version of Amber: error message Mingfeng Yang
- Re: AMBER: Parallel version of Amber: error message Mark Williamson
- AMBER: Parallel error in Amber 8 snoze pa
- Re: AMBER: Parallel error in Amber 8 snoze pa
- Re: AMBER: Parallel error in Amber 8 Wei Zhang
- Re: AMBER: Parallel error in Amber 8 snoze pa
- Re: AMBER: Parallel error in Amber 8 David A. Case
- AMBER: soft-core potential in amber? Lydia
- Re: AMBER: Parallel error in Amber 8 snoze pa
- AMBER: non bond list overflow Kenley Barrett
- Re: AMBER: non bond list overflow David A. Case
Tuesday, 7 February 2006
- AMBER: format of qusaiharmonic eigenvector file in AMBER7 Phineus Markwick
- Re: AMBER: format of qusaiharmonic eigenvector file in AMBER7 Chris Moth
- Re: AMBER: soft-core potential in amber? David Mobley
- Re: AMBER: non bond list overflow Kenley Barrett
- Re: AMBER: Hessian matrix David A. Case
- Re: AMBER: Hessian matrix mbrut.laas.fr
- Re: AMBER: non bond list overflow David A. Case
Wednesday, 8 February 2006
- AMBER: Ask for your help to install Amber8 software Cao Tran
- Re: AMBER: Ask for your help to install Amber8 software Cenk Andac
- RE: AMBER: Ask for your help to install Amber8 software CaoTran
- RE: AMBER: Ask for your help to install Amber8 software Lei Wang
- AMBER: DNA tutorial xleap help Amanda Jonsson
- AMBER: desc related issue snoze pa
- Re: AMBER: DNA tutorial xleap help Wei Zhang
- Re: AMBER: DNA tutorial xleap help Bill Ross
- AMBER: PMED in AMBER snoze pa
Thursday, 9 February 2006
- AMBER: Acetyl CoA Satyan Sharma
- AMBER: Distortion in parallelploied Varsha Goyal
- AMBER: EAMBER Mingfeng Yang
- Re: AMBER: EAMBER Carlos Simmerling
Friday, 10 February 2006
- RE: AMBER: Ask for your help to install Amber8 software Cao Tran
- RE: AMBER: Ask for your help to install Amber8 software Cenk Andac
- AMBER: PMEMD MPI_Finalize() error Mingfeng Yang
- Re: AMBER: PMEMD MPI_Finalize() error Robert Duke
- Re: AMBER: PMEMD MPI_Finalize() error Mingfeng Yang
- Re: AMBER: Distortion in parallelploied David A. Case
- AMBER: minization: outputing intermediate snapshots Vlad Cojocaru
- AMBER: minization: outputing intermediate snapshots Vlad Cojocaru
Sunday, 12 February 2006
- AMBER: Problem in running umbrella sampling Sai Kumar Ramadugu
- Re: AMBER: Problem in running umbrella sampling David A. Case
- Re: AMBER: Problem in running umbrella sampling Sai Kumar Ramadugu
Monday, 13 February 2006
- AMBER: shuli kang
- AMBER: MM_PBSA problem (No values for MM_GAS ) Bing Liu
- Re: AMBER: Distortion in parallelploied Angelo Pugliese
- AMBER: Error when installing Brian Stupi
- Re: AMBER: Error when installing Brian Stupi
- Re: AMBER: MM_PBSA problem (No values for MM_GAS ) Scott Pendley
- Re: AMBER: Scott Pendley
- AMBER: 2D-topology Baldoni Hector Armando
- AMBER: mm_pbsa output lucas luquitas
- AMBER: script advice A D
Tuesday, 14 February 2006
- AMBER: double stranded polyribocytidylic acid Kateryna Miroshnychenko
- AMBER: Istallation AMBER8 Dr.Rudolf Friedemann
- Re: AMBER: double stranded polyribocytidylic acid Jiri Sponer
- AMBER: paralelization and sander problems cristian obiol
- Re: AMBER: double stranded polyribocytidylic acid Kateryna Miroshnychenko
- Re: AMBER: double stranded polyribocytidylic acid Jiri Sponer
- Re: AMBER: paralelization and sander problems Carlos Simmerling
- Re: AMBER: paralelization and sander problems David A. Case
- AMBER: Organic molecules Marie Brut
- AMBER: Xleap crash Scott Pendley
- Re: AMBER: Xleap crash David A. Case
- RE: AMBER: Organic molecules Ross Walker
- RE: AMBER: paralelization and sander problems Ross Walker
- Re: AMBER: Xleap crash Scott Pendley
- Re: AMBER: Xleap crash Scott Pendley
- RE: AMBER: Error when installing Ross Walker
- RE: AMBER: minization: outputing intermediate snapshots Ross Walker
- Re: AMBER: Xleap crash David A. Case
- Re: AMBER: double stranded polyribocytidylic acid Bill Ross
- Re: AMBER: 2D-topology David A. Case
- AMBER: Absoft Pro Fortran and AMBER 8 on MacOS X 10.4.4 Jingyuan Luke
- Re: AMBER: Absoft Pro Fortran and AMBER 8 on MacOS X 10.4.4 David A. Case
- Re: AMBER: Istallation AMBER8 David A. Case
Wednesday, 15 February 2006
- AMBER: negative T_solv values Markus O Kaukonen
- Re: AMBER: double stranded polyribocytidylic acid Jiri Sponer
- Re: AMBER: script advice JunJun Liu
- Re: AMBER: negative T_solv values David A. Case
- Re: AMBER: double stranded polyribocytidylic acid Bill Ross
- Re: AMBER: double stranded polyribocytidylic acid Jiri Sponer
- AMBER: m4 error with Amber8 on SUN Amber admin
- Re: AMBER: m4 error with Amber8 on SUN David A. Case
- AMBER: Charge of the phosphorylated Ser/Thr in MM_PBSA calculation zgleo
Thursday, 16 February 2006
- Re: AMBER: double stranded polyribocytidylic acid Kateryna Miroshnychenko
- Re: AMBER: Charge of the phosphorylated Ser/Thr in MM_PBSA calculation german
- AMBER: sander problem bala
- Re: AMBER: sander problem snoze pa
- Re: AMBER: sander problem Carlos Simmerling
- Re: AMBER: sander problem JunJun Liu
- RE: AMBER: sander problem Ross Walker
- Re: AMBER: double stranded polyribocytidylic acid Bill Ross
- Re: AMBER: double stranded polyribocytidylic acid Bill Ross
- RE: AMBER: sander problem Brian Stupi
- RE: AMBER: sander problem Thomas E. Cheatham, III
- RE: AMBER: sander problem Ross Walker
- AMBER: process_mdout.perl Brian Stupi
Friday, 17 February 2006
- Re: AMBER: paralelization and sander problems cristian obiol
- Re: AMBER: paralelization and sander problems Carlos Simmerling
- AMBER: Torsional restraints for groups of atoms Supat Jiranusornkul
- AMBER: Question about renaming a residue Kara Di Giorgio
- Re: AMBER: Question about renaming a residue Thomas E. Cheatham, III
- Re: AMBER: Question about renaming a residue Ilyas Yildirim
- AMBER: mm_pbsa problem in IBM-aix Jiten
Saturday, 18 February 2006
- AMBER: instructions for making a library file for an unusual residue? Kenley Barrett
Sunday, 19 February 2006
- AMBER: antechamber for a database of organic molecules Yogesh Sabnis
- Re: AMBER: antechamber for a database of organic molecules FyD
- Re: AMBER: instructions for making a library file for an unusual residue? FyD
- Re: AMBER: mm_pbsa problem in IBM-aix Ray Luo
- AMBER: Phosphorylated amino acid andy ng
- RE: AMBER: antechamber for a database of organic molecules Junmei Wang
Monday, 20 February 2006
- Re: AMBER: Phosphorylated amino acid Tim Meyer
- Re: AMBER: paralelization and sander problems cristian obiol
- AMBER: parallel problem of amber8 linfu
- AMBER: charge redistribution in .prep files Stefano Federico Massimiliano Pieraccini (Stefano.Pieraccini)
- AMBER: Truncated octahedral box as triclinic lattice vectors Markus O Kaukonen
- AMBER: amber 8 problem Abd Ghani Abd Aziz
- Re: AMBER: amber 8 problem JunJun Liu
- Re: AMBER: amber 8 problem Abd Ghani Abd Aziz
- Re: AMBER: amber 8 problem Andreas Svrcek-Seiler
- Re: AMBER: charge redistribution in .prep files David A. Case
- Re: AMBER: amber 8 problem David A. Case
- RE: AMBER: parallel problem of amber8 Ross Walker
- RE: AMBER: amber 8 problem Ross Walker
- AMBER: Ti calculations in dmso solvent Vitor Manuel Sousa F?x
- AMBER: Error in RST files in long simulations! lucas luquitas
- Re: AMBER: Error in RST files in long simulations! Carlos Simmerling
- Re: AMBER: Error in RST files in long simulations! lucas luquitas
- Re: AMBER: instructions for making a library file for an unusual residue? Kenley Barrett
- AMBER: NMR restraints and LES Sivakolundu, Sivashankar
- Re: AMBER: NMR restraints and LES David A. Case
- RE: AMBER: amber 8 problem Abd Ghani Abd Aziz
- Re: AMBER: Phosphorylated amino acid andy ng
- Re: AMBER: instructions for making a library file for an unusual residue? Ilyas Yildirim
- AMBER: About WHAM Atsutoshi Okabe
Tuesday, 21 February 2006
- Re: AMBER: Error in RST files in long simulations! Carlos Simmerling
- Re: AMBER: paralelization and sander problems Carlos Simmerling
- Re: AMBER: instructions for making a library file for an unusual residue? FyD
- AMBER: does anyone have library file for methylated histidine, 2003 ff? Kenley Barrett
- AMBER: CARNAL: H-BOND Specifying side chains only Kay Kunes
- Re: AMBER: CARNAL: H-BOND Specifying side chains only Bill Ross
- AMBER: Problem with file size of sander outputs Cenk Andac
Wednesday, 22 February 2006
- Re: AMBER: Problem with file size of sander outputs shuli kang
- Re: AMBER: Problem with file size of sander outputs german
- AMBER: Free energy perturbation Angelo Pugliese
- AMBER: AMBER force field with namd Fabien Cailliez
- Re: AMBER: Problem with file size of sander outputs JunJun Liu
- RE: AMBER: Problem with file size of sander outputs Ross Walker
- RE: AMBER: Problem with file size of sander outputs Cenk Andac
Thursday, 23 February 2006
- Re: AMBER: AMBER force field with namd Vlad Cojocaru
- Re: AMBER: AMBER force field with namd Carlos Simmerling
- Re: AMBER: AMBER force field with namd Vlad Cojocaru
- Re: AMBER: Ti calculations in dmso solvent David Mobley
- RE: AMBER: Problem with file size of sander outputs Feng X Zhou
- Re: AMBER: Ti calculations in dmso solvent David A. Case
- RE: AMBER: Problem with file size of sander outputs Ross Walker
- AMBER: generating parameters for the NADH analogue H4NAD Simon Whitehead
- Re: AMBER: generating parameters for the NADH analogue H4NAD Vlad Cojocaru
- RE: AMBER: generating parameters for the NADH analogue H4NAD Ross Walker
- AMBER: TI cal Steve Seibold
- RE: AMBER: TI cal Ross Walker
- Re: AMBER: Ti calculations in dmso solvent David Mobley
- RE: AMBER: TI cal Steve Seibold
- AMBER: A problem with Amber force field new parameter derivation Vidana.Epa.csiro.au
- Re: AMBER: A problem with Amber force field new parameter derivation FyD
Friday, 24 February 2006
- AMBER: entropic energy Nina Fischer
- AMBER: Antechamber Package Announcement Junmei Wang
- Re: AMBER: entropic energy David A. Case
- AMBER: Constant pressure - restart - Amber8 Jennie Thomas
- Re: AMBER: Constant pressure - restart - Amber8 David A. Case
- Re: AMBER: Constant pressure - restart - Amber8 Jennie Thomas
- AMBER: specifying RSOLV when calculating 2003 force field charges Kenley Barrett
- Re: AMBER: Constant pressure - restart - Amber8 David A. Case
Saturday, 25 February 2006
- AMBER: How to explain the meaning of the mmpbsa/DC result? zhli_2000.126.com
Sunday, 26 February 2006
- AMBER: dynamic memory allocation problem in nmode Cenk Andac
- Re: AMBER: dynamic memory allocation problem in nmode Cenk Andac
- Re: AMBER: dynamic memory allocation problem in nmode Jiten
- AMBER: ptraj atomicfluct: is it possible to calculate atomic fluctations from a reference structure Magne Olufsen
- AMBER: Sulfonamides and GAFF Varsha Goyal
- Re: AMBER: Constant pressure - restart - Amber8 Jennie Thomas
- Re: AMBER: dynamic memory allocation problem in nmode David A. Case
Monday, 27 February 2006
- AMBER: ptraj warning while loading reference Vlad Cojocaru
- AMBER: MD job stopped without any error information? ying xiong
- Re: AMBER: MD job stopped without any error information? Melinda Layten
- Re: AMBER: MD job stopped without any error information? Guanglei Cui
- AMBER: RE: about compiling errors for Leap Ross Walker
- RE: AMBER: MD job stopped without any error information? Ross Walker
- Re: AMBER: ptraj warning while loading reference David A. Case
- Re: AMBER: ptraj warning while loading reference Vlad Cojocaru
- AMBER: sander testing problem mdione.fcq.unc.edu.ar
Tuesday, 28 February 2006
- AMBER: mask issues Claire Zerafa
- Re: AMBER: mask issues Vlad Cojocaru
- AMBER: failed to save prm and xyz using ff96 Abd Ghani Abd Aziz
- RE: AMBER: failed to save prm and xyz using ff96 Ross Walker
- Re: AMBER: failed to save prm and xyz using ff96 Carlos Simmerling
- AMBER: Compiling the parallel version of amber 8 in a beowulf linux cluster Carlos Silva Lopez
- Re: AMBER: Compiling the parallel version of amber 8 in a beowulf linux cluster Wei Zhang
- AMBER: How to develop charge for my deprotonated glycine Jianzhong Liu
- AMBER: Angle restraint venditti2.unisi.it
- Re: AMBER: Compiling the parallel version of amber 8 in a beowulf linux cluster Carlos Silva Lopez
- Re: AMBER: Angle restraint David A. Case
- Re: AMBER: failed to save prm and xyz using ff96 Abd Ghani Abd Aziz

Last message date: Sun Mar 05 2006 - 06:10:12 PST
Archived on: Mon Nov 03 2025 - 05:53:31 PST

Amber Archive Feb 2006 by date