Amber Archive Nov 2006: by date

Wednesday, 1 November 2006
- AMBER: Mass weights Sergey Samsonov
- Re: AMBER: Closest(closest water) Sergey Samsonov
- AMBER: How to start a Simulation of a peptide in bilayer nur avneet
- AMBER: ab initio terminology query HL Eastwood
- Re: AMBER: ab initio terminology query Jiri Sponer
- AMBER: PCA and projections Miguel Ferreira
- AMBER: Amber 9 parallel test fail on 4096wat/Run.column_fft Yu Chen
- AMBER: grid output Sergey Samsonov
- AMBER: GBSA implicit chloroform nadiav.soton.ac.uk
- RE: AMBER: ab initio terminology query Ross Walker
- Re: AMBER: ab initio terminology query Gustavo Seabra
- Re: AMBER: Amber 9 parallel test fail on 4096wat/Run.column_fft David A. Case
- Re: AMBER: GBSA implicit chloroform David A. Case
- AMBER: NEWPDB.PDB from antechamber Esther Brugger
- AMBER: too big EEL values in the minimisation output Rachel
- Re: AMBER: Amber 9 parallel test fail on 4096wat/Run.column_fft Yu Chen
- Re: AMBER: GBSA implicit chloroform nadiav.soton.ac.uk
- RE: AMBER: NEWPDB.PDB from antechamber Junmei Wang
- RE: AMBER: Amber 9 parallel test fail on 4096wat/Run.column_fft Ross Walker
- Re: AMBER: GBSA implicit chloroform Adrian Roitberg
- Re: AMBER: ab initio terminology query David A. Case
- Re: AMBER: mm_pbsa does not terminate Holly Freedman
- Re: AMBER: too big EEL values in the minimisation output darden
- Re: AMBER: ab initio terminology query Jiri Sponer
- Re: AMBER: ab initio terminology query Jiri Sponer
- RE: AMBER: ab initio terminology query Yong Duan
- Re: AMBER: ab initio terminology query Adrian Roitberg
- RE: AMBER: NEWPDB.PDB from antechamber Esther Brugger
- Re: AMBER: mm_pbsa does not terminate Holly Freedman
- Re: AMBER: ab initio terminology query Jiri Sponer
- RE: AMBER: NEWPDB.PDB from antechamber Junmei Wang
- AMBER: Problem of QM/MM calculation with amber 9 parallel version Lee Kyung-koo
- RE: AMBER: ab initio terminology query Hayden Eastwood
- Re: AMBER: ab initio terminology query David A. Case
- RE: AMBER: ab initio terminology query Ilyas Yildirim
- RE: AMBER: ab initio terminology query Ross Walker
- RE: AMBER: Problem of QM/MM calculation with amber 9 parallel version Ross Walker
- AMBER: How the ensemble average calculated in Gibbs, AMBER7? Yongmei Pan
- RE: AMBER: ab initio terminology query Yong Duan
- [RE]RE: AMBER: Problem of QM/MM calculation with amber 9 parallel version Lee Kyung-koo
- RE: AMBER: Problem of QM/MM calculation with amber 9 parallel version Ross Walker
- Re: AMBER: problem installing amber9 with g95 gcc on a fc5 m/c Sayandeep Purkayasth
Thursday, 2 November 2006
- [RE]RE: AMBER: Problem of QM/MM calculation with amber 9 parallel version Lee Kyung-koo
- RE: AMBER: Problem of QM/MM calculation with amber 9 parallel version Rafi Ahmad
- AMBER: leap usage Stefano Federico Massimiliano Pieraccini (Stefano.Pieraccini)
- AMBER: Can we use the distance restraint in Replica-exchange simulation with AMBER8 wenfei Li
- Re: AMBER: leap usage Mark Williamson
- Re: AMBER: leap usage Angelo
- RE: AMBER: Problem of QM/MM calculation with amber 9 parallel version Ross Walker
- RE: AMBER: Problem of QM/MM calculation with amber 9 parallel version Ross Walker
- Re: AMBER: too big EEL values in the minimisation output Rachel
- Re: AMBER: too big EEL values in the minimisation output darden
- Re: AMBER: Can we use the distance restraint in Replica-exchange simulation with AMBER8 Carlos Simmerling
- AMBER: Interaction Energy Calculation Varsha Goyal
- Re: AMBER: Interaction Energy Calculation Vitor Manuel Sousa F?x
- Re: AMBER: Interaction Energy Calculation Varsha Goyal
- AMBER: ntt=1 in simulated annealing Tanya Johannsen
Friday, 3 November 2006
- AMBER: how to choose the parameter for the production/sampling run after the equilibration run hbluo
- Re: AMBER: ntt=1 in simulated annealing Carlos Simmerling
- Re: AMBER: too big EEL values in the minimisation output Rachel
- Re: AMBER: Amber 9 parallel test fail on 4096wat/Run.column_fft Yu Chen
- Re: AMBER: Amber 9 parallel test fail on 4096wat/Run.column_fft Ross Walker
- AMBER: Problems with equilibrating the starting density Markus Weingarth
- AMBER: Simulation a small chain of amino acids - error in MD simulation Dave, Sonya
- Re: AMBER: Simulation a small chain of amino acids - error in MD simulation Carlos Simmerling
- RE: AMBER: Simulation a small chain of amino acids - error in MD simulation Ross Walker
- AMBER: pmemd installation problem Ed Pate
- Re: AMBER: Amber 9 parallel test fail on 4096wat/Run.column_fft Yu Chen
- Re: AMBER: pmemd installation problem Robert Duke
- RE: AMBER: Simulation a small chain of amino acids - error in MD simulation Dave, Sonya
- RE: AMBER: Problems with equilibrating the starting density Ross Walker
- AMBER: Re: Fluorine and Bromine Parameters in Amber 9 Philip Cheung
- Re: AMBER: ntt=1 in simulated annealing Tanya Johannsen
- RE: AMBER: ntt=1 in simulated annealing Ross Walker
- AMBER: I got the error meassage in testcase of QMMM Lee Kyung-koo
Saturday, 4 November 2006
- AMBER: PTRAJ RMS: dumping RMSd vs time data r. a.
- AMBER: PTRAJ RMS: dumping RMSd vs time data r. a.
- AMBER: Unable to find solution for an error - "cannot successfully assign bond type" Rama krishnan
- Re: AMBER: PTRAJ RMS: dumping RMSd vs time data Adrian Roitberg
- AMBER: Ross Walker
- AMBER: RE: I got the error meassage in testcase of QMMM Ross Walker
- AMBER: ACS Chicago potential symposia and OASYS abstracts Thomas Cheatham
- AMBER: Amber: disufide bond Fenghui Fan
- Re: AMBER: PTRAJ RMS: dumping RMSd vs time data Fenghui Fan
Sunday, 5 November 2006
- RE: AMBER: Amber: disufide bond hayden
- RE: AMBER: Amber: disufide bond Fenghui Fan
- AMBER: trajout script Fenghui Fan
- AMBER: Combine amber-force field and gaff94 for one molecule? Michel Becker
- Re: AMBER: Combine amber-force field and gaff94 for one molecule? Fenghui Fan
- Re: AMBER: Combine amber-force field and gaff94 for one molecule? M. L. Dodson
- Re: AMBER: Combine amber-force field and gaff94 for one molecule? Fenghui Fan
- Re: AMBER: Combine amber-force field and gaff94 for one molecule? M. L. Dodson
- Re: AMBER: Combine amber-force field and gaff94 for one molecule? Jiri Sponer
- AMBER: no g77 in Fedora Core 5. how to get around with this problem in Fedora Core 5? Margaret S. Cheung
- Re: AMBER: no g77 in Fedora Core 5. how to get around with this problem in Fedora Core 5? Peter Gannett
- Re: AMBER: no g77 in Fedora Core 5. how to get around with this problem in Fedora Core 5? Fenghui Fan
- Re: AMBER: How the ensemble average calculated in Gibbs, AMBER7? David A. Case
- AMBER: Zn metal library Fenghui Fan
- AMBER: Mutual exclusion of atoms Nitin Bhardwaj
- RE: AMBER: Zn metal library Ross Walker
Monday, 6 November 2006
- Re: AMBER: no g77 in Fedora Core 5. how to get around with this problem in Fedora Core 5? Andreas Svrcek-Seiler
- AMBER: Potential Energy Calculation sangeeta
- Re: AMBER: Zn metal library Carlos Simmerling
- Re: AMBER: Potential Energy Calculation Carlos Simmerling
- RE: AMBER: Potential Energy Calculation Hayden Eastwood
- AMBER: problem with NAD+ parameters Urszula Uciechowska
- Re: AMBER: no g77 in Fedora Core 5. how to get around with this problem in Fedora Core 5? Margaret S. Cheung
- AMBER: PCA results with explicit Vs Implicit solvation Keerthi Gottipati
- Re: AMBER: PCA results with explicit Vs Implicit solvation Angelo
- Re: AMBER: no g77 in Fedora Core 5. how to get around with this problem in Fedora Core 5? Andreas Svrcek-Seiler
- Re: AMBER: no g77 in Fedora Core 5. how to get around with this problem in Fedora Core 5? Scott Pendley
- Re: AMBER: no g77 in Fedora Core 5. how to get around with this problem in Fedora Core 5? Scott Pendley
- Re: AMBER: trajout script Thomas Cheatham
- Re: AMBER: Potential Energy Calculation Mingfeng Yang
- AMBER: Mutual exclusion of atoms Nitin Bhardwaj
- Re: AMBER: Mutual exclusion of atoms Thomas Steinbrecher
- Re: AMBER: problem with NAD+ parameters Cenk Andac
- Re: AMBER: Mutual exclusion of atoms Nitin Bhardwaj
- AMBER: top2mol2.c scanf format string bug Chris Moth
- Re: AMBER: PTRAJ RMS: dumping RMSd vs time data Thomas Cheatham
- Re: AMBER: grid output Thomas Cheatham
- Re: AMBER: Mass weights Thomas Cheatham
- Re: AMBER: PTRAJ RMS: dumping RMSd vs time data r. a.
- Re: AMBER: PTRAJ RMS: dumping RMSd vs time data David A. Case
- Re: AMBER: PTRAJ RMS: dumping RMSd vs time data r. a.
Tuesday, 7 November 2006
- Re: AMBER: Mass weights Sergey Samsonov
- Re: AMBER: grid output Sergey Samsonov
- AMBER: leap - compilation error Tomas Kubar
- Re: AMBER: ntt=1 in simulated annealing Steven Winfield
- AMBER: klambda for TI method. Biswa Ranjan Meher
- Re: AMBER: klambda for TI method. David A. Case
- Re: AMBER: top2mol2.c scanf format string bug David A. Case
- Re: AMBER: grid output Thomas Cheatham
- Re: AMBER: grid output Sergey Samsonov
- [RE]AMBER: RE: I got the error meassage in testcase of QMMM Lee Kyung-koo
- AMBER: building a box kepa koldo burusco
- [RE]AMBER: RE: I got the error meassage in testcase of QMMM Lee Kyung-koo
- Re: AMBER: building a box Fenghui Fan
- AMBER: error about the number of snapshots AYTUG TUNCEL
- AMBER: Format of the prmtop file (NUMBER_EXCLUDED_ATOMS) & (EXCLUDED_ATOMS_LIST) Nitin Bhardwaj
- Re: AMBER: Format of the prmtop file (NUMBER_EXCLUDED_ATOMS) & (EXCLUDED_ATOMS_LIST) David A. Case
- Re: AMBER: leap - compilation error David A. Case
- AMBER: Atom Exclusion Nitin Bhardwaj
- AMBER: Re: Unit of force Kakali Sen
Wednesday, 8 November 2006
- AMBER: question about the topology file J. Zhang
- AMBER: Unit of force Kakali Sen
- Re: AMBER: question about the topology file Carlos Simmerling
- Re: AMBER: building a box kepa koldo burusco
- Re: AMBER: Unit of force Adrian Roitberg
- AMBER: vlimit exceeded for step 0, vmax = infinity Rachel
- Re: AMBER: Unit of force Kakali Sen
- AMBER: NAD ?? Urszula Uciechowska
- Re: AMBER: NAD ?? David A. Case
- AMBER: Flag for removal of translational and rotational center-of-mass (COM) motion Rajesh Murarka
- AMBER: simulating a small chain protein in water box Dave, Sonya
- Re: AMBER: Flag for removal of translational and rotational center-of-mass (COM) motion David A. Case
- AMBER: Problems amber mask in distance? Sergey Samsonov
- AMBER: big bond energy change from minimization and md (heating) Rachel
- Re: AMBER: vlimit exceeded for step 0, vmax = infinity David A. Case
- Re: AMBER: Problems amber mask in distance? Viktor Hornak
- Re: AMBER: Problems amber mask in distance? Sergey Samsonov
- Re: AMBER: vlimit exceeded for step 0, vmax = infinity Rachel
- Re: AMBER: vlimit exceeded for step 0, vmax = infinity Carlos Simmerling
- Re: AMBER: simulating a small chain protein in water box Carlos Simmerling
- Re: AMBER: vlimit exceeded for step 0, vmax = infinity Carlos Simmerling
- Re: AMBER: vlimit exceeded for step 0, vmax = infinity David A. Case
- AMBER: problem in calculating EGB using sander for ligand containing F atom VANDANA KUMARI
Thursday, 9 November 2006
- AMBER: Amber H-bond print? Andres Palencia
- AMBER: Probelm with running Amber 9 parallelly Rafi Ahmad
- AMBER: Biomolecular Simulation 2007 Angelo
- Re: AMBER: problem in calculating EGB using sander for ligand containing F atom David A. Case
- AMBER: Building Library Steve Seibold
- AMBER: Steve Seibold
- AMBER: saltconc for explicit solvent calculation. a a
- Re: AMBER: David A. Case
- Re: AMBER: saltconc for explicit solvent calculation. David A. Case
- Re: AMBER: saltconc for explicit solvent calculation. Carlos Simmerling
- Re: AMBER: Building Library Fenghui Fan
- AMBER: antechamber:tutorial Lwin, ThuZar
- AMBER: FW: antechamber:tutorial Lwin, ThuZar
- Re: AMBER: antechamber:tutorial Mark Williamson
- Re: AMBER: antechamber:tutorial Fenghui Fan
- AMBER: Building Library Steve Seibold
- AMBER: strange temperature behavior when changing to constant pressure Joshua
- RE: AMBER: antechamber:tutorial. . Lwin, ThuZar
Friday, 10 November 2006
- Re: AMBER: NAD ?? Urszula Uciechowska
- AMBER: sander error: rst file crash jitrayut jitonnom
- Re: AMBER: sander error: rst file crash Carlos Simmerling
- Re: AMBER: vlimit exceeded for step 0, vmax = infinity Rachel
- Re: AMBER: vlimit exceeded for step 0, vmax = infinity Carlos Simmerling
- Fwd: AMBER: sander error: rst file crash jitrayut jitonnom
- Re: AMBER: vlimit exceeded for step 0, vmax = infinity Rachel
- Re: AMBER: vlimit exceeded for step 0, vmax = infinity David A. Case
- AMBER: PTRAJ: radius of gyration kepa koldo burusco
- Re: AMBER: PTRAJ: radius of gyration Bill Ross
- Re: AMBER: sander error: rst file crash David A. Case
- RE: AMBER: vlimit exceeded for step 0, vmax = infinity Yong Duan
- Re: AMBER: NAD ?? Cenk Andac
- Re: AMBER: NAD ?? Cenk Andac
- AMBER: bond command between Zn and a CYM residue in one chain of a protein complex Fenghui Fan
Saturday, 11 November 2006
- Fwd: AMBER: sander error: rst file crash jitrayut jitonnom
- Re: Fwd: AMBER: sander error: rst file crash Carlos Simmerling
- Re: AMBER: sander error: rst file crash jitrayut jitonnom
Sunday, 12 November 2006
- Re: Re: AMBER: question about the topology file J. Zhang
- AMBER: ZN-CYS prepin and frcmd file Fenghui Fan
- Re: Fwd: AMBER: sander error: rst file crash David A. Case
- AMBER: The plc.frcmod file in the old version tutorial Fenghui Fan
Monday, 13 November 2006
- Re: AMBER: NAD ?? Urszula Uciechowska
- AMBER: <kein Betreff> Michel Becker
- Re: AMBER: NAD ?? Cenk Andac
- RE: AMBER: The plc.frcmod file in the old version tutorial Ross Walker
- RE: AMBER: <kein Betreff> Ross Walker
- Re: AMBER: vlimit exceeded for step 0, vmax = infinity Rachel
- Re: AMBER: <kein Betreff> Gustavo Seabra
- RE: AMBER: vlimit exceeded for step 0, vmax = infinity Yong Duan
Tuesday, 14 November 2006
- AMBER: what to do with the counter ions when minimizing average structure of DNA? Chengwen Chen
- AMBER: how to remove the rotation of system in periodic condition? 张勇
- AMBER: gfortran/gcc versus ifort/icc Lachele Foley (Lists)
- Re: AMBER: gfortran/gcc versus ifort/icc Fenghui Fan
- AMBER: Ptraj: radial distribution and correlation coefficient Austin B. Yongye
- AMBER: Acetone box SERGIO MIGUEL FERNANDES DOS SANTOS
- Re: AMBER: Ptraj: radial distribution and correlation coefficient Thomas Cheatham
- Re: AMBER: Ptraj: radial distribution and correlation coefficient Austin B. Yongye
- Re: AMBER: Ptraj: radial distribution and correlation coefficient Austin B. Yongye
- Re: AMBER: Ptraj: radial distribution and correlation coefficient Thomas Cheatham
- AMBER: Restraints of the strand-endings? Michel Becker
- Re: AMBER: Ptraj: radial distribution and correlation coefficient Andres Palencia
- Re: AMBER: Restraints of the strand-endings? Bill Ross
- Re: AMBER: vlimit exceeded for step 0, vmax = infinity Rachel
- RE: AMBER: vlimit exceeded for step 0, vmax = infinity Yong Duan
- Re: AMBER: ntt=1 in simulated annealing Tanya Johannsen
- AMBER: error in tleap test Christian Roth
- Re: AMBER: ntt=1 in simulated annealing Sergey Samsonov
Wednesday, 15 November 2006
- Re: AMBER: ntt=1 in simulated annealing kepa koldo burusco
- Re: AMBER: gfortran/gcc versus ifort/icc Lachele Foley (Lists)
- Re: AMBER: how to remove the rotation of system in periodic condition? David A. Case
- Re: AMBER: ntt=1 in simulated annealing David A. Case
- RE: AMBER: gfortran/gcc versus ifort/icc Jordi Camps
- Re: AMBER: error in tleap test Scott Brozell
- RE: AMBER: error in tleap test Christian Roth
- Re: AMBER: gfortran/gcc versus ifort/icc Luis Gracia
- AMBER: ptraj and mdvel question Jianhui
- AMBER: H-Bond Terms in amber force field Ilyas Yildirim
- AMBER: Error in compliling LEAP on Fedora 5 Pankaj Daga
- Re: AMBER: H-Bond Terms in amber force field Jiri Sponer
- Re: AMBER: ptraj and mdvel question Thomas Cheatham
- Re: AMBER: H-Bond Terms in amber force field Thomas Cheatham
- Re: AMBER: H-Bond Terms in amber force field Ilyas Yildirim
- Re: AMBER: Error in compliling LEAP on Fedora 5 Steven Winfield
- Re: AMBER: H-Bond Terms in amber force field Jiri Sponer
- Re: AMBER: Error in compliling LEAP on Fedora 5 David A. Case
- AMBER: MM_PBSA Varsha Goyal
Thursday, 16 November 2006
- AMBER: erroneous placement of TER card Gregory Sandala
- Re: AMBER: erroneous placement of TER card Robert Duke
- AMBER: opls_aa in amber Vitor Manuel Sousa F?x
- RE: AMBER: gfortran/gcc versus ifort/icc Jordi Camps
- Re: AMBER: erroneous placement of TER card David A. Case
- Re: AMBER: MM_PBSA Thomas Steinbrecher
- AMBER: pqr file Seth Lilavivat
- Re: AMBER: erroneous placement of TER card Robert Duke
- Re: AMBER: pqr file David A. Case
- AMBER: GLYCAM and ff98 atom-types Gabbar S. Daaku
- AMBER: Xleap woes Shozeb Haider
- Re: AMBER: Xleap woes David A. Case
- Re: AMBER: erroneous placement of TER card Bill Ross
- Re: AMBER: erroneous placement of TER card David A. Case
- Re: AMBER: erroneous placement of TER card Bill Ross
- Re: AMBER: GLYCAM and ff98 atom-types Fenghui Fan
- Re: AMBER: Xleap woes Fenghui Fan
- AMBER: parameters for beta peptides yipinl.umich.edu
- Re: AMBER: GLYCAM and ff98 atom-types] Austin B. Yongye
- Re: AMBER: Xleap woes M. L. Dodson
- Re: AMBER: gfortran/gcc versus ifort/icc Lachele Foley (Lists)
- AMBER: optimatized structure is so much different from the original pdb structure emilia wu
Friday, 17 November 2006
- AMBER: Ethanol Rita Cassia
- AMBER: dihedral angle equation Vitor Manuel Sousa F?x
- Re: AMBER: Ethanol FyD
- Re: AMBER: dihedral angle equation Igor Schapiro
- Re: AMBER: dihedral angle equation Igor Schapiro
- Re: AMBER: optimatized structure is so much different from the original pdb structure Gabbar S. Daaku
- AMBER: reading psf file jojartb.pharm.u-szeged.hu
- AMBER: Amber9 installation error Keerthi Gottipati
- Re: AMBER: reading psf file Thomas Cheatham
Saturday, 18 November 2006
- Re: AMBER: reading psf file jojartb.pharm.u-szeged.hu
- RE: AMBER: Amber9 installation error Ross Walker
- AMBER: gfortran and amber9 success on FreeBSD M. L. Dodson
Sunday, 19 November 2006
- AMBER: parameters for silicon atom Chengwen Chen
Saturday, 18 November 2006
- Re: AMBER: reading psf file jojartb.pharm.u-szeged.hu
Monday, 20 November 2006
- AMBER: problems with saving self-built molecules parameters Rachel
- Re: AMBER: problems with saving self-built molecules parameters Fenghui Fan
- Re: AMBER: problems with saving self-built molecules parameters Rachel
- Re: AMBER: problems with saving self-built molecules parameters Fenghui Fan
- AMBER: Combining Residues in LEaP for Lipid Bilayers Matthew Tessier
- Re: AMBER: problems with saving self-built molecules parameters Rachel
- Re: AMBER: problems with saving self-built molecules parameters David A. Case
- Re: AMBER: Combining Residues in LEaP for Lipid Bilayers David A. Case
- RE: AMBER: Combining Residues in LEaP for Lipid Bilayers Matthew Tessier
- Re: AMBER: problems with saving self-built molecules parameters Fenghui Fan
- Re: AMBER: problems with saving self-built molecules parameters Rachel
- Re: AMBER: problems with saving self-built molecules parameters Bill Ross
- RE: AMBER: Combining Residues in LEaP for Lipid Bilayers Bill Ross
- AMBER: the energy and temperature both increasing during the simulation with NTT=0 Xiaowei (David) Li
- Re: AMBER: the energy and temperature both increasing during the simulation with NTT=0 David A. Case
Tuesday, 21 November 2006
- AMBER: matrix correl Jardas sucuriba
- AMBER: Quantifying pi-pi interactions zachary hartman
- Re: AMBER: Quantifying pi-pi interactions Jiri Sponer
- Re: AMBER: Combining Residues in LEaP for Lipid Bilayers David A. Case
- AMBER: ff03 GLY HAs atom type Sandro Fornili
- RE: AMBER: ff03 GLY HAs atom type Yong Duan
- AMBER: compile amber8 on IBM-sp4 Rachel
- Re: AMBER: compile amber8 on IBM-sp4 Scott Brozell
- AMBER: Ptraj: diffusion rate Austin B. Yongye
- AMBER: Ptraj: correlation time Austin B. Yongye
- RE: AMBER: ff03 GLY HAs atom type mahdi fathi
Wednesday, 22 November 2006
- AMBER: Some warning !!! during SANDER ? jitrayut jitonnom
- Re: AMBER: Ethanol Rita Cassia
- AMBER: Ptraj syntax change Amber8->Amber9 ? Markus Kaukonen
- Re: AMBER: compile amber8 on IBM-sp4 Rachel
- AMBER: Radius of gyration r. a.
- AMBER: SHAKE problem after minimization Rachel
- Re: AMBER: Ethanol FyD
- Re: AMBER: SHAKE problem after minimization Rachel
- AMBER: Re: installation instructions David A. Case
- RE: AMBER: Some warning !!! during SANDER ? Ross Walker
- RE: AMBER: compile amber8 on IBM-sp4 Ross Walker
- RE: AMBER: SHAKE problem after minimization Ross Walker
- Re: AMBER: compile amber8 on IBM-sp4 Rachel
- Re: AMBER: SHAKE problem after minimization Rachel
- RE: AMBER: SHAKE problem after minimization Hayden Eastwood
- AMBER: Problem with mask when using distance in ptraj Christopher Gaughan
- Re: AMBER: SHAKE problem after minimization Rachel
- RE: AMBER: SHAKE problem after minimization Hayden Eastwood
- RE: AMBER: SHAKE problem after minimization Hayden Eastwood
- Re: AMBER: Problem with mask when using distance in ptraj David A. Case
- Re: AMBER: Problem with mask when using distance in ptraj Thomas Cheatham
- Re: AMBER: Ptraj syntax change Amber8->Amber9 ? David A. Case
- Re: AMBER: SHAKE problem after minimization Steven Winfield
- Re: AMBER: SHAKE problem after minimization David A. Case
- AMBER: problem of the REMD with nmr constraints wenfei Li
- Re: AMBER: compile amber8 on IBM-sp4 Xuebin Qiao
Thursday, 23 November 2006
- AMBER: ammonia parameters Peter Trodler
- Re: AMBER: compile amber8 on IBM-sp4 Rachel
- Re: AMBER: compile amber8 on IBM-sp4 Xuebin Qiao
- Re: AMBER: compile amber8 on IBM-sp4 Xuebin Qiao
- Re: AMBER: compile amber8 on IBM-sp4 Rachel
- Re: AMBER: compile amber8 on IBM-sp4 Xuebin Qiao
- Re: AMBER: ammonia parameters Fenghui Fan
- Re: AMBER: compile amber8 on IBM-sp4 Rachel
- AMBER: Restarting with new topology Sergey Samsonov
- AMBER: Snapshots (pdbs) from a trajectory. Jordi Rodrigo De Losada
- Re: AMBER: compile amber8 on IBM-sp4 Martin Peters
- Re: AMBER: Snapshots (pdbs) from a trajectory. Carlos Simmerling
- Re: AMBER: compile amber8 on IBM-sp4 Rachel
- Re: AMBER: SHAKE problem after minimization Rachel
- AMBER: Unable to find mopac charges in divcon.out Rachel
- Re: AMBER: Unable to find mopac charges in divcon.out Mark Williamson
- Re: AMBER: Unable to find mopac charges in divcon.out Rachel
- Re: AMBER: Snapshots (pdbs) from a trajectory. David A. Case
- AMBER: NTR for implicit solvent? How to defin restrain for two disconnected sequences? a a
- Re: AMBER: NTR for implicit solvent? How to defin restrain for two disconnected sequences? David A. Case
Friday, 24 November 2006
- Re: AMBER: NTR for implicit solvent? How to defin restrain for two disconnected sequences? a a
- Re: AMBER: NTR for implicit solvent? How to defin restrain for two disconnectedsequences? cristian obiol
- RE: AMBER: Radius of gyration kepa koldo burusco
- RE: AMBER: Combining Residues in LEaP for Lipid Bilayers kepa koldo burusco
- RE: AMBER: Radius of gyration Andy Purkiss-Trew
- Re: AMBER: Unable to find mopac charges in divcon.out Mark Williamson
- Re: AMBER: problem of the REMD with nmr constraints Carlos Simmerling
- RE: AMBER: Radius of gyration kepa koldo burusco
- AMBER: failure in testing amber8 parallel parts on IBM-SP4 machines Rachel
- Re: RE: AMBER: Radius of gyration Carles Jaime Cardiel
- Re: AMBER: failure in testing amber8 parallel parts on IBM-SP4 machines Nicolas Lux Fawzi
- RE: AMBER: Radius of gyration Andy Purkiss-Trew
- Re: RE: AMBER: Radius of gyration Andy Purkiss-Trew
- Re: AMBER: failure in testing amber8 parallel parts on IBM-SP4 machines Rachel
- Re: RE: AMBER: Radius of gyration Elijah Gregory
- AMBER: Antechamber and gaussian questions Fenghui Fan
- AMBER: amber9 serial compile with pathscale on SuSe10.1/AMD64 In Hee Park
- AMBER: bondtype problem Fenghui Fan
- Re: AMBER: amber9 serial compile with pathscale on SuSe10.1/AMD64 David A. Case
- Re: AMBER: NTR for implicit solvent? How to defin restrain for two disconnectedsequences? a a
- Re: AMBER: failure in testing amber8 parallel parts on IBM-SP4 machines Xuebin Qiao
- AMBER: respin file Fenghui Fan
Saturday, 25 November 2006
- Re: AMBER: NTR for implicit solvent? How to defin restrain for two disconnectedsequences? David A. Case
- Re: AMBER: respin file M. L. Dodson
- AMBER: resp Fenghui Fan
- AMBER: respin file Fenghui Fan
- Re: AMBER: respin file Ilyas Yildirim
- Re: AMBER: respin file Fenghui Fan
- Re: AMBER: problem of the REMD with nmr constraints wenfei Li
- Re: AMBER: respin file Ilyas Yildirim
- Re: AMBER: respin file Fenghui Fan
- AMBER: how to get complete prepin file Fenghui Fan
Sunday, 26 November 2006
- Re: AMBER: respin file Ilyas Yildirim
- Re: AMBER: Problem with mask when using distance in ptraj Christopher Gaughan
- AMBER: how can i treat with long "mask" in ptraj analysis. Changge Ji
- Re: AMBER: respin file Fenghui Fan
- Re: AMBER: respin file Ilyas Yildirim
- Re: AMBER: respin file M. L. Dodson
- AMBER: ZN prepin Fenghui Fan
- Re: AMBER: respin file Fenghui Fan
- AMBER: bond information Fenghui Fan
- AMBER: ptraj grid Hannes Loeffler
Monday, 27 November 2006
- AMBER: Did Antechamber support tertiary amines? How can I get the prepin file for it? a a
- Re: AMBER: NTR for implicit solvent? How to defin restrain for two disconnectedsequences? a a
- AMBER: helices in GB simulations Marie-Pierre Durrieu
- Re: AMBER: helices in GB simulations Carlos Simmerling
- AMBER: minimization of Hydrogens with xLeaP rebeca.mmb.pcb.ub.es
- AMBER: Problem Installing Amber in SGI Irix 6.5 trudy.uoguelph.ca
- AMBER: phantom sander8 in dmesg Lachele Foley (Lists)
- Re: AMBER: helices in GB simulations Ilyas Yildirim
- Re: AMBER: Problem Installing Amber in SGI Irix 6.5 David A. Case
- Re: AMBER: minimization of Hydrogens with xLeaP David A. Case
- AMBER: prepin file nan Fenghui Fan
- AMBER: Problem about dummy atoms when running antechamber 한 민우
- Re: RE: AMBER: Radius of gyration r. a.
Tuesday, 28 November 2006
- Re: AMBER: prepin file nan linfu
Monday, 27 November 2006
- AMBER: protonated phosphate Einar Uggerud
- AMBER: NONB values adjusted? Dave S Walker
- AMBER: energy minimizations in amber8 vs. amber9 Seongeun Yang
Tuesday, 28 November 2006
- AMBER: How to specify user defined force fields or its parameters in amber?? Gobind Singh Bisht
- Re: AMBER: How to specify user defined force fields or its parameters in amber?? Carlos Simmerling
- Re: AMBER: How to specify user defined force fields or its parameters in amber?? Gobind Singh Bisht
- Re: AMBER: How to specify user defined force fields or its parameters in amber?? Carlos Simmerling
- Re: AMBER: How to specify user defined force fields or its parameters in amber?? Gobind Singh Bisht
- AMBER: xleap Steve Seibold
- AMBER: uccadco.ucl.ac.uk
- Re: AMBER: prepin file nan Fenghui Fan
- Re: AMBER: How to specify user defined force fields or its parameters in amber?? Gustavo Seabra
- AMBER: Modifying a Force Field Seth Lilavivat
- Re: AMBER: Problem Installing Amber in SGI Irix 6.5 trudy.uoguelph.ca
- Re: AMBER: David A. Case
- AMBER: nmode output with ptraj nadiav.soton.ac.uk
- Re: AMBER: xleap David A. Case
- Re: AMBER: NONB values adjusted? Thomas Steinbrecher
- Re: AMBER: How to specify user defined force fields or its parameters in amber?? Gobind Singh Bisht
- AMBER: Charge fitting in Amber Changge Ji
- AMBER: Amber9 patch bugfix.all issue on SunOS 5.1 Michael John Hanby
- Re: AMBER: NONB values adjusted? Dave S Walker
- AMBER: ambpdb -pqr Seth Lilavivat
- RE: AMBER: Amber9 patch bugfix.all issue on SunOS 5.1 Michael John Hanby
- Re: AMBER: ambpdb -pqr harianto
- Re: AMBER: ambpdb -pqr Carlos Simmerling
- Re: AMBER: Amber9 patch bugfix.all issue on SunOS 5.1 Mark Williamson
- Re: AMBER: ambpdb -pqr Ilyas Yildirim
- RE: AMBER: Amber9 patch bugfix.all issue on SunOS 5.1 Michael John Hanby
- RE: AMBER: prepin file nan Junmei Wang
- RE: AMBER: Problem about dummy atoms when running antechamber Junmei Wang
- RE: AMBER: bond information Junmei Wang
- AMBER: RE: Amber: ZN-complex file Junmei Wang
- Re: AMBER: RE: Amber: ZN-complex file Fenghui Fan
- RE: AMBER: RE: Amber: ZN-complex file Junmei Wang
- AMBER: Periodic simulations with net charge Jennie Thomas
- Re: AMBER: Periodic simulations with net charge David A. Case
- Re: AMBER: nmode output with ptraj David A. Case
- Re: AMBER: nmode output with ptraj a a
- AMBER: DNA helix end stable? a a
- AMBER: How to apply a force to some atom in a residues? a a
- Re: AMBER: Charge fitting in Amber FyD
- Re: AMBER: RE: Amber: ZN-complex file FyD
Wednesday, 29 November 2006
- Re: AMBER: How to apply a force to some atom in a residues? Carlos Simmerling
- Re: AMBER: DNA helix end stable? Carlos Simmerling
- Re: AMBER: Problem Installing Amber in SGI Irix 6.5 Joe Nolan
- AMBER: Solvation Energies Ivelin Georgiev
- Re: AMBER: Problem Installing Amber in SGI Irix 6.5 trudy.uoguelph.ca
- AMBER: Confusion about PBC anna.schrey.gmx.de
- Re: AMBER: Confusion about PBC Thomas Steinbrecher
- AMBER: Langevin temperature control vs berendson heat bath Hayden Eastwood
- Re: AMBER: Langevin temperature control vs berendson heat bath Carlos Simmerling
- AMBER: ptraj----radial output files Esther Brugger
- Re: AMBER: How to apply a force to some atom in a residues? a a
- AMBER: How to run MD simulation of a silicon containing complex with AMBER9? Chengwen Chen
- AMBER: How to specify a box with few walls rigid and others with periodic boundary conditions and then apply a pressure gradient across it? Gobind Singh Bisht
Thursday, 30 November 2006
- AMBER: How to run QM/MM simulation of DNA duplex bound with platinum moietes Chengwen Chen
- AMBER: Performing Interactive Essential Dynamics in Ptraj hbluo
- RE: AMBER: Langevin temperature control vs berendson heat bath Hayden Eastwood
- Re: AMBER: Langevin temperature control vs berendson heat bath Andreas Svrcek-Seiler
- Re: AMBER: How to apply a force to some atom in a residues? Carlos Simmerling
- Re: AMBER: Langevin temperature control vs berendson heat bath Carlos Simmerling
- Re: AMBER: How to run QM/MM simulation of DNA duplex bound with platinum moietes Gustavo Seabra
- Re: AMBER: Problem Installing Amber in SGI Irix 6.5 trudy.uoguelph.ca
- Re: AMBER: How to specify user defined force fields or its parameters in amber?? Gustavo Seabra
- AMBER: amber9 parralel compiling Nikola Trbovic
- Re: AMBER: amber9 parralel compiling David A. Case
- Re: AMBER: amber9 parralel compiling Nikola Trbovic
- AMBER: How to recompile sander for single-processor use in AMBER 8? Peter Anderson
- AMBER: watershell and image commands Esther Brugger
- Re: AMBER: How to recompile sander for single-processor use in AMBER 8? David A. Case
- AMBER: watershell command Esther Brugger
- Re: AMBER: watershell and image commands Thomas Cheatham
- Re: AMBER: amber9 parralel compiling David A. Case
- Re: AMBER: watershell and image commands Esther Brugger
- AMBER: H-bond analysis (Ptraj) Esther Brugger

Last message date: Sun Dec 03 2006 - 06:07:40 PST
Archived on: Wed Apr 24 2024 - 05:53:32 PDT

Amber Archive Nov 2006 by date