Amber Archive Feb 2004: by date

Monday, 2 February 2004
- AMBER: DNA Beale, John
- AMBER: convert restart to mdcrd? Karin Schleinkofer
- Re: AMBER: convert restart to mdcrd? Dr. Yong Duan
- Re: AMBER: convert restart to mdcrd? Vlad Cojocaru
- Re: AMBER: convert restart to mdcrd? Vlad Cojocaru
- Re: AMBER: convert restart to mdcrd? Vlad Cojocaru
- Re: AMBER: convert restart to mdcrd? Dr. Yong Duan
- Re: AMBER: convert restart to mdcrd? Teletchéa Stéphane
- AMBER: ptraj & LES Vlad Cojocaru
- Re: AMBER: DNA David A. Case
- AMBER: LEaP- Error reading frcmod parameters. Miguel de Federico
- Re: AMBER: ptraj & LES Michael Trieb
- Re: AMBER: ptraj & LES Vlad Cojocaru
- Re: AMBER: NVE&polarizable force field Martina Roeselova
- Re: AMBER: LEaP- Error reading frcmod parameters. David A. Case
- Re: AMBER: ANAL problem. David A. Case
- AMBER: TI, angle parameters for nitrogen, frcmod Carsten Detering
- AMBER: nucleic acid bases nonplanar during LES sim Vlad Cojocaru
- AMBER: cell dimensions Dave S Walker
- Re: AMBER: nucleic acid bases nonplanar during LES sim Carlos Simmerling
- AMBER: temperature in DelPhi for MM-PBSA calculation Qing Zhang
- RE: AMBER: temperature in DelPhi for MM-PBSA calculation S. Frank Yan
- RE: AMBER: temperature in DelPhi for MM-PBSA calculation Qing Zhang
- AMBER: leap - orientation of sequenced residues Sarah Wittkopp
- Re: AMBER: temperature in DelPhi for MM-PBSA calculation rluo.uci.edu
- AMBER: Installing Amber on IBM AIX cluster Wayne Dawson
Tuesday, 3 February 2004
- AMBER: xleap & antechamber L Jin
- AMBER: protonation Nikolai Smolin
- AMBER: the uses for Amber FFs a b
- Re: AMBER: the uses for Amber FFs Vlad Cojocaru
- AMBER: What does this error message mean? nie beining
- Re: AMBER: What does this error message mean? David A. Case
- AMBER: Carnal Herbert Georg
- Re: AMBER: What does this error message mean? Carlos Simmerling
- Re: AMBER: leap - orientation of sequenced residues David A. Case
- Re: AMBER: NVE&polarizable force field Byungchan Kim
- Re: AMBER: Carnal Bill Ross
- AMBER: Amber on Redhat Enterprise Mingfeng Yang
- Re: AMBER: What does this error message mean? Bill Ross
- Re: AMBER: Carnal Herbert Georg
- Re: AMBER: What does this error message mean? Martina Roeselova
- AMBER: A general question aini.UMDNJ.EDU
- Re: AMBER: A general question Carlos Simmerling
- Re: AMBER: A general question aini.UMDNJ.EDU
Wednesday, 4 February 2004
- AMBER: NMODE for protein via MM-PBSA-cntd ML
- Re: AMBER: NMODE for protein via MM-PBSA-cntd David A. Case
- Re: AMBER: NMODE for protein via MM-PBSA-cntd ML
- AMBER: rstdip Martina Roeselova
- Re: AMBER: rstdip Scott Brozell
- Re: AMBER: sander and mpich (which compilers/mpich work) Viktor Hornak
- AMBER: carnal Herbert Georg
- Re: AMBER: carnal Bill Ross
- AMBER: antechamber + mopac error Carsten Detering
Thursday, 5 February 2004
- AMBER: ptraj Julien Pecher
- Re: AMBER: ptraj Bill Ross
- AMBER: PMEMD and nmropt=1 aldo jongejan
- Re: AMBER: PMEMD and nmropt=1 Robert Duke
- RE: AMBER: antechamber + mopac error Meg McCarrick
- Re: AMBER: antechamber + mopac error David A. Case
- Re: AMBER: Re: ANAL problem David A. Case
- Re: AMBER: xleap & antechamber David A. Case
- Re: AMBER: TI, angle parameters for nitrogen, frcmod David A. Case
- Re: AMBER: cell dimensions David A. Case
- Re: AMBER: Re: ANAL problem Bill Ross
- AMBER: antechamber error in test / differences in prmtop files Carsten Detering
- Re: AMBER: antechamber error in test / differences in prmtop files David A. Case
- RE: AMBER: PMEMD and nmropt=1 Kristina Furse
- Re: AMBER: PMEMD and nmropt=1 Robert Duke
- AMBER: ptraj and dipoles Herbert Georg
- Re: AMBER: PMEMD and nmropt=1 David A. Case
- AMBER: MCSS Chen, Ya
- Re: AMBER: MCSS David A. Case
- Re: AMBER: ptraj and dipoles David A. Case
- Re: AMBER: questions parm94/99 ff secondary structure Wayne Dawson
Friday, 6 February 2004
- AMBER: How to remove Cl- ions Do Anh Tuan
- Re: AMBER: How to remove Cl- ions Itziar Maestre Asenjo
- Re: AMBER: How to remove Cl- ions Vlad Cojocaru
- AMBER: How to remove Cl- ions Wayne Dawson
- AMBER: water as a "ligand" in GBSA and MM-PBSA? Giulio Rastelli
- Re: AMBER: ptraj and dipoles Herbert Georg
- AMBER: How to remove Cl- ions Do Anh Tuan
- Re: AMBER: questions parm94/99 ff secondary structure Carlos Simmerling
- Re: AMBER: How to remove Cl- ions Bill Ross
- AMBER: off-subject ROCKS/Qbank James W. Caldwell
- AMBER: ptraj and dipoles.... Herbert Georg
- Fwd: Re: AMBER: Lattice structures in xleap Brandon Tefft
- Re: Fwd: Re: AMBER: Lattice structures in xleap David A. Case
- Re: Fwd: Re: AMBER: Lattice structures in xleap Bill Ross
- AMBER: antechamber + mopac +scf failed Carsten Detering
- AMBER: antechamber + mopac + MAXIMUM NUMBER OF ATOMIC ORBITALS EXCEEDED Carsten Detering
Saturday, 7 February 2004
- Re: AMBER: antechamber + mopac + MAXIMUM NUMBER OF ATOMIC ORBITALS EXCEEDED David A. Case
Sunday, 8 February 2004
- AMBER: adding ions to nucleic acids a b
- Re: AMBER: adding ions to nucleic acids Vlad Cojocaru
- AMBER: question about the average structure from ptraj aini.UMDNJ.EDU
- Re: AMBER: adding ions to nucleic acids Bill Ross
- Re: AMBER: question about the average structure from ptraj Bill Ross
- Re: AMBER: question about the average structure from ptraj Thomas E. Cheatham, III
- AMBER: dipole moment in ptraj Herbert Georg
- Re: AMBER: dipole moment in ptraj Thomas E. Cheatham, III
Monday, 9 February 2004
- AMBER: Aldo's PMEMD bug Robert Duke
- AMBER: antechamber error jwfang
- Re: AMBER: Aldo's PMEMD bug aldo jongejan
- Re: AMBER: antechamber error David A. Case
- Re: AMBER: antechamber error Carsten Detering
- RE: AMBER: antechamber error Fang, Jianwen
- AMBER: antechamber + FAILED TO ACHIEVE SCF Carsten Detering
- Re: AMBER: antechamber + FAILED TO ACHIEVE SCF Junmei Wang
- Re: AMBER: antechamber + FAILED TO ACHIEVE SCF Carsten Detering
- Re: AMBER: antechamber + FAILED TO ACHIEVE SCF David A. Case
- AMBER: Nmode convergence ML
Tuesday, 10 February 2004
- Re: AMBER: Nmode convergence ML
- AMBER: Temperature in Nmode ML
- AMBER: minimization output L Jin
- Re: AMBER: Nmode convergence David A. Case
- Re: AMBER: Temperature in Nmode David A. Case
- Re: AMBER: Temperature in Nmode ML
- AMBER: LES question Lishan Yao
- Re: AMBER: LES question Vlad Cojocaru
- Re: AMBER: LES question Lishan Yao
- AMBER: Nitrogen vdw type Terry Downing
- Re: AMBER: minimization output David A. Case
- AMBER: Installing AMBER on SGI Octane 2-CPU - erfcfun.c compile prob. Joseph E. Maxwell
- Re: AMBER: Installing AMBER on SGI Octane 2-CPU - erfcfun.c compile prob. David A. Case
- Re: AMBER: LES question xiaolin cheng
- AMBER: Box of mixed solvant FyD
- Re: AMBER: adding ions to nucleic acids Dr. Yong Duan
- Re: AMBER: Box of mixed solvant Dr. Yong Duan
Wednesday, 11 February 2004
- Re: AMBER: Nmode convergence ML
- Re: AMBER: LES question Carlos Simmerling
- Re: AMBER: LES question Lishan Yao
- AMBER: atom type for GBSA aini.UMDNJ.EDU
- Re: AMBER: atom type for GBSA David A. Case
- Re: AMBER: LES question Carlos Simmerling
- Re: AMBER: LES question Lishan Yao
- Re: AMBER: LES question Carlos Simmerling
- Re: AMBER: LES question Lishan Yao
- Re: AMBER: LES question Carlos Simmerling
- AMBER: GBSA frequency update Sergio E. Wong
- Re: AMBER: GBSA frequency update David A. Case
Thursday, 12 February 2004
- AMBER: Run calculations for protein in Amber Małgorzata Jarończyk
- AMBER: ptraj Karin Schleinkofer
- Re: AMBER: ptraj Vlad Cojocaru
- Re: AMBER: Run calculations for protein in Amber Carlos Simmerling
- Re: AMBER: LES question Lishan Yao
- Re: AMBER: Run calculations for protein in Amber-distance dependent dielectric function Małgorzata Jarończyk
- Re: AMBER: Run calculations for protein in Amber-distance dependent dielectric function Vlad Cojocaru
- AMBER: TER in amber Lishan Yao
- AMBER: MM-PBSA: molecular charges and active site water Anselm Horn
- Re: AMBER: TER in amber Vlad Cojocaru
- AMBER: center of mass in CARNAL Herbert Georg
- Re: AMBER: TER in amber Lishan Yao
- Re: AMBER: Run calculations for protein in Amber-distance dependent dielectric function David A. Case
- Re: AMBER: TER in amber David A. Case
- Re: AMBER: ptraj Thomas E. Cheatham, III
- Re: AMBER: TER in amber Lishan Yao
- Re: AMBER: TER in amber Lishan Yao
- AMBER: neutrality of charge in AMBER 7 Sichun Yang
- Re: AMBER: MM-PBSA: molecular charges and active site water David A. Case
- Re: AMBER: MM-PBSA: molecular charges and active site water ML
Friday, 13 February 2004
- Re: AMBER: TER in amber Vlad Cojocaru
- Re: AMBER: minimization output L Jin
- AMBER: Re: To David Case Małgorzata Jarończyk
Saturday, 14 February 2004
- Re: AMBER: neutrality of charge in AMBER 7 David A. Case
Sunday, 15 February 2004
- AMBER: minimizating complex-protein with AMBER susan.costantini.unina2.it
- AMBER: problem with tleap in Amber donna j
- Re: AMBER: problem with tleap in Amber David A. Case
- Re: AMBER: minimizating complex-protein with AMBER David A. Case
Monday, 16 February 2004
- AMBER: MM-PBSA:??Decomposition of receptor energies?? ML
- Re: AMBER: MM-PBSA:??Decomposition of receptor energies?? Holger Gohlke
- AMBER: SIGSEGV John
- AMBER: TIP4P Nikolai Smolin
- AMBER: IFC COMPILER Obdulia Rabal
- Re: AMBER: IFC COMPILER Robert Duke
- AMBER: carnal Julien Pecher
- AMBER: DIELC L Jin
- AMBER: bad crd file John
- Re: AMBER: MM-PBSA:??Decomposition of receptor energies?? ML
- AMBER: image in ptraj Lishan Yao
- Re: AMBER: SIGSEGV David A. Case
- Re: AMBER: TIP4P David A. Case
- AMBER: TIP4P extended Nikolai Smolin
- AMBER: TIP4P extended Nikolai Smolin
- Re: AMBER: TIP4P extended Sarah Wittkopp
- Re: AMBER: TIP4P extended David A. Case
- Re: AMBER: carnal Bill Ross
- Re: AMBER: bad crd file Bill Ross
Sunday, 15 February 2004
- AMBER: problem with tleap in Amber donna j
Monday, 16 February 2004
- AMBER: saveamberparm warning in leap? opitz.che.udel.edu
- AMBER: multiple messages on the amber reflector David A. Case
- Re: AMBER: saveamberparm warning in leap? David A. Case
- AMBER: moil-view question S. Frank Yan
- Re: AMBER: MM-PBSA:??Decomposition of receptor energies?? Holger Gohlke
Tuesday, 17 February 2004
- AMBER: John
- AMBER: flexible water potential Herbert Georg
- Re: AMBER: moil-view question Carlos Simmerling
- Re: AMBER: moil-view question Teletchéa Stéphane
- AMBER: Close contact warnings L Jin
- AMBER: RESP charges for protein fragment Tom Turner
- Re: AMBER: Close contact warnings David A. Case
- Re: AMBER: Close contact warnings L Jin
- Re: AMBER: Close contact warnings David A. Case
- AMBER: How to add H+ ion in leap? xinchen
- Re: AMBER: center of mass in CARNAL Bill Ross
- Re: AMBER: How to add H+ ion in leap? Bill Ross
- Re: AMBER: How to add H+ ion in leap? xinchen
- AMBER: (no subject) ThuZar Lwin
- Re: AMBER: How to add H+ ion in leap? Bill Ross
- Re: AMBER: (no subject) Bill Ross
- Re: AMBER: (no subject) ThuZar Lwin
- AMBER: multiple messages on the amber reflector Amber Administration
- AMBER: contributed parameters (modified base - PSU) Shau Grossman
- RE: AMBER: contributed parameters (modified base - PSU) S. Frank Yan
- AMBER: Segmentation fault in SaveAmberParm xinchen
Wednesday, 18 February 2004
- Re: AMBER: Close contact warnings L Jin
- Re: AMBER: Close contact warnings Michael George Lerner
- AMBER: histidine and its various forms Stern, Julie
- Re: AMBER: histidine and its various forms David A. Case
- Re: AMBER: Close contact warnings L Jin
- Re: AMBER: contributed parameters FyD
- Re: AMBER: histidine and its various forms Peter Oelschlaeger
- Re: AMBER: Close contact warnings Bill Ross
- Re: AMBER: Close contact warnings L Jin
- RE: AMBER: Close contact warnings Yong Duan
- Re: AMBER: Segmentation fault in SaveAmberParm Xin Chen
- AMBER: sander + ewald bomb Carsten Detering
- Re: AMBER: Close contact warnings Bill Ross
- Re: AMBER: Close contact warnings David A. Case
- AMBER: GLYCAM web site Scott Brozell
- AMBER: MD simulations with 2 molecules Joey Harriman
- Re: AMBER: sander + ewald bomb Michael Crowley
- Re: AMBER: sander + ewald bomb David A. Case
- Re: AMBER: MD simulations with 2 molecules David A. Case
- AMBER: check unit + saveamberparm Carsten Detering
- AMBER: tmd question hj zou
- AMBER: mm_pbsa question hj zou
- AMBER: pmf calculation using gibbs. Myunggi Yi
- Re: AMBER: pmf calculation using gibbs. David A. Case
- Re: AMBER: compiling software(RESP) on MAC G5 Scott Brozell
Thursday, 19 February 2004
- AMBER: LCPO parameters in gbsa Giulio Rastelli
- AMBER: distance-aromatic ring John
- Re: AMBER: pmf calculation using gibbs. Myunggi Yi
- RE: AMBER: Close contact warnings L Jin
- Re: AMBER: tmd question Carlos Simmerling
- Re: AMBER: pmf calculation using gibbs. David A. Case
- Re: AMBER: compiling software(RESP) on MAC G5 FyD
- Re: AMBER: Close contact warnings David A. Case
- AMBER: prep files for modified bases Wen Li
- Re: AMBER: compiling software(RESP) on MAC G5 James W. Caldwell
- AMBER: LES Petr Jeřábek
- RE: AMBER: Close contact warnings Bill Ross
- AMBER: Build a H+ ion in Leap? Xin Chen
- Re: AMBER: distance-aromatic ring Bill Ross
- Re: AMBER: Build a H+ ion in Leap? Bill Ross
- Re: AMBER: Build a H+ ion in Leap? xinchen
- Re: AMBER: compiling software(RESP) on MAC G5 David A. Case
- Re: AMBER: prep files for modified bases David A. Case
- AMBER: how to add force field parameters Ioana Cozmuta
- Re: AMBER: LES Carlos Simmerling
- Re: AMBER: compiling software(RESP) on MAC G5 Lifeng Tian.PantherServer
- Re: AMBER: LES Petr Jeřábek
- Re: AMBER: LES Carlos Simmerling
- Re: AMBER: Build a H+ ion in Leap? Bill Ross
- Re: AMBER: LES Viktor Hornak
- Re: AMBER: LES Petr Jeřábek
- Re: AMBER: LES Carlos Simmerling
- Re: AMBER: sander output Dave S Walker
- Re: AMBER: contributed parameters Shau Grossman
- Re: AMBER: sander output David A. Case
Friday, 20 February 2004
- Re: AMBER: minimization output Anna Schrey
- Re: AMBER: minimization output L Jin
- AMBER: The charge given by xleap from amber 5 Ben Cossins
- AMBER: LES methodology question Vlad Cojocaru
- Re: AMBER: LES methodology question Carlos Simmerling
- AMBER: ions94.lib file Wen Li
- Re: AMBER: contributed parameters FyD
- Re: AMBER: contributed parameters Shau Grossman
- Re: AMBER: sander output Dave S Walker
- Re: AMBER: contributed parameters FyD
- re: AMBER: check unit + saveamberparm S. Frank Yan
Saturday, 21 February 2004
- AMBER: Defining residues opitz.che.udel.edu
Sunday, 22 February 2004
- AMBER: xleap don't recognize my residue/atom scopio
- Re: AMBER: xleap don't recognize my residue/atom Rhonda Torres
- AMBER: Can anybody help me with CHARMM Gabbar Daaku
- Re: AMBER: Can anybody help me with CHARMM Piotr Cieplak
Monday, 23 February 2004
- AMBER: How to add ACE and NME groups? Małgorzata Jarończyk
- AMBER: protein - fractional native contacts uddhavesh bhaskar sonavane
- AMBER: pka calculation hj zou
- Re: AMBER: How to add ACE and NME groups? David A. Case
- Re: AMBER: Defining residues David A. Case
- AMBER: Thermostat comparison ? MD Tyka, Biochemistry
- Re: AMBER: Defining residues Bill Ross
- Re: AMBER: LCPO parameters in gbsa David A. Case
- Re: AMBER: Defining residues opitz.che.udel.edu
- AMBER: how to use prep file Fang, Jianwen
- Re: AMBER: Defining residues Bill Ross
- RE: AMBER: how to use prep file Kristina Furse
- Re: AMBER: how to use prep file David A. Case
- RE: AMBER: how to use prep file Bill Ross
- Re: AMBER: Defining residues John Bushnell
- Re: AMBER: Defining residues opitz.che.udel.edu
- AMBER: problem with frcmod file donna j
- Re: AMBER: Defining residues opitz.che.udel.edu
- Re: AMBER: Defining residues John Bushnell
- Re: AMBER: Defining residues Bill Ross
- Re: AMBER: problem with frcmod file David A. Case
- Re: AMBER: problem with frcmod file Bill Ross
- Re: AMBER: Defining residues John Bushnell
- AMBER: R.E.D. Shau Grossman
- Re: AMBER: R.E.D. FyD
- Re: AMBER: R.E.D. Shau Grossman
Tuesday, 24 February 2004
- AMBER: Can you write me how can I add the ACE and NMe groups in the Xleap? Małgorzata Jarończyk
- Re: AMBER: How to add ACE and NME groups? Ben Cossins
- Re: AMBER: R.E.D. FyD
- AMBER: carnal Youyi Peng
- Re: AMBER: carnal Bill Ross
- AMBER: add Na+ L Jin
- RE: AMBER: add Na+ Ross Walker
- RE: AMBER: add Na+ Bill Ross
- RE: AMBER: add Na+ L Jin
- RE: AMBER: add Na+ Bill Ross
- Re: AMBER: add Na+ David A. Case
- AMBER: Star like (branching) molecule opitz.che.udel.edu
- Re: AMBER: Star like (branching) molecule John Bushnell
- Re: AMBER: Star like (branching) molecule Bill Ross
- Re: AMBER: Star like (branching) molecule Bill Ross
Wednesday, 25 February 2004
- RE: AMBER: add Na+ L Jin
- Re: AMBER: Can anybody help me with CHARMM Tru Huynh
- AMBER: PGA Beale, John
- AMBER: NMR restraints-Floating point exception John
- AMBER: pmf calculation using gibbs Myunggi Yi
- Re: AMBER: NMR restraints-Floating point exception David A. Case
- RE: AMBER: NMR restraints-Floating point exception John
- RE: AMBER: add Na+ Bill Ross
- AMBER: Errors when running tleap Ann P
- Re: AMBER: Errors when running tleap Bill Ross
- AMBER: averaged structure with unknown elements Youyi Peng
- Re: AMBER: averaged structure with unknown elements Bill Ross
- Re: AMBER: averaged structure with unknown elements David A. Case
- AMBER: mmpbsa qustion hj zou
- Re: AMBER: mmpbsa qustion Holger Gohlke
Thursday, 26 February 2004
- Re: AMBER: pmf calculation using gibbs David Smith
- Re: AMBER: mmpbsa qustion James W. Caldwell
- Re: AMBER: problem with frcmod file donna j
- Re: AMBER: problem with frcmod file James W. Caldwell
- RE: AMBER: Errors when running tleap Ann P
- RE: AMBER: Errors when running tleap Bill Ross
- AMBER: size.h error Emmanuel Giudice
- Re: AMBER: size.h error Surjit Dixit
- Re: AMBER: size.h error David A. Case
- AMBER: sander + vlimit exceed... Carsten Detering
Friday, 27 February 2004
- AMBER: pka calculation hj zou
Saturday, 28 February 2004
- Re: AMBER: pka calculation Florian Barth
- AMBER: PB in mm-pbsa Sue Heavner
Sunday, 29 February 2004
- Re: AMBER: PB in mm-pbsa Holger Gohlke
- Re: AMBER: problem with frcmod file donna j
Thursday, 26 February 2004
- AMBER: Problems with xleap Javier Perez Miron

Last message date: Mon Mar 01 2004 - 22:53:00 PST
Archived on: Fri Apr 26 2024 - 05:53:21 PDT

Amber Archive Feb 2004 by date