Amber Archive Jun 2006: by date

Wednesday, 31 May 2006
- AMBER: offset? Tonda March
- AMBER: Bond Force Conctants in Amber Force Fields Егоров Д.А.
Thursday, 1 June 2006
- Re: AMBER: offset? Angelo
- Re: AMBER: Different results for TI calculation David A. Case
- AMBER: Amber 8 QMMM tests fail on AIX Shan-ho Tsai
- Re: AMBER: AMBER mdcrd file bigger than 2GB snoze pa
- Re: AMBER: Installation of Amber8 on Fedora Core 5. . Don.Bashford.stjude.org
- Re: AMBER: AMBER mdcrd file bigger than 2GB Thomas Cheatham
- RE: AMBER: Amber 8 QMMM tests fail on AIX Ross Walker
- RE: AMBER: Amber 8 QMMM tests fail on AIX Shan-ho Tsai
- AMBER: Another Installation Problem Seth Lilavivat
- RE: AMBER: Another Installation Problem Ross Walker
- AMBER: compile error with pgf90 Evan Kelly
Friday, 2 June 2006
- AMBER: some questions and problems about antechamber and divcon Zhihong Yu
- AMBER: How to analyze the trajectory generated by LES simulation pang zhao
- AMBER: attachments for my last mail Zhihong Yu
- Re: AMBER: How to analyze the trajectory generated by LES simulation Vlad Cojocaru
- AMBER: Programes to calculate ligand RMSD nag raj
- Re: AMBER: Programes to calculate ligand RMSD Carlos Simmerling
- Re: AMBER: some questions and problems about antechamber and divcon Martin Peters
- AMBER: individual torsion/bond energies from a minimization Thomas Pochapsky
- AMBER: distance restraints Myunggi Yi
- RE: AMBER: compile error with pgf90 Ross Walker
- Re: AMBER: Another Installation Problem Scott Pendley
- AMBER: bugfix for frcmod.ff03 in Amber 9 David A. Case
- AMBER: NMR restraint Myunggi Yi
- Re: AMBER: NMR restraint Myunggi Yi
- Re: AMBER: NMR restraint Myunggi Yi
- Re: AMBER: Installation of Amber8 on Fedora Core 5. . David A. Case
- Re: AMBER: Thermodynamic integration using the amber 9 Ilyas Yildirim
- Re: AMBER: Namelists in input files David A. Case
- AMBER: trouble adding mdcrd files together Adam Pelzer
- Re: AMBER: trouble adding mdcrd files together Carlos Simmerling
- Re: AMBER: trouble adding mdcrd files together David A. Case
- Re: AMBER: trouble adding mdcrd files together Carlos Simmerling
- Re: AMBER: some questions and problems about antechamber and divcon David A. Case
- Re: AMBER: NMR restraint David A. Case
- AMBER: manual docking mathew k varghese
- AMBER: manual docking mathew k varghese
Saturday, 3 June 2006
- AMBER: How to use the prmtop and inpcrd files of ligand in a complex system? Zhihong Yu
- Re: AMBER: manual docking linfu
- Re: AMBER: NMR restraint Myunggi Yi
- Re: AMBER: trouble adding mdcrd files together Adam Pelzer
Sunday, 4 June 2006
- Re: AMBER: manual docking snoze pa
Monday, 5 June 2006
- Re: AMBER: How to use the prmtop and inpcrd files of ligand in a complex system? Navnit Kumar Mishra
- Re: AMBER: How to use the prmtop and inpcrd files of ligand in acomplex system? Zhihong Yu
- Re: AMBER: How to use the prmtop and inpcrd files of ligand in acomplex system? Navnit Kumar Mishra
- AMBER: MM-PBSA and first solvation shell Andrea Bortolato
- AMBER: process_mdout Navnit Kumar Mishra
- Re: AMBER: individual torsion/bond energies from a minimization David A. Case
- RE: AMBER: process_mdout Ross Walker
- Re: AMBER: MM-PBSA and first solvation shell Thomas Cheatham
- AMBER: Amber: Segfault while running sander sethl.gatech.edu
- RE: AMBER: Amber: Segfault while running sander Ross Walker
- AMBER: does the Amber8 or Amber9 contains Br,I and Sulfur parameter for MM-PBSA or MM-GBSA. linfu
Tuesday, 6 June 2006
- AMBER: How to submit a job in cluster pkb bioinfo
- AMBER: calculating box dimensions during MD Vlad Cojocaru
- Re: AMBER: calculating box dimensions during MD Ananda Rama Krishnan Selvaraj
- AMBER: antechamber and FMN David Mobley
- AMBER: Amber: Can't get sander to run sethl.gatech.edu
- AMBER: xleap problem Hashem Taha
- Re: AMBER: Amber: Can't get sander to run David A. Case
- Re: AMBER: xleap problem Myunggi Yi
- Re: AMBER: xleap problem Myunggi Yi
- Re: AMBER: xleap problem Ilyas Yildirim
Wednesday, 7 June 2006
- Re: AMBER: xleap problem Myunggi Yi
- AMBER: compiler error for Amber9 Weihua Li
- Re: AMBER: compiler error for Amber9 Robert Duke
- RE: AMBER: compiler error for Amber9 Ross Walker
- Re: AMBER: compiler error for Amber9 David A. Case
- AMBER: antechamber Steve Seibold
- Re: AMBER: antechamber Myunggi Yi
- RE: AMBER: antechamber Ross Walker
- AMBER: RE: antechamber and FMN Junmei Wang
- AMBER: pmemd_parallel_ins_prob pkmukher
- Re: AMBER: pmemd_parallel_ins_prob Robert Duke
- Re: AMBER: does the Amber8 or Amber9 contains Br,I and Sulfur parameter for MM-PBSA or MM-GBSA. David A. Case
- AMBER: problem with amber 9 and igb=5 M. Scott Shell
- Re: AMBER: problem with amber 9 and igb=5 Carlos Simmerling
- Re: AMBER: problem with amber 9 and igb=5 John Mongan
Thursday, 8 June 2006
- AMBER: How to build N-terminal of alanine : NH2 jitrayut jitonnom
- Re: AMBER: How to build N-terminal of alanine : NH2 FyD
- AMBER: save coordinates during SANDER minimisation Hannes Barsch
- Re: AMBER: save coordinates during SANDER minimisation Ilyas Yildirim
- Fwd: AMBER: How to build N-terminal of alanine : NH2 jitrayut jitonnom
- AMBER: Ask for help in pbsa error in AMBER9 Cheng Luo, Ph.D.
- Re: AMBER: problem with amber 9 and igb=5 M. Scott Shell
- Re: AMBER: problem with amber 9 and igb=5 M. Scott Shell
- AMBER: GB and protein backbone parameters Carlos Simmerling
- AMBER: software to visualize normal modes Douali, Latifa
- RE: AMBER: software to visualize normal modes Ross Walker
- Re: AMBER: software to visualize normal modes David A. Case
- Re: AMBER: pmemd_parallel_ins_prob pkmukher
- Re: AMBER: Ask for help in pbsa error in AMBER9 Ray Luo
- AMBER: AMD 64 Installation / configuration clarification sethl.gatech.edu
- Re: AMBER: AMD 64 Installation / configuration clarification David LeBard
- Re: AMBER: AMD 64 Installation / configuration clarification sethl.gatech.edu
- Re: AMBER: save coordinates during SANDER minimisation David A. Case
- Re: AMBER: AMD 64 Installation / configuration clarification David LeBard
- AMBER: COM khn _
- Re: AMBER: COM Thomas Cheatham
- AMBER: charmm force field in amber9 soo
- AMBER: Problem with Leap jitrayut jitonnom
- Re: AMBER: problem with amber 9 and igb=5 M. Scott Shell
- Re: Fwd: AMBER: How to build N-terminal of alanine : NH2 FyD
Friday, 9 June 2006
- AMBER: use ptraj and two differenct prmtop file to analyze LES trajectory pang zhao
- AMBER: MMPBSA problem jitrayut jitonnom
- Re: AMBER: charmm force field in amber9 David A. Case
- Re: AMBER: MMPBSA problem Thomas Steinbrecher
- AMBER: ptraj Marcela Madrid
- Re: AMBER: problem with amber 9 and igb=5 David A. Case
- AMBER: Why the result from sander minimization (epsilon=4r) is not same with that from nmode, when restraint is applied? Yongmei Pan
- AMBER: Why the energy from sander minimization (epsilon=4r) is not same with that from nmode, when restraint is applied? Yongmei Pan
- AMBER: is seems that The SAS in MMPBSA is SES , not SAS. ???? linfu
Saturday, 10 June 2006
- AMBER: MD stopped Miguel Ferreira
- AMBER: Umbrella sampling Atsutoshi Okabe
- Re: AMBER: Umbrella sampling Ilyas Yildirim
- Re: AMBER: Why the energy from sander minimization (epsilon=4r) is not same with that from nmode, when restraint is applied? David A. Case
- Re: AMBER: is seems that The SAS in MMPBSA is SES , not SAS. ???? Ray Luo
- Re: AMBER: is seems that The SAS in MMPBSA is SES , not SAS. ???? David A. Case
- Re: AMBER: problem with amber 9 and igb=5 M. Scott Shell
- RE: AMBER: problem with amber 9 and igb=5 Ross Walker
- AMBER: parmchk error Evan Kelly
- Re: Re: AMBER:it seems that The SAS in MMPBSA is SES , not SAS. ???? linfu
Sunday, 11 June 2006
- AMBER: mm_pbsa calculation for calcium Navnit Kumar Mishra
Monday, 12 June 2006
- AMBER: switching function for electrostatic interactions Fabien Cailliez
- RE: AMBER: switching function for electrostatic interactions Ross Walker
- RE: AMBER: parmchk error Ross Walker
- RE: AMBER: MD stopped Ross Walker
- Re: AMBER: switching function for electrostatic interactions Thomas Cheatham
- AMBER: How to calculate the mmpbsa for explicit MD ? jitrayut jitonnom
- Re: AMBER: How to calculate the mmpbsa for explicit MD ? Thomas Steinbrecher
- Fwd: AMBER: How to calculate the mmpbsa for explicit MD ? jitrayut jitonnom
- Re: Fwd: AMBER: How to calculate the mmpbsa for explicit MD ? Thomas Steinbrecher
- Fwd: Fwd: AMBER: How to calculate the mmpbsa for explicit MD ? jitrayut jitonnom
- Re: AMBER: How to calculate the mmpbsa for explicit MD ? Chris Moth
- Re: AMBER: How to strip waters in trajectorie ? Gustavo Seabra
- AMBER: How to strip waters in trajectorie ? jitrayut jitonnom
- Re: AMBER: How to strip waters in trajectorie ? David A. Case
- Re: AMBER: mm_pbsa calculation for calcium Scott Pendley
- AMBER: Nmode memory allocation problem JunJun Liu
- RE: AMBER: Nmode memory allocation problem Ross Walker
- Re: AMBER: parmchk error Evan Kelly
Tuesday, 13 June 2006
- Re: AMBER: mm_pbsa calculation for calcium Navnit Kumar Mishra
- Re: AMBER: How to strip waters in trajectorie ? simon whitehead
- AMBER: SGI compiler problems Peter Gannett
- AMBER: MMPBSA error jitrayut jitonnom
- Re: AMBER: MMPBSA error Heike.Meiselbach.chemie.uni-erlangen.de
- Re: AMBER: Nmode memory allocation problem JunJun Liu
- Re: AMBER: mm_pbsa calculation for calcium Scott Pendley
- Fwd: AMBER: MMPBSA error jitrayut jitonnom
- Re: Fwd: AMBER: MMPBSA error JunJun Liu
- Re: AMBER: mm_pbsa calculation for calcium Navnit Kumar Mishra
- AMBER: Difficulty loading a pdb file Kara Di Giorgio
- AMBER: LEaP Warning ... when do NH2-neutral fragment jitrayut jitonnom
- Re: AMBER: LEaP Warning ... when do NH2-neutral fragment FyD
- Re: AMBER: mm_pbsa calculation for calcium Scott Pendley
- Re: AMBER: Difficulty loading a pdb file Ilyas Yildirim
- Re: AMBER: LEaP Warning ... when do NH2-neutral fragment Ilyas Yildirim
- AMBER: Problem of Ptraj in AMBER9 Chunhu Tan
- AMBER: compiler requirement for SGI Fuel To install AMBER9 S.Sundar Raman
Wednesday, 14 June 2006
- AMBER: How to simplify this big system rationally to perform MD studies Zhihong Yu
- Fwd: Fwd: AMBER: MMPBSA error jitrayut jitonnom
- AMBER: problems on mm_pbsa Giovanni
- AMBER: saveamberparams error in Amber9 Weihua Li
- RE: AMBER: Difficulty loading a pdb file Ross Walker
- AMBER: ptraj: rms per residue simon whitehead
- Re: AMBER: saveamberparams error in Amber9 Thomas Steinbrecher
- AMBER: Fully QM periodic runs Steven Winfield
- RE: AMBER: Fully QM periodic runs Ross Walker
- Re: AMBER: Fully QM periodic runs Wei Zhang
Tuesday, 13 June 2006
- Re: AMBER: problems on mm_pbsa Ray Luo
Wednesday, 14 June 2006
- Re: AMBER: Fully QM periodic runs Gustavo Seabra
- Re: AMBER: Difficulty loading a pdb file (Modified by Kara Di Giorgio) Kara Di Giorgio
- Re: AMBER: Difficulty loading a pdb file (Modified by Kara Di Giorgio) Ilyas Yildirim
- Re: AMBER: Difficulty loading a pdb file (Modified by Kara Di Giorgio) Knut Langsetmo
- RE: AMBER: Difficulty loading a pdb file (Modified by Kara Di Giorgio) Ross Walker
- AMBER: best way to customize linkages sethl.gatech.edu
- Re: AMBER: ptraj: rms per residue Mingfeng Yang
- Re: AMBER: saveamberparams error in Amber9 Weihua Li
- Re: AMBER: saveamberparams error in Amber9 David A. Case
- Re: AMBER: parmchk error David A. Case
- AMBER: Re: Problem in compiling sander with MMTSB Scott Brozell
- Re: AMBER: saveamberparams error in Amber9 Weihua Li
Thursday, 15 June 2006
- AMBER: RMS FLUCTUATIONS Jiang Jianwen
- Re: AMBER: Fully QM periodic runs Ken Merz
- RE: AMBER: RMS FLUCTUATIONS Yong Duan
- RE: AMBER: parmchk error Junmei Wang
- Re: AMBER: Difficulty loading a pdb file (Modified by Kara Di Giorgio) Kara Di Giorgio
- Re: AMBER: pmemd_parallel_ins_prob Amber admin
- AMBER: GBSA of nonstandard cations Martin LEPSIK
- AMBER: Re: Problem in compiling sander with MMTSB Scott Brozell
- AMBER: repeat use of a trimer lib file Eric Hu
- AMBER: MPICH and Sander Andrew Box
- Re: AMBER: MPICH and Sander David A. Case
- Re: AMBER: RMS FLUCTUATIONS David A. Case
Friday, 16 June 2006
- RE: AMBER: RMS FLUCTUATIONS Jiang Jianwen
- AMBER: LEaP error : unbalanced charge jitrayut jitonnom
- Re: AMBER: LEaP error : unbalanced charge Thomas Steinbrecher
- Fwd: AMBER: LEaP error : unbalanced charge jitrayut jitonnom
- Fwd: Fwd: AMBER: LEaP error : unbalanced charge jitrayut jitonnom
- AMBER: Antechamber - NH2 and C not planar when it should be on one of my ligand Christophe Guilbert
Saturday, 17 June 2006
- Re: AMBER: Antechamber - NH2 and C not planar when it should be on one of my ligand Ilyas Yildirim
- AMBER: Problems with restart file from pmemd sim. anna.schrey.gmx.de
- Re: AMBER: Problems with restart file from pmemd sim. Robert Duke
- AMBER: charge in LEaP step jitrayut jitonnom
- Fwd: Fwd: AMBER: LEaP error : unbalanced charge jitrayut jitonnom
Sunday, 18 June 2006
- Re: Fwd: Fwd: AMBER: LEaP error : unbalanced charge Ilyas Yildirim
- RE: AMBER: Umbrella sampling Atsutoshi Okabe
- Fwd: Fwd: Fwd: AMBER: LEaP error : unbalanced charge jitrayut jitonnom
- RE: AMBER: Umbrella sampling Ilyas Yildirim
- AMBER: Non bond list overflow in amber8.0 program. nag raj
Monday, 19 June 2006
- Re: AMBER: LEaP error : unbalanced charge FyD
- AMBER: Post-MD minimization sangeeta.bioinfo.ernet.in
- Re: AMBER: Post-MD minimization Carlos Simmerling
- RE: AMBER: Post-MD minimization Ross Walker
- AMBER: Amber7-CHARMM22-TRIPOS force fields opitz.che.udel.edu
- AMBER: help with custom RNA molecule sethl.gatech.edu
- AMBER: Antechamber poorly define atom angles of a five ring system which causes NH2 and C not to be planar as expected Christophe Guilbert
- AMBER: ions+proteins Hannes Loeffler
- AMBER: RE: Antechamber poorly define atom angles of a five ring system whichcauses NH2 and C not to be planar as expected Junmei Wang
Tuesday, 20 June 2006
- AMBER: second derivative matrix Marie Brut
- AMBER: why has "ELE " a large fluctuation in MMP BSA? yxiong99
- RE: AMBER: checkoverlap doubt [was: Post-MD minimization] sangeeta.bioinfo.ernet.in
- AMBER: why has "ELE " a large fluctuation in MMPBSA? JunJun Liu
- AMBER: ptraj vector Myunggi Yi
- Re: AMBER: ptraj vector Myunggi Yi
- Re: AMBER: ptraj vector Thomas Cheatham
- Re: AMBER: ptraj vector Myunggi Yi
- Re: AMBER: second derivative matrix David A. Case
- Re: AMBER: ptraj vector David A. Case
- Re: AMBER: ptraj vector Myunggi Yi
- Re: AMBER: ptraj vector Thomas Cheatham
- Re: AMBER: ptraj vector Thomas Cheatham
- RE: AMBER: checkoverlap doubt [was: Post-MD minimization] Thomas Cheatham
- Re: AMBER: why has "ELE " a large fluctuation in MMP BSA? JunJun Liu
- Re: AMBER: why has "ELE " a large fluctuation in MMP BSA? Carlos Simmerling
- Re: AMBER: why has "ELE " a large fluctuation in MMP BSA? Thomas Cheatham
- Re: AMBER: why has "ELE " a large fluctuation in MMP BSA? JunJun Liu
- AMBER: amber9 hostfile snoze pa
- Re: AMBER: why has "ELE " a large fluctuation in MMP BSA? Carlos Simmerling
- Re: AMBER: why has "ELE " a large fluctuation in MMP BSA? Carlos Simmerling
- Re: AMBER: why has "ELE " a large fluctuation in MMP BSA? JunJun Liu
- Re: AMBER: why has "ELE " a large fluctuation in MMP BSA? Carlos Simmerling
- Re: AMBER: why has "ELE " a large fluctuation in MMP BSA? JunJun Liu
Wednesday, 21 June 2006
- AMBER: Tutorial 2: Production MD. a a
- AMBER: Amber9 under SGI Prism (Altix) with Intel 8.0 error in pbpgb test David McGiven
- Re: AMBER: SGI compiler problems Atro Tossavainen
- AMBER: MMTSB: phi-pdi-based clustering sangeeta.bioinfo.ernet.in
- Re: AMBER: Amber9 under SGI Prism (Altix) with Intel 8.0 error in pbpgb test Roberto Gomperts
- Re: AMBER: SGI compiler problems Roberto Gomperts
- Re: AMBER: Tutorial 2: Production MD. Thomas Steinbrecher
- AMBER: terms in mm-pbsa Lwin, ThuZar
- Re: AMBER: Amber9 under SGI Prism (Altix) with Intel 8.0 error in pbpgb test David McGiven
- AMBER: openmpi snoze pa
- AMBER: problems with cpinutil.pl Abhilash Mohan
- AMBER: What's the meaning of NTYPES? JunJun Liu
- Re: AMBER: What's the meaning of NTYPES? JunJun Liu
Thursday, 22 June 2006
- AMBER: problems about compiling a parallel version of AMBER 9 Chengwen Chen
- AMBER: kill job command? a a
- AMBER: Restraint internal coordinates in Amber 8.0 Guillaume Bollot
- AMBER: average struct.problem bala
- AMBER: can i use unusual amino acid priya priya
- AMBER: RESP charge fitting problems with capping group hayden
- Re: AMBER: kill job command? JunJun Liu
- Re: AMBER: average struct.problem Thomas Cheatham
- Re: AMBER: What's the meaning of NTYPES? Wei Zhang
- Re: AMBER: problems about compiling a parallel version of AMBER 9 Wei Zhang
- Re: AMBER: RESP charge fitting problems with capping group FyD
- AMBER: help creating RNA sethl.gatech.edu
- Re: AMBER: help creating RNA Ilyas Yildirim
- Re: AMBER: help creating RNA David A. Case
- AMBER: ANN: APBS/Amber interface released Robert Konecny
- RE: AMBER: Post-MD minimization sangeeta.bioinfo.ernet.in
Friday, 23 June 2006
- AMBER: Ptraj reimage truncated octahedral box simulation with AMBER8 Ricardo J. F. Branco
- Re: AMBER: help creating RNA Vlad Cojocaru
- AMBER: Tutorial 2: Minimise and equlibrium error NaN a a
- AMBER: references simon whitehead
- Re: AMBER: references Ricardo J. F. Branco
- RE: AMBER: Tutorial 2: Minimise and equlibrium error NaN Ross Walker
- RE: AMBER: references Ross Walker
- RE: AMBER: Ptraj reimage truncated octahedral box simulation with AMBER8 Ross Walker
- RE: AMBER: Post-MD minimization Ross Walker
- AMBER: constant pressure equillibration simon whitehead
- AMBER: Implicit solvent question Anthony Cruz
- RE: AMBER: constant pressure equillibration Ross Walker
- Re: AMBER: Implicit solvent question John Mongan
- AMBER: problems with cpinutil.pl Abhilash Mohan
- AMBER: how to create 2'-5' RNA sethl.gatech.edu
- Re: AMBER: references simon whitehead
- Re: AMBER: how to create 2'-5' RNA FyD
Saturday, 24 June 2006
- AMBER: Second derivative matrix mbrut.laas.fr
Sunday, 25 June 2006
- AMBER: about GBSA sishi.tang.utoronto.ca
- Re: AMBER: Difficulty loading a pdb file (Modified by Kara Di Giorgio) Mengjuei Hsieh
Monday, 26 June 2006
- AMBER: periodic boundary condition in the X and Y dimensions only hbluo
- AMBER: periodic boundary condition in the X and Y dimensions only hbluo
- AMBER: Can we submit jobs in sequences to amber? a a
- Re: AMBER: Can we submit jobs in sequences to amber? Ilyas Yildirim
- Re: AMBER: Can we submit jobs in sequences to amber? Roberto Gomperts
- AMBER: Minizsation strange error message! Please help. a a
- AMBER:Checkoverlap query sangeeta.bioinfo.ernet.in
- Re: AMBER: help creating RNA sethl.gatech.edu
- AMBER: Amber minimization with multiple restraints Qingning Shu
- AMBER: Curves and Average Structures Lauren O'Neil
- AMBER: Review. Chunhu Tan
- Re: AMBER: Curves and Average Structures David E. Konerding
- AMBER: manual/prmtop/missing bonds section David Mobley
- AMBER: creating RNA, nucgen / leap sethl.gatech.edu
- Re: AMBER: how to create 2'-5' RNA Ilyas Yildirim
- Re: AMBER: problems about compiling a parallel version of AMBER 9 Chengwen Chen
Tuesday, 27 June 2006
- Re: AMBER: Second derivative matrix David A. Case
- Re: AMBER: problems about compiling a parallel version of AMBER 9 Kateryna Miroshnychenko
- Re: AMBER: Curves and Average Structures Angelo
- AMBER: MM-PBSA and gaff atom types anna ferrari
- AMBER: Leap: neutralising the charge Miguel Ferreira
- Re: AMBER: Leap: neutralising the charge FyD
- Re: AMBER: MM-PBSA and gaff atom types Ray Luo
- AMBER: rgbmax--something wrong with my input file? Kenley Barrett
- RE: AMBER: rgbmax--something wrong with my input file? Ross Walker
Wednesday, 28 June 2006
- AMBER: Question about ptraj setup for phase angles (P) of ribose sugar puckering Cenk Andac
- AMBER: REM test failures on IA-64 architecture Glass, Kevin A
- Re: AMBER: Question about ptraj setup for phase angles (P) of ribose sugar puckering Thomas Cheatham
- Re: AMBER: MM-PBSA and gaff atom types anna ferrari
- Re: AMBER: Amber minimization with multiple restraints Myunggi Yi
- Re: AMBER: Amber minimization with multiple restraints Myunggi Yi
- Re: AMBER: REM test failures on IA-64 architecture Asim Okur
- AMBER: remlog option changed in amber9? Alik Widge
- Re: AMBER: remlog option changed in amber9? Carlos Simmerling
- Re: AMBER: remlog option changed in amber9? Alik Widge
- Re: AMBER: remlog option changed in amber9? Carlos Simmerling
- Re: AMBER: rgbmax--something wrong with my input file? tmarch.coin.org
- AMBER: problem with pattern searching in mm_pbsa_calceneent.pm, Amber8, when salt>0 using delphi version 4 Lwin, ThuZar
- AMBER: MM-PBSA questions Miguel Ferreira
Thursday, 29 June 2006
- Re: AMBER: MM-PBSA questions Ray Luo
- AMBER: How to calculate binding free energy using MM-PBSA Xioling Chuang
- Re: AMBER: How to calculate binding free energy using MM-PBSA Cenk Andac
- AMBER: Strange problems with PMEMD on Intel Xeons with Infiniband Fabian Boes
- Re: AMBER: Implicit solvent question Anthony Cruz
- Re: AMBER: Strange problems with PMEMD on Intel Xeons with Infiniband Robert Duke
- Re: AMBER: Strange problems with PMEMD on Intel Xeons with Infiniband Fabian Boes
- Re: AMBER: Strange problems with PMEMD on Intel Xeons with Infiniband Robert Duke
- AMBER: Having trouble getting Iron parameters for QM/MM zachary hartman
- Re: AMBER: Having trouble getting Iron parameters for QM/MM Ken Merz
- AMBER: inconsistence in MM_PBSA between mm_pbsa .pl and mm_pbsa_statistics.pl yxiong99
- Re: AMBER: Having trouble getting Iron parameters for QM/MM FyD
- Re: AMBER: inconsistence in MM_PBSA between mm_pbsa .pl and mm_pbsa_statistics.pl Ray Luo
- AMBER: RDII and epsilon of ho and hw wrong in gaff.dat ??!!! Christophe Guilbert
- Re: AMBER: RDII and epsilon of ho and hw wrong in gaff.dat ??!!! Bill Ross
- Re: AMBER: inconsistence in MM_PBSA between mm_pbsa .pl and mm_pbsa_statistics.pl JunJun Liu
- AMBER: general question about hydrogen bond energy vs electrostatic energy Eric Hu
- Re: AMBER: RDII and epsilon of ho and hw wrong in gaff.dat ??!!! Christophe Guilbert
- AMBER: tleap BUG to write a pdb file if atom name contains 4 chars. Christophe Guilbert
- Re: AMBER: How to calculate binding free energy using MM-PBSA Xioling Chuang
Friday, 30 June 2006
- RE: AMBER: Having trouble getting Iron parameters for QM/MM Ross Walker
- Re: AMBER: How to calculate binding free energy using MM-PBSA Cenk Andac
- AMBER: GB simulation problem Anthony Cruz
- Re: AMBER: RDII and epsilon of ho and hw wrong in gaff.dat ??!!! Bill Ross
- AMBER: NAMOT sethl.gatech.edu
Tuesday, 13 June 2006
- AMBER: Compiling / Installing Amber 8 on SUSE 10.1 Seth Lilavivat
Saturday, 17 June 2006
- AMBER: Creating an Intercalation site Seth Lilavivat

Last message date: Wed Jul 19 2006 - 06:07:08 PDT
Archived on: Wed May 08 2024 - 05:53:21 PDT

Amber Archive Jun 2006 by date