Amber Archive Nov 2005: by date

Monday, 31 October 2005
- AMBER: mm_pbsa problem emilia wu
Tuesday, 1 November 2005
- Re: AMBER: mm_pbsa problem Cenk Andac
- Re: AMBER: mm_pbsa problem Scott Pendley
- AMBER: About WHAM program Atsutoshi Okabe
Wednesday, 2 November 2005
- Re: AMBER: About WHAM program Guanglei Cui
- AMBER: fedora installation problem Simon Whitehead
- Re: AMBER: Improper Torsional Parameters David A. Case
- RE: AMBER: fedora installation problem Ross Walker
- Re: AMBER: rounding in xleap when using saveoff command... David A. Case
- AMBER: ptraj distance mask Peter Gannett
- Re: AMBER: ptraj distance mask Thomas E. Cheatham, III
- Re: AMBER: Improper Torsional Parameters Ilyas Yildirim
- AMBER: Leap error: Could not find atom type: CE Vlad Cojocaru
- Re: AMBER: Leap error: Could not find atom type: CE Ilyas Yildirim
- Re: AMBER: Leap error: Could not find atom type: CE David A. Case
- Re: AMBER: rounding in xleap when using saveoff command... Wei Zhang
- Re: AMBER: rounding in xleap when using saveoff command... Ilyas Yildirim
- RE: AMBER: fedora installation problem Scott Brozell
- AMBER: Density of Cyclohexane box chaiann ng
- RE: AMBER: Improper Torsional Parameters Ross Walker
- AMBER: EEL and EAMBER values Andrew Box
- RE: AMBER: Density of Cyclohexane box Ross Walker
- RE: AMBER: EEL and EAMBER values Ross Walker
- Re: AMBER: Density of Cyclohexane box FyD
Thursday, 3 November 2005
- Re: AMBER: Metals with Amber Marc Baaden
- Re: AMBER: fedora installation problem caoch.cherry.bio.titech.ac.jp
- AMBER: REM difficulties Peter Varnai
- Re: AMBER: REM difficulties Carlos Simmerling
- Re: AMBER: REM difficulties David A. Case
- Re: AMBER: fedora installation problem David A. Case
- Re: AMBER: REM difficulties Peter Varnai
- Re: AMBER: REM difficulties Carlos Simmerling
- AMBER: Ask for helpf to get examples for MM-PBSA with AMBER8 Peng Tao
- Re: AMBER: Ask for helpf to get examples for MM-PBSA with AMBER8 Wei Chen
- Re: AMBER: Antechamber error David A. Case
- Re: AMBER: Improper Torsional Parameters David A. Case
- AMBER: How to generate a RMSd-residue number graph using AMBER8 ptraj? Jiapu.Zhang.csiro.au
- Re: AMBER: How to generate a RMSd-residue number graph using AMBER8 ptraj? Carlos Simmerling
- RE: AMBER: Density of Cyclohexane box chaiann ng
- AMBER: MM_PBSA problem haixiao jin
- Re: AMBER: MM_PBSA problem Magne Olufsen
Friday, 4 November 2005
- Re: AMBER: MM_PBSA problem haixiao jin
- AMBER: Leap task Vlad Cojocaru
- AMBER: just one more try:) xleap, opteron, pgi and segmentation fault. (fwd) Lars Packschies
- Re: AMBER: restart file and crd file Heiko Meyer
- Re: AMBER: restart file and crd file Heiko Meyer
- RE: AMBER: restart file and crd file Ross Walker
- Re: AMBER: MM_PBSA problem Scott Pendley
- AMBER: PMEMD limitation on NFFT Chng Choon-Peng
- Re: AMBER: PMEMD limitation on NFFT Robert Duke
- Re: AMBER: PMEMD limitation on NFFT Chng Choon-Peng
Saturday, 5 November 2005
- AMBER: About WHAM program Atsutoshi Okabe
- AMBER: bug report Ye Mei
Sunday, 6 November 2005
- AMBER: bugfix 49 Lihua Wang
- AMBER: rluo.uci.edu
- AMBER: DNA simulations Andrew Box
Monday, 7 November 2005
- Re: AMBER: MM_PBSA problem haixiao jin
- AMBER: AMBER 8 compilation with lahey F95 ! Pradipta Bandyopadhyay
- AMBER: addition to the last mail (lahey F95) ! Pradipta Bandyopadhyay
- AMBER: XRED II error while initializing tomjas.poczta.onet.pl
- Re: AMBER: XRED II error while initializing FyD
- AMBER: tRNA's modified bases in the Amber parameters database Whitney Allen
- AMBER: Making movie from AMBER trajectory Varsha Goyal
- Re: AMBER: tRNA's modified bases in the Amber parameters database David A. Case
- Re: AMBER: Making movie from AMBER trajectory Carlos Simmerling
- Re: AMBER: bug report David A. Case
- AMBER: calculating time correlation functions with ptraj John S Zintsmaster
- RE: AMBER: Making movie from AMBER trajectory Ross Walker
- RE: AMBER: Making movie from AMBER trajectory Varsha Goyal
- Re: AMBER: Making movie from AMBER trajectory Varsha Goyal
- Re: AMBER: Making movie from AMBER trajectory Carlos Simmerling
- Re: AMBER: Making movie from AMBER trajectory Varsha Goyal
- Re: AMBER: Making movie from AMBER trajectory Carlos Simmerling
- Re: AMBER: Making movie from AMBER trajectory Knut Langsetmo
- Re: AMBER: Making movie from AMBER trajectory David Bevan
- Re: AMBER: AMBER 8 compilation with lahey F95 ! Amber admin
- Re: AMBER: Making movie from AMBER trajectory caoch.cherry.bio.titech.ac.jp
Tuesday, 8 November 2005
- Re: AMBER: Making movie from AMBER trajectory Carlos Simmerling
- Re: AMBER: Making movie from AMBER trajectory YoungJin Cho
- Re: AMBER: Making movie from AMBER trajectory Mingfeng Yang
- AMBER: Time Correlation Functions with Amber John S Zintsmaster
- Re: AMBER: Time Correlation Functions with Amber David A. Case
- Re: AMBER: tkbc2 David A. Case
- Re: AMBER: Time Correlation Functions with Amber John S Zintsmaster
- Re: AMBER: Time Correlation Functions with Amber David A. Case
- Re: AMBER: Making movie from AMBER trajectory David E. Konerding
- Re: AMBER: Time Correlation Functions with Amber John S. Zintsmaster
- Re: AMBER: Making movie from AMBER trajectory David E. Konerding
- Re: Re: AMBER: bug report Ye Mei
- Re: AMBER: XRED II error while initializing tomjas
Wednesday, 9 November 2005
- Re: AMBER: XRED II error while initializing FyD
- Re: AMBER: Making movie from AMBER trajectory using UCSF Chimera David E. Konerding
- AMBER: mm_pbsa Wei Chen
Tuesday, 8 November 2005
- Re: AMBER: mm_pbsa Ray Luo
Wednesday, 9 November 2005
- AMBER: Resp install problem Jianzhong Liu
- Re: AMBER: Resp install problem David A. Case
- AMBER: LoadPdb Error: In file [chirality.c], line 121 Message: Atom C67 is not in the first list Nitin Bhardwaj
- Re: AMBER: LoadPdb Error: In file [chirality.c], line 121 Message: Atom C67 is not in the first list Bill Ross
- Re: AMBER: LoadPdb Error: In file [chirality.c], line 121 Message: Atom C67 is not in the first list Ilyas Yildirim
Thursday, 10 November 2005
- AMBER: ESP exceeds the MAXESP(20000), nag raj
- AMBER: restart coordinate file s0344557.sms.ed.ac.uk
- Re: AMBER: mm_pbsa Cenk Andac
- Re: AMBER: restart coordinate file Carlos Simmerling
- RE: AMBER: ESP exceeds the MAXESP(20000), Junmei Wang
- Re: AMBER: restart coordinate file Bill Ross
- AMBER: Resp install problem, again Jianzhong Liu
- Re: AMBER: restart coordinate file s0344557.sms.ed.ac.uk
- Re: AMBER: LoadPdb Error: In file [chirality.c], line 121 Message: Atom C67 is not in the first list Nitin Bhardwaj
- Re: AMBER: LoadPdb Error: In file [chirality.c], line 121 Message: Atom C67 is not in the first list David A. Case
- Re: AMBER: LoadPdb Error: In file [chirality.c], line 121 Message: Atom C67 is not in the first list Nitin Bhardwaj
- Re: AMBER: Resp install problem, again David A. Case
- Re: AMBER: Resp install problem, again FyD
- Re: AMBER: LoadPdb Error: In file [chirality.c], line 121 Message: Atom C67 is not in the first list Ilyas Yildirim
Friday, 11 November 2005
- Re: AMBER: LoadPdb Error: In file [chirality.c], line 121 Message: Atom C67 is not in the first list Nitin Bhardwaj
- Re: AMBER: mm_pbsa Wei Chen
- Re: AMBER: mm_pbsa Wei Chen
- Re: AMBER: mm_pbsa Ray Luo
- Re: AMBER: LoadPdb Error: In file [chirality.c], line 121 Message: Atom C67 is not in the first list David A. Case
Saturday, 12 November 2005
- CORRENDUM: Re: AMBER: mm_pbsa Cenk Andac
- Re: AMBER: mm_pbsa Wei Chen
- Re: AMBER: mm_pbsa Ray Luo
Monday, 14 November 2005
- AMBER: Error message Sukjoon Yoon
- AMBER: RESP problem RESP laura zan
- Re: AMBER: RESP problem RESP FyD
- RE: AMBER: Error message Ross Walker
- Re: AMBER: LoadPdb Error: In file [chirality.c], line 121 Message: Atom C67 is not in the first list David A. Case
- AMBER: iwork array for nmr Peter Varnai
- Re: AMBER: mm_pbsa Wei Chen
- Re: AMBER: iwork array for nmr Guanglei Cui
- AMBER: Antechamber/Leap, problem with Improper angles Christophe Guilbert
- AMBER: ew_legal.h Yam
- RE: AMBER: ew_legal.h Ross Walker
- RE: AMBER: ew_legal.h Yam
- Re: AMBER: ew_legal.h David A. Case
- Re: AMBER: ew_legal.h Yam
Tuesday, 15 November 2005
- AMBER: calculating end-end distance C Balasubramanian
- Re: AMBER: ew_legal.h darden
- Re: AMBER: calculating end-end distance David A. Case
- Re: AMBER: Antechamber/Leap, problem with Improper angles David A. Case
- AMBER: recent Chimera MD enhancements Eric Pettersen
- Re: AMBER: recent Chimera MD enhancements Eric Pettersen
- AMBER: pH=1 MD simulation Harianto Tjong
- Re: AMBER: LoadPdb Error: In file [chirality.c], line 121 Message: Atom C67 is not in the first list Nitin Bhardwaj
- AMBER: Quantifying DNA perterbation Kara Di Giorgio
- Re: AMBER: LoadPdb Error: In file [chirality.c], line 121 Message: Atom C67 is not in the first list Ilyas Yildirim
- Re: AMBER: Quantifying DNA perterbation Thomas Cheatham
Wednesday, 16 November 2005
- Re: AMBER: Quantifying DNA perterbation Carlos Simmerling
- AMBER: anal and periodic boundary conditions Rachel Burdge
- Re: AMBER: LoadPdb Error: In file [chirality.c], line 121 Message: Atom C67 is not in the first list David A. Case
- Re: AMBER: anal and periodic boundary conditions Bill Ross
- AMBER: using periodic boundary conditions to create infinite double helix Kenley Barrett
- Re: AMBER: Resp install problem, again Jianzhong Liu
- Re: AMBER: Resp install problem, again David A. Case
- Re: AMBER: Resp install problem, again Jianzhong Liu
- Re: AMBER: Resp install problem, again David A. Case
- Re: AMBER: using periodic boundary conditions to create infinite double helix David A. Case
- Re: AMBER: using periodic boundary conditions to create infinite double helix Bill Ross
- AMBER: ptraj Hbond analysis mathew k varghese
- Re: AMBER: ptraj Hbond analysis Thomas Cheatham
Thursday, 17 November 2005
- AMBER: FATAL error with ATP, MG2 residue Michael Mazanetz
- AMBER: need clarification on EWALD BOMB error S.Sundar Raman
- AMBER: FATAL error with ATP and MG2 - fixed Michael Mazanetz
- RE: AMBER: need clarification on EWALD BOMB error Ross Walker
- Re: AMBER: need clarification on EWALD BOMB error Thomas Cheatham
- AMBER: Question about using MM_PBSA gtg549i.mail.gatech.edu
- Re: AMBER: Question about using MM_PBSA Wei Chen
- Re: AMBER: need clarification on EWALD BOMB error S.Sundar Raman
- Re: AMBER: ptraj Hbond analysis mathew k varghese
- Re: AMBER: ptraj Hbond analysis Thomas Cheatham
Friday, 18 November 2005
- AMBER: RED and EP from GAMESS Vlad Cojocaru
- AMBER: Polarization & energy analysis GUILBAUD Philippe 153683
- AMBER: RED and EP from GAMESS FyD
- AMBER: RED&GAMESS: sorry ... my mistake Vlad Cojocaru
- AMBER: MM/PBSA basic questions Peng Tao
- Re: AMBER: MM/PBSA basic questions Wei Chen
- Re: AMBER: Polarization & energy analysis David A. Case
- Re: AMBER: MM/PBSA basic questions David A. Case
- Re: AMBER: MM/PBSA basic questions Peng Tao
Saturday, 19 November 2005
- AMBER: Question about PDB format FyD
- Re: AMBER: ptraj Hbond analysis mathew k varghese
- RE: AMBER: Question about PDB format Ross Walker
- Re: AMBER: Question about PDB format David A. Case
- Re: AMBER: Question about PDB format Andy Purkiss
Sunday, 20 November 2005
- Re: AMBER: Question about PDB format FyD
- AMBER: RED: extra variable definition Vlad Cojocaru
- Re: AMBER: ptraj Hbond analysis Thomas Cheatham
- AMBER: How to use XLEAP to link one atom in a monomer to another atom in another monomer? (where both the 2 monomers are in a same pdb file) Jiapu.Zhang.csiro.au
- AMBER: Will Amber 9 available? Xioling Chuang
- Re: AMBER: Will Amber 9 available? David A. Case
- RE: AMBER: How to use XLEAP to link one atom in a monomer to another atom in another monomer? (where both the 2 monomers are in a same pdb file) Ross Walker
Monday, 21 November 2005
- AMBER: temprature and restraint in constant volumm MD tonglei
- Re: AMBER: Will Amber 9 available? bmbbjm.bmb.leeds.ac.uk
- Re: AMBER: Will Amber 9 available? Barbault Florent
- Re: AMBER: temprature and restraint in constant volumm MD Carlos Simmerling
- AMBER: average struct without solvent C Balasubramanian
- Re: AMBER: temprature and restraint in constant volumm MD tonglei
- Re: AMBER: average struct without solvent mcpreto.fc.up.pt
- Re: AMBER: RED: extra variable definition FyD
- RE: AMBER: average struct without solvent Ross Walker
- Re: AMBER: Will Amber 9 available? David A. Case
- RE: AMBER: How to use XLEAP to link one atom in a monomer to another atom in another monomer? (where both the 2 monomers are in a same pdb file) Ross Walker
- Re: AMBER: average struct without solvent Thomas Cheatham
- AMBER: ANAL problem Sébastien Fiorucci
- RE: AMBER: How to use XLEAP to link one atom in a monomer to another atom in ano Andrew Box
- AMBER: how to extract the residues of first solvation shell from the simulated system after the production? gtg549i.mail.gatech.edu
- Re: AMBER: ANAL problem David A. Case
- AMBER: Question about PB bomb zgleo
- Re: AMBER: how to extract the residues of first solvation shell from the simulated system after the production? Thomas Cheatham
- AMBER: Question of PB bomb zgleo
Tuesday, 22 November 2005
- AMBER: sp0 console message after using addAtomTypes Lorna Stimson
- Re: AMBER: RED: extra variable definition Vlad Cojocaru
- Re: AMBER: RED: extra variable definition FyD
- Re: AMBER: RED: extra variable definition FyD
- AMBER: Leap handling crystallographic waters Vlad Cojocaru
- Re: AMBER: Leap handling crystallographic waters Andy Purkiss
- Re: AMBER: RED: extra variable definition Vlad Cojocaru
- AMBER: GRID program used to add ions and solvate AMBER minimized structures Vlad Cojocaru
- Re: AMBER: how to extract the residues of first solvation shell from the simulated system after the production? gtg549i.mail.gatech.edu
- AMBER: MM_PBSA problem Zhang Bing
- AMBER: Using OPLS atom types Lorna Stimson
- Re: AMBER: sp0 console message after using addAtomTypes David A. Case
- Re: AMBER: MM_PBSA problem David A. Case
- Re: AMBER: sp0 console message after using addAtomTypes Lorna Stimson
- Re: AMBER: Using OPLS atom types Furse, Kristina Elisabet
- Re: AMBER: Leap handling crystallographic waters Furse, Kristina Elisabet
- RE: AMBER: Leap handling crystallographic waters Ross Walker
- Re: AMBER: Using OPLS atom types Bill Ross
- RE: AMBER: Leap handling crystallographic waters Furse, Kristina Elisabet
- AMBER: RE: gaff sugar residue instability hayden
- Re: AMBER: RE: gaff sugar residue instability David A. Case
- RE: AMBER: Leap handling crystallographic waters Ross Walker
- Re: AMBER: Leap handling crystallographic waters David A. Case
- Re: AMBER: how to extract the residues of first solvation shell from the simulated system after the production? gtg549i.mail.gatech.edu
- AMBER: MM_PBSA problem---Illegal division by zero at ... Zhang Bing
- Re: AMBER: how to extract the residues of first solvation shell from the simulated system after the production? Thomas Cheatham
- AMBER: cluster analysis mathew k varghese
Wednesday, 23 November 2005
- RE: AMBER: cluster analysis Ross Walker
- AMBER: MM_PBSA_parameter Wei Chen
- Re: AMBER: MM_PBSA_parameter Ray Luo
- Re: AMBER: MM_PBSA_parameter Wei Chen
- Re: AMBER: MM_PBSA_parameter Ray Luo
Thursday, 24 November 2005
- AMBER: MM_PBSA question Tiziano Tuccinardi
- AMBER: Parameters for S-substituted nucleic acids E.A.Moore
- AMBER: gaff sugar residue instability hayden
- AMBER: My model loses its motion in MD Lukasz Bielecki
- Re: AMBER: My model loses its motion in MD Thomas Cheatham
- Re: AMBER: My model loses its motion in MD Andreas Svrcek-Seiler
- Re: AMBER: MM_PBSA question David A. Case
- Re: AMBER: gaff sugar residue instability David A. Case
- Re: AMBER: gaff sugar residue instability Bill Ross
- Re: AMBER: gaff sugar residue instability Bill Ross
Friday, 25 November 2005
- AMBER: aloks.mbu.iisc.ernet.in
- AMBER: PARM-99 Angelo Pugliese
- Re: AMBER: PARM-99 Carlos Simmerling
- AMBER: reordering atoms after antechamber Vlad Cojocaru
- Re: AMBER: reordering atoms after antechamber David A. Case
- Re: AMBER: PARM-99 Piotr Cieplak
Saturday, 26 November 2005
- Re: AMBER: PARM-99 Claire Zerafa
- AMBER: How to wrap a truncated octahedron water box into the primary box? Xioling Chuang
- AMBER: input for mm_pbsa Xioling Chuang
Sunday, 27 November 2005
- AMBER: Comparing EELEC from amber and that calculated in the trivial fashion. Pavan G
- AMBER: How to check for water mediated hydrogen bonds? Hannes Loeffler
- Re: AMBER: Comparing EELEC from amber and that calculated in the trivial fashion. David A. Case
Monday, 28 November 2005
- AMBER: Cluster - input files Ananda Rama Krishnan Selvaraj
- Re: AMBER: Comparing EELEC from amber and that calculated in the trivial fashion. Carlos Simmerling
- AMBER: CD spectrum Anthony Cruz
- Re: AMBER: reordering atoms after antechamber FyD
- Re: AMBER: CD spectrum Adrian Roitberg
- AMBER: antechamber charge methods Sagar S. Rane
- Re: AMBER: Cluster - input files David A. Case
- Re: AMBER: Cluster - input files Ananda Rama Krishnan Selvaraj
- Re: AMBER: Cluster - input files David A. Case
- Re: AMBER: Cluster - input files Bill Ross
- AMBER: MM_PBSA stopped at some snapshot Xioling Chuang
Tuesday, 29 November 2005
- AMBER: AMBER compilation with -DREM Sergey Krishtal
- AMBER: some problems with Antechamber David Mobley
- Re: AMBER: some problems with Antechamber Wei Zhang
- Re: AMBER: AMBER compilation with -DREM David A. Case
Sunday, 27 November 2005
- Re: AMBER: MM_PBSA stopped at some snapshot Ray Luo
Tuesday, 29 November 2005
- AMBER: constant pressure vs. constant volume heating Vlad Cojocaru
- Re: AMBER: some problems with Antechamber David Mobley
- Re: AMBER: constant pressure vs. constant volume heating David Mobley
- RE: AMBER: constant pressure vs. constant volume heating Ross Walker
- Re: AMBER: constant pressure vs. constant volume heating Bill Ross
- AMBER: Solvation in trifluoroethanol Ann Vilan Tran
- AMBER: rdparm bug David Mobley
- AMBER: question convert crd files to pdb files Zhuang
- AMBER: parmchk segfaulting David A. Case
- RE: AMBER: question convert crd files to pdb files Ross Walker
Wednesday, 30 November 2005
- Re[2]: AMBER: AMBER compilation with -DREM Sergey Krishtal
- AMBER: more data points on the parmchk problem David A. Case
- AMBER: ifort compiling problem Simon Whitehead
- Re: AMBER: ifort compiling problem Andy Purkiss
- AMBER: Targeted MD Whitney Allen
- RE: Re[2]: AMBER: AMBER compilation with -DREM Ross Walker
- Re: AMBER: more data points on the parmchk problem David Mobley
- AMBER: Residual Dipolar Refinement RadhaKumari Yadav
Tuesday, 29 November 2005
- Re: AMBER: MM_PBSA stopped at some snapshot Ray Luo
Wednesday, 30 November 2005
- Re: AMBER: Targeted MD Viktor Hornak
- Re: AMBER: Targeted MD Carlos Simmerling
- AMBER: MM-PBSA: plot the "Ggas+Gsol" vs time Lihong Song
- Re: AMBER: more data points on the parmchk problem John Mongan
- Re: AMBER: MM-PBSA: plot the "Ggas+Gsol" vs time Nelson Fonseca
- AMBER: Any way to get different charge on same type atom Jianzhong Liu
- Re: AMBER: Any way to get different charge on same type atom rpaduri.chem.wayne.edu
- Re: AMBER: Mg2+ issues of using MM-PB/GBSA Ray Luo
- Re: AMBER: Questions about MM-PBSA in Amber8 Ray Luo
- Re: AMBER: Mg2+ issues of using MM-PB/GBSA Ray Luo
- Re: AMBER: Mg2+ issues of using MM-PB/GBSA Ray Luo

Last message date: Fri Dec 02 2005 - 21:53:01 PST
Archived on: Sun Nov 02 2025 - 05:53:26 PST

Amber Archive Nov 2005 by date