Amber Archive Jun 2007: by date

Friday, 1 June 2007
- Re: AMBER: Solvent models Francesco Pietra
- AMBER: problem in installing amber9 Syed Tarique Moin
- AMBER: rms in nmode Marie Brut
- Re: AMBER: rms in nmode cristian
- Re: AMBER: Solvent models FyD
- AMBER: Question about separating bonded force Shawn yy
- Re: AMBER: Question about separating bonded force David A. Case
- Re: AMBER: rms in nmode David A. Case
- AMBER: equilibrium constants via MMPBSA Sean Rathlef
- Re: AMBER: equilibrium constants via MMPBSA Julien Michel
- Re: AMBER: Reg restraint value obtained during umbrella sampling D.Usharani
- AMBER: BUG? Does TLEAP understand SPC/E water? David Cerutti
- RE: AMBER: BUG? Does TLEAP understand SPC/E water? Ross Walker
- Re: AMBER: BUG? Does TLEAP understand SPC/E water? Thomas Steinbrecher
- Re: AMBER: BUG? Does TLEAP understand SPC/E water? David A. Case
- Re: AMBER: BUG? Does TLEAP understand SPC/E water? David A. Case
- AMBER: RE: process_mdout.perl Ross Walker
- Re: AMBER: problem in installing amber9 David A. Case
- Re: AMBER: Reg restraint value obtained during umbrella sampling David A. Case
Saturday, 2 June 2007
- AMBER: "distance" command in ptraj Roberto Veiga
- Re: AMBER: "distance" command in ptraj Carlos Simmerling
- Re: AMBER: Reg restraint value obtained during umbrella sampling D.Usharani
- Re: AMBER: "distance" command in ptraj Barbault Florent
- Re: AMBER: Reg restraint value obtained during umbrella sampling David A. Case
Sunday, 3 June 2007
- AMBER: pdb flie format Mr Defang Ouyang
- AMBER: dihedral simulation lishan yao
- AMBER: MM-GBSA: pairwise decompose energy calculation can't read snapshot_com.all.out jitrayut jitonnom
- Re: AMBER: pdb flie format Fenghui Fan
- Re: AMBER: pdb flie format David A. Case
- Re: AMBER: dihedral simulation David A. Case
- Re: AMBER: RESTRAINTMASK Sandeep Kaushik
Monday, 4 June 2007
- Re: AMBER: equilibrium constants via MMPBSA David Mobley
- AMBER: LES problem Urszula Uciechowska
- AMBER: Installation Question Chrystal Bruce
- AMBER: Once again, "distance" command in ptraj Roberto Veiga
- Re: AMBER: Once again, "distance" command in ptraj Carlos Simmerling
- Re: AMBER: Installation Question Carlos Simmerling
- Re: AMBER: Once again, "distance" command in ptraj Roberto Veiga
- Re: AMBER: Installation Question Jianmin Feng
- AMBER: Once again, "distance" command in ptraj Roberto Veiga
- AMBER: Amber9's sander.MPI on x86_64 kkirschn.hamilton.edu
- Re: AMBER: Amber9's sander.MPI on x86_64 Thomas Steinbrecher
- RE: AMBER: Amber9's sander.MPI on x86_64 Ross Walker
- AMBER: Problem about prepare the model when running antechamber Liang, Lei
- Re: AMBER: RESTRAINTMASK Roberto Veiga
- RE: AMBER: Problem about prepare the model when running antechamber Ross Walker
- Re: AMBER: Problem about prepare the model when running antechamber Carlos Simmerling
- Re: AMBER: Problem about prepare the model when running antechamber Liang, Lei
- Re: AMBER: Problem about prepare the model when running antechamber Liang, Lei
- Re: AMBER: pdb flie format j j
- AMBER: Nucleic acid analyse : base pair parameters, backbone torsions... Sophie Barbe
- Re: AMBER: Nucleic acid analyse : base pair parameters, backbone torsions... Cenk Andac
- Re: AMBER: Once again, "distance" command in ptraj Thomas Cheatham
- Re: AMBER: Nucleic acid analyse : base pair parameters, backbone torsions... Thomas Cheatham
Tuesday, 5 June 2007
- Re: AMBER: Nucleic acid analyse : base pair parameters, backbone torsions... Stéphane Téletchéa
- Re: AMBER: Once again, "distance" command in ptraj Roberto Veiga
- Re: AMBER: LES problem Carlos Simmerling
- Re: AMBER: LES problem Vlad Cojocaru
- AMBER: problem with starting REM on amber9 priya priya
- Re: AMBER: problem with starting REM on amber9 Carlos Simmerling
- Re: AMBER: problem with starting REM on amber9 priya priya
- AMBER: Ptraj hbond analysis Achuth Prabhu
- RE: AMBER: problem with starting REM on amber9 Ross Walker
- Re: AMBER: Amber9's sander.MPI on x86_64 Steve Young
- AMBER: problem running parallel jobs Nikola Trbovic
- Re: AMBER: problem running parallel jobs Robert Konecny
- AMBER: REMD and mpiexec Steve Young
Wednesday, 6 June 2007
- RE: AMBER: problem with starting REM on amber9 priya priya
- AMBER: g(r) in mixtures? BJÖRN KARLSSON
- AMBER: Restraining valence angles Abi Ghanem josephine
- AMBER: Reg COM restraint to DNA D.Usharani
- Re: AMBER: Restraining valence angles David A. Case
- AMBER: GB vs. Invacuo Energies Seth Lilavivat
- RE: AMBER: REMD and mpiexec Ross Walker
- RE: AMBER: Amber9's sander.MPI on x86_64 Ross Walker
- AMBER: Hardware recommendations please Jeremy Weedon
- RE: AMBER: problem running parallel jobs Nikola Trbovic
- Re: AMBER: problem running parallel jobs Robert Duke
- RE: AMBER: problem running parallel jobs Nikola Trbovic
- Re: AMBER: problem running parallel jobs Robert Duke
- AMBER: Ptraj: reading PDB files Austin B. Yongye
Thursday, 7 June 2007
- RE: AMBER: problem running parallel jobs Andy Purkiss-Trew
- Re: AMBER: Ptraj: reading PDB files Austin B. Yongye
- RE: AMBER: problem running parallel jobs Nikola Trbovic
- AMBER: How to fix two angle but do umberlla sampling for distance? Catein Catherine
- AMBER: Should we just vary one parameter at a time only for PMF calculations? Catein Catherine
- Re: AMBER: Hardware recommendations please Jeremy Weedon
- Re: AMBER: How to fix two angle but do umberlla sampling for distance? Jerome.GOLEBIOWSKI.unice.fr
- RE: AMBER: REMD and mpiexec Steve Young
- AMBER: extracting starting structures from equilibration trajectory Nikola Trbovic
- Re: AMBER: Hardware recommendations please David LeBard
- Re: AMBER: extracting starting structures from equilibration trajectory Ilyas Yildirim
- RE: AMBER: extracting starting structures from equilibration trajectory Nikola Trbovic
- Re: AMBER: extracting starting structures from equilibration trajectory Carlos Simmerling
- RE: AMBER: extracting starting structures from equilibration trajectory Ilyas Yildirim
- RE: AMBER: extracting starting structures from equilibration trajectory Nikola Trbovic
- RE: AMBER: extracting starting structures from equilibration trajectory Ilyas Yildirim
- RE: AMBER: extracting starting structures from equilibration trajectory Nikola Trbovic
- AMBER: Dihedral driver Beale, John
- Re: AMBER: Dihedral driver Ilyas Yildirim
- AMBER: amber94 parameters for cholesterol paula lario
- AMBER: Trouble on wiki about GAFF j j
- Re: AMBER: Trouble on wiki about GAFF David A. Case
- Re: AMBER: Reg restraint value obtained during umbrella sampling D.Usharani
Friday, 8 June 2007
- Re: AMBER: Trouble on wiki about GAFF j j
- AMBER: Potential of mean force. Catein Catherine
- Re: AMBER: Potential of mean force. Carlos Simmerling
- AMBER: mmpbsa decomposition error cristian
- Re: AMBER: Should we just vary one parameter at a time only for PMF calculations? David A. Case
- Re: AMBER: Trouble on wiki about GAFF David A. Case
- AMBER: Compiling openmpi/icc/icpc Francesco Pietra
- AMBER: Taryn Hartley
- Re: AMBER: Carlos Simmerling
- AMBER: RE: Need your gudiance Ross Walker
- AMBER: RE: Need your gudiance Ross Walker
- RE: AMBER: Compiling openmpi/icc/icpc Ross Walker
- RE: AMBER: Compiling openmpi/icc/icpc Francesco Pietra
Sunday, 10 June 2007
- AMBER: antechamber/charges/conformation Francesco Pietra
- AMBER: amber9 compile problem hmeij.wesleyan.edu
- AMBER: problem installing amber7 Saiful Islam
- Re: AMBER: problem installing amber7 Carlos Simmerling
- Re: AMBER: amber9 compile problem Mark Williamson
- RE: AMBER: amber9 compile problem Ross Walker
- AMBER: Rdf question BJÖRN KARLSSON
- AMBER: Installing on windows Colby C
- Re: AMBER: Installing on windows Carlos Simmerling
- Re: AMBER: Installing on windows Gustavo Seabra
- Re: AMBER: Installing on windows Colby C
- Re: AMBER: Installing on windows Gustavo Seabra
- AMBER: Input files for the Potential of mean force. Catein Catherine
- Re: AMBER: problem installing amber7 David A. Case
- Re: AMBER: Installing on windows Colby C
- Re: AMBER: Installing on windows David A. Case
Monday, 11 June 2007
- Re: AMBER: antechamber/charges/conformation FyD
- Re: AMBER: antechamber/charges/conformation Francesco Pietra
- Re: AMBER: Installing on windows Colby C
- Re: AMBER: amber9 compile problem Henk Meij
- Re: AMBER: amber9 compile problem Mark Williamson
- Re: AMBER: amber9 compile problem Henk Meij
- Re: AMBER: Installing on windows Gustavo Seabra
- Re: AMBER: Installing on windows Colby C
- Re: AMBER: Installing on windows Colby C
- Re: AMBER: Installing on windows Gustavo Seabra
- RE: AMBER: amber9 compile problem Ross Walker
- Re: AMBER: Installing on windows Colby C
- AMBER: Steve Seibold
- Re: AMBER: Installing on windows Gustavo Seabra
- Re: AMBER: Installing on windows Bill Ross
- Re: AMBER: amber9 compile problem Henk Meij
- Re: AMBER: Installing on windows Bill Ross
- AMBER: Question about MPI-IO David LeBard
- Re: AMBER: Question about MPI-IO Thomas Cheatham III
- Re: AMBER: Question about MPI-IO Robert Duke
- RE: AMBER: amber9 compile problem Ross Walker
- AMBER: dihedral parameters Jardas sucuriba
- RE: AMBER: Question about MPI-IO Ross Walker
- AMBER: Amber 9 on IRIX 6.5 Colby C
- Re: AMBER: Question about MPI-IO David LeBard
- AMBER: xleap on cygwin Colby C
- AMBER: NMR vs. X-ray structures Sally Pias
- Re: AMBER: NMR vs. X-ray structures Marc Baaden
- AMBER: Amber: Number density profile, pucker..reg Praveena Gopal
Tuesday, 12 June 2007
- AMBER: building water box with desired number of molecules Vijay Manickam Achari
- Re: AMBER: problem in installing amber9 Syed Tarique Moin
- Re: AMBER: building water box with desired number of molecules gurpreet singh
- Re: AMBER: NMR vs. X-ray structures Carlos Simmerling
- AMBER: Internal dielectric and MMPBSA Ileana Stoica
- Re: AMBER: xleap on cygwin Wei Chen
- AMBER: Metal ions in GBSA Wei Chen
- AMBER: Using position restraints during constant pressure equilibration priya priya
- AMBER: MM-PBSA calcuation for drug dna complex in 2:1 ratio saurabh agrawal
- Re: AMBER: amber9 compile problem Henk Meij
- AMBER: Steve Seibold
- Re: AMBER: xleap on cygwin Colby C
- Re: AMBER: xleap on cygwin Steven Winfield
- RE: AMBER: amber9 compile problem Ross Walker
- RE: AMBER: Atom types Taryn Hartley
- Re: AMBER: Atom types Melinda Layten
- Re: AMBER: David A. Case
- Re: AMBER: dihedral parameters David A. Case
- AMBER: box size bomb in QMMM calculation M. L. Dodson
- AMBER: frcmod Brooke Elizabeth Adams
- AMBER: metal ions Wei Chen
- Re: AMBER: problem in installing amber9 David A. Case
- Re: AMBER: frcmod David A. Case
- RE: AMBER: box size bomb in QMMM calculation Ross Walker
- Re: AMBER: box size bomb in QMMM calculation M. L. Dodson
- Re: AMBER: xleap on cygwin Colby C
- AMBER: Installing amber9 in IBM P5? Du, Shiyu
- RE: AMBER: dihedral parameters Jardas sucuriba
- RE: AMBER: Installing amber9 in IBM P5? Ross Walker
- RE: AMBER: box size bomb in QMMM calculation Ross Walker
- RE: AMBER: problem in installing amber9 Ross Walker
- Re: AMBER: Installing amber9 in IBM P5? Du, Shiyu
Wednesday, 13 June 2007
- AMBER: hydrogen bond Guillaume Renvez
- Re: AMBER: box size bomb in QMMM calculation M. L. Dodson
- AMBER: problems using TIP4PBOX john chen
- Re: AMBER: problems using TIP4PBOX David A. Case
- AMBER: [Fwd: Tr: H bonds] Guillaume Renvez
- Re: AMBER: problems using TIP4PBOX Andy Purkiss-Trew
- AMBER: Hbonds mbrut.laas.fr
- Re: AMBER: problem in installing amber9 Henk Meij
- AMBER: S-nitrocysteine Anthony Cruz Balberdi
- Re: AMBER: Installing amber9 in IBM P5? Jed W Pitera
- RE: AMBER: Installing amber9 in IBM P5? Ross Walker
- RE: AMBER: problem in installing amber9 Ross Walker
- AMBER: g(r) khn _
- Re: AMBER: problem in installing amber9 Henk Meij
Tuesday, 12 June 2007
- Re: AMBER: amber9 compile problem Henk Meij
Wednesday, 13 June 2007
- Re: AMBER: Installing amber9 in IBM P5? Du, Shiyu
- Re: AMBER: amber9 compile problem Robert Duke
- RE: AMBER: problem in installing amber9 Ross Walker
- Re: AMBER: problem in installing amber9 Robert Duke
- Re: AMBER: problem in installing amber9 Henk Meij
- Re: AMBER: problem in installing amber9 SOLVED! Henk Meij
- Re: AMBER: Hbonds David A. Case
- Re: AMBER: Installing amber9 in IBM P5? Du, Shiyu
- Re: AMBER: S-nitrocysteine FyD
- AMBER: SANDER error: 'angles are not correct' Fred Baba
- RE: AMBER: Installing amber9 in IBM P5? Ross Walker
- AMBER: Regarding conversion of CHARMM force field parameters to AMBER parameters. nag raj
- THANKS -- Re: AMBER: NMR vs. X-ray structures Sally Pias
- AMBER: (no subject) Catein Catherine
Thursday, 14 June 2007
- AMBER: Hbonds mbrut.laas.fr
- AMBER: spring constant for restraint Catein Catherine
- Re: AMBER: (no subject) Franck Vendeix
- AMBER: ff99 vs ff99SB for RNA Brent Krueger
- Re: AMBER: ff99 vs ff99SB for RNA Carlos Simmerling
- Re: AMBER: ff99 vs ff99SB for RNA j j
- Re: AMBER: ff99 vs ff99SB for RNA Carlos Simmerling
- Re: AMBER: ff99 vs ff99SB for RNA Thomas Cheatham III
- AMBER: [ProblemSolved]Re: SANDER error: 'angles are not correct' Fred Baba
- AMBER: Compile openmpi Francesco Pietra
- AMBER: umbrella sampling dihedral restraint question Cen Gao
- AMBER: pair distribution function khn _
- Re: AMBER: pair distribution function Thomas Cheatham III
Friday, 15 June 2007
- AMBER: isolated NTP Steve Seibold
- Re: AMBER: Hbonds David A. Case
- AMBER: Saving a structuring from trajectory Seth Lilavivat
- Re: AMBER: Amber Installation Error David A. Case
- Re: AMBER: Saving a structuring from trajectory Ilyas Yildirim
- Re: AMBER: frcmod Brooke Elizabeth Adams
- RE: AMBER: Amber Installation Error Ross Walker
- AMBER: .lib files Taryn Hartley
- Re: AMBER: .lib files Ilyas Yildirim
- AMBER: performance with implicit solvent Kijeong Kwac
- AMBER: PDB problems Taryn Hartley
- Re: AMBER: performance with implicit solvent Carlos Simmerling
- Re: AMBER: performance with implicit solvent David A. Case
- Re: AMBER: PDB problems David A. Case
- Re: AMBER: Saving a structuring from trajectory Bill Ross
- AMBER: MMPBSA-nmode .top question Matthew Danielson
- Re: AMBER: frcmod David A. Case
- Re: AMBER: PDB problems Ilyas Yildirim
- AMBER: Energy outputs in TI Approach Ilyas Yildirim
Saturday, 16 June 2007
- AMBER: distance scan Miguel Ferreira
- AMBER: distance scan Miguel Ferreira
- Re: AMBER: distance scan David A. Case
- Re: AMBER: Energy outputs in TI Approach David A. Case
Sunday, 17 June 2007
- Re: AMBER: pair distribution function khn _
- AMBER: implementation of GB model in AMBER john chen
- Re: AMBER: implementation of GB model in AMBER Carlos Simmerling
- AMBER: explanation to edit and use the script Syed Tarique Moin
- Re: AMBER: MMPBSA-nmode .top question David A. Case
- Re: AMBER: isolated NTP David A. Case
- Re: AMBER: umbrella sampling dihedral restraint question David A. Case
Monday, 18 June 2007
- AMBER: error due to exceeding left-hand side digital numbers in restart output Cenk Andac
- RE: AMBER: isolated NTP Steve Seibold
- AMBER: problem with running rem on amber9 priya priya
- Re: AMBER: problem with running rem on amber9 Carlos Simmerling
- Re: AMBER: problem with running rem on amber9 priya priya
- AMBER: Charge not integral. Head-to-tail cyclic peptides Giacomo Bastianelli
- Re: AMBER: Charge not integral. Head-to-tail cyclic peptides Melinda Layten
- Re: AMBER: Charge not integral. Head-to-tail cyclic peptides Laurent Chiche
- RE: AMBER: Amber Installation Error Joe Nolan
- Re: AMBER: problem with running rem on amber9 priya priya
- Re: AMBER: problem with running rem on amber9 Carlos Simmerling
- Re: AMBER: problem with running rem on amber9 priya priya
- Re: AMBER: problem with running rem on amber9 (NOT A REMD PROBLEM) Carlos Simmerling
- Re: AMBER: isolated NTP David A. Case
- Re: AMBER: Amber Installation Error Mark Williamson
- Re: AMBER: shell model MD Carlos Simmerling
- AMBER: shell model MD Stern, Julie
- Re: AMBER: Amber Installation Error David A. Case
- Re: AMBER: Amber Installation Error Joe Nolan
- Re: AMBER: error due to exceeding left-hand side digital numbers in restart output David A. Case
- Re: AMBER: Amber Installation Error Mark Williamson
- Re: AMBER: problem with running rem on amber9 David A. Case
- AMBER: Questions about how ptraj calculates solvent shells Roberto Veiga
- Re: AMBER: frcmod Brooke Elizabeth Adams
- Re: AMBER: frcmod David A. Case
- Re: AMBER: frcmod Brooke Elizabeth Adams
- Re: AMBER: Amber Installation Error Joe Nolan
- AMBER: unres Carra, Claudio (JSC-SK)[USRA]
- Re: AMBER: unres Piotr Cieplak
Tuesday, 19 June 2007
- AMBER: H bond Guillaume Renvez
- Re: AMBER: H bond Carlos Simmerling
- AMBER: Re: Strange shape in my MD simulations Pavan G
- Re: AMBER: Re: Strange shape in my MD simulations Adrian Roitberg
- Re: AMBER: Re: Strange shape in my MD simulations Pavan G
- Re: AMBER: Re: Strange shape in my MD simulations Adrian Roitberg
- AMBER: How to add semi-experience parameter in divcon? clarkzhy
- Re: AMBER: Re: Strange shape in my MD simulations Pavan G
- RE: AMBER: Re: Strange shape in my MD simulations Ross Walker
- RE: AMBER: How to add semi-experience parameter in divcon? Ross Walker
- Re: AMBER: How to add semi-experience parameter in divcon? Seth Hayik
- Re: AMBER: Re: Strange shape in my MD simulations Pavan G
- AMBER: Reply regarding PCA with ptraj and IED Steve Spronk
- Re: AMBER: Reply regarding PCA with ptraj and IED Hannes Loeffler
Wednesday, 20 June 2007
- Re: AMBER: Re: Strange shape in my MD simulations gurpreet singh
- Re: AMBER: explanation to edit and use the script Syed Tarique Moin
- AMBER: problems in adding ACE and NME group backy
- AMBER: Re: Fwd: joshua j j
- Re: AMBER: problems in adding ACE and NME group Carlos Simmerling
- Re: AMBER: Re: Fwd: joshua j j
- Re: AMBER: problems in adding ACE and NME group backy
- RE: AMBER: problems in adding ACE and NME group Gustavo Seabra
- RE: AMBER: Re: Strange shape in my MD simulations Ross Walker
- Re: AMBER: problems in adding ACE and NME group Carlos Simmerling
- Re: AMBER: problems in adding ACE and NME group David A. Case
- AMBER: 5 Ligands and 1 Protein Colby C
- AMBER: Algorithm for integration of equations of motion Roberto Veiga
- RE: AMBER: Algorithm for integration of equations of motion Ross Walker
- Re: AMBER: 5 Ligands and 1 Protein David A. Case
- Re: AMBER: 5 Ligands and 1 Protein Colby C
- Re: AMBER: 5 Ligands and 1 Protein Scott Brozell
- Re: AMBER: 5 Ligands and 1 Protein David A. Case
- Re: AMBER: 5 Ligands and 1 Protein Colby C
- AMBER: sander core dumped during minimization zgleo
- Re: AMBER: problems in adding ACE and NME group backy
- Re: AMBER: problems in adding ACE and NME group backy
- Re: AMBER: problems in adding ACE and NME group Carlos Simmerling
- Re: AMBER: problems in adding ACE and NME group backy
- Re: AMBER: 5 Ligands and 1 Protein David A. Case
- Re: AMBER: sander core dumped during minimization David A. Case
- Re: AMBER: problems in adding ACE and NME group David A. Case
- Re: AMBER: problems in adding ACE and NME group backy
Thursday, 21 June 2007
- AMBER: set up system solution with 3 different components, each with multiple copies Nicolas Lux Fawzi
- AMBER: ptray segfault: vector out Nicolas Lux Fawzi
- Re: AMBER: 5 Ligands and 1 Protein Colby C
- To Mr. Ross Walker Re: RE: AMBER: How to add semi-experience parameter in divcon? clarkzhy
- AMBER: testing protein stability Sally Pias
Friday, 22 June 2007
- AMBER: Limitation in number of atoms/residues Sascha Rehm
- Re: AMBER: testing protein stability Carlos Simmerling
- Re: AMBER: Limitation in number of atoms/residues Robert Duke
- Re: AMBER: Limitation in number of atoms/residues Sascha Rehm
- Re: AMBER: 5 Ligands and 1 Protein David A. Case
- AMBER: radius of gyration priya priya
- Re: AMBER: radius of gyration Carlos Simmerling
- Re: AMBER: radius of gyration priya priya
- Re: AMBER: radius of gyration Carlos Simmerling
- Re: AMBER: radius of gyration Thomas Cheatham III
- AMBER: remd/rdc's McElheny, Dan
- Re: AMBER: testing protein stability Sally Pias
- AMBER: radial distribution function in ptraj khn _
Saturday, 23 June 2007
- Re: AMBER: remd/rdc's Carlos Simmerling
- AMBER: SPCFW water: angle problems in leap Thomas Hofer
- RE: AMBER: SPCFW water: angle problems in leap Ross Walker
- Re: AMBER: remd/rdc's David A. Case
Monday, 25 June 2007
- AMBER: Antechamber--Boron Parameters brmeher.iitg.ernet.in
- Re: AMBER: radius of gyration priya priya
- Re: AMBER: radius of gyration priya priya
- Re: AMBER: problems in adding ACE and NME group backy
- AMBER: how to calculate energy of the peptide priya priya
- Re: AMBER: problems in adding ACE and NME group priya priya
- AMBER: environment variables Francesco Pietra
- AMBER: RDF of pure chloroform BJÖRN KARLSSON
- Re: AMBER: remd/rdc's McElheny, Dan
- AMBER: sander MPI fails included tests Sergio Wong
- RE: AMBER: sander MPI fails included tests Ross Walker
- AMBER: prepin for metal centre Mattias Blomberg
- RE: AMBER: sander MPI fails included tests Sergio Wong
- AMBER: Re: ff02 and ff03 parameters Pavan G
- RE: AMBER: environment variables Ross Walker
- AMBER: PMF calculation Jena M
- AMBER: Simulated Annealing Joseph Maxwell
- Re: AMBER: Re: ff02 and ff03 parameters Carlos Simmerling
- Re: AMBER: Simulated Annealing David A. Case
- Re: AMBER: prepin for metal centre David A. Case
- Re: AMBER: PMF calculation David A. Case
- Re: AMBER: Antechamber--Boron Parameters David A. Case
- RE: AMBER: sander MPI fails included tests Ross Walker
Tuesday, 26 June 2007
- RE: AMBER: Simulated Annealing Hayden Eastwood
- Re: AMBER: Simulated Annealing Carlos Simmerling
- AMBER: Offending restraints???? saccenti.cerm.unifi.it
- Re: AMBER: Offending restraints???? Carlos Simmerling
- AMBER: PBSA Error Pankaj R. Daga
- RE: AMBER: Offending restraints???? Gustavo Seabra
- RE: AMBER: Offending restraints???? saccenti.cerm.unifi.it
- AMBER: rst overflow for implicit REMD In Hee Park
- Re: AMBER: Offending restraints???? saccenti.cerm.unifi.it
- Re: AMBER: set up system solution with 3 different components, each with multiple copies David A. Case
- Re: AMBER: set up system solution with 3 different components, each with multiple copies Nicolas Lux Fawzi
- Re: AMBER: set up system solution with 3 different components, each with multiple copies M. L. Dodson
- Re: AMBER: Offending restraints???? David A. Case
- Re: AMBER: rst overflow for implicit REMD David A. Case
- Re: AMBER: Offending restraints???? Carlos Simmerling
- Re: AMBER: rst overflow for implicit REMD Carlos Simmerling
- Re: AMBER: Offending restraints???? saccenti.cerm.unifi.it
- Re: AMBER: Offending restraints???? saccenti.cerm.unifi.it
- Re: AMBER: Offending restraints???? David A. Case
- AMBER: $AMBERHOME on PATH Francesco Pietra
- AMBER: "FATAL: Atom xxx does not have a type." Fred Baba
- Re: AMBER: $AMBERHOME on PATH David A. Case
- AMBER: Unexpected Failure in XLeap Jason Brown
- Re: AMBER: problems in adding ACE and NME group Melinda Layten
- Re: AMBER: $AMBERHOME on PATH Francesco Pietra
- Re: AMBER: Unexpected Failure in XLeap David A. Case
- RE: AMBER: sander MPI fails included tests Sergio Wong
- RE: AMBER: sander MPI fails included tests Ross Walker
- Re: AMBER: "FATAL: Atom xxx does not have a type." David A. Case
- AMBER: Does Chimera support AMBER file formats? Ilyas Yildirim
- Re: AMBER: Does Chimera support AMBER file formats? Mingfeng Yang
- Re: AMBER: problems in adding ACE and NME group backy
Wednesday, 27 June 2007
- Re: AMBER: Offending restraints???? saccenti.cerm.unifi.it
- Fwd: Re: AMBER: $AMBERHOME on PATH Francesco Pietra
- Fwd: Re: AMBER: $AMBERHOME on PATH Francesco Pietra
- Re: AMBER: problems in adding ACE and NME group Melinda Layten
- RE: AMBER: problems in adding ACE and NME group Ross Walker
- Fwd: Re: AMBER: $AMBERHOME on PATH & compilations Francesco Pietra
- RE: Re: AMBER: $AMBERHOME on PATH Ross Walker
- Re: AMBER: problems in adding ACE and NME group David A. Case
- Re: Fwd: Re: AMBER: $AMBERHOME on PATH & compilations David A. Case
- AMBER: bugfix.all Francesco Pietra
- Re: AMBER: bugfix.all M. L. Dodson
- Re: AMBER: bugfix.all Carlos Simmerling
- Re: AMBER: bugfix.all David A. Case
- RE: AMBER: bugfix.all Ross Walker
- AMBER: how to stop ptraj atom renumbering Russell Green
- Re: AMBER: problems in adding ACE and NME group backy
- Re: AMBER: bugfix.all Francesco Pietra
Thursday, 28 June 2007
- AMBER: Math libraries Francesco Pietra
- AMBER: conversion of Macromodel substructure format to .frcmod file brmeher.iitg.ernet.in
- Re: AMBER: Math libraries Robert Duke
- RE: Re: AMBER: $AMBERHOME on PATH Francesco Pietra
- RE: Re: AMBER: $AMBERHOME on PATH Ross Walker
- Re: RE: Re: AMBER: $AMBERHOME on PATH Alexandar T Tzanov
- Re: AMBER: remd/rdc's David A. Case
- AMBER: configure question Steve Young
- Re: RE: Re: AMBER: $AMBERHOME on PATH David A. Case
- Re: AMBER: problems in adding ACE and NME group David A. Case
- AMBER: Improving pmemd parallel scaling Alessandro Nascimento
- Re: AMBER: Improving pmemd parallel scaling Mark Williamson
- Re: AMBER: configure question David A. Case
- Re: AMBER: Math libraries Andreas Svrcek-Seiler
- Re: AMBER: configure question Andreas Svrcek-Seiler
- RE: Problems with Ifort 9.1.047 on Altix (Was: RE: Re: AMBER: $AMBERHOME on PATH) Ross Walker
- RE: AMBER: configure question Ross Walker
- RE: Re: AMBER: $AMBERHOME on PATH Francesco Pietra
- RE: Re: AMBER: $AMBERHOME on PATH Ross Walker
- Re: Re: AMBER: $AMBERHOME on PATH David A. Case
- RE: AMBER: sander MPI fails included tests Sergio Wong
- RE: Re: AMBER: $AMBERHOME on PATH Francesco Pietra
- Re: AMBER: Math libraries Francesco Pietra
- RE: Re: AMBER: $AMBERHOME on PATH Francesco Pietra
- RE: AMBER: sander MPI fails included tests Ross Walker
- Re: AMBER: configure question Robert Duke
- Re: AMBER: Improving pmemd parallel scaling Robert Duke
- RE: AMBER: sander MPI fails included tests Sergio Wong
- AMBER: Problem with leaprc yen li
- RE: AMBER: sander MPI fails included tests Ross Walker
- Fwd: RE: Re: AMBER: $AMBERHOME on PATH Francesco Pietra
Friday, 29 June 2007
- Re: AMBER: radius of gyration priya priya
- Re: AMBER: radius of gyration Carlos Simmerling
- Re: AMBER: radius of gyration priya priya
- Re: Fwd: RE: Re: AMBER: $AMBERHOME on PATH M. L. Dodson
- RE: AMBER: configure question Steve Young
- AMBER: Re: RE: Problems with Ifort 9.1.047 on Altix (Was: RE: Re: AMBER: $AMBERHOME on PATH) Alexandar T Tzanov
- AMBER: Sander Error Colby C
- RE: AMBER: Sander Error Ross Walker
- Re: AMBER: Sander Error Phineus Markwick
- Re: AMBER: Sander Error Phineus Markwick
- Re: AMBER: Problem with leaprc David A. Case
- Re: Fwd: RE: Re: AMBER: $AMBERHOME on PATH David A. Case
- RE: AMBER: Sander Error Ross Walker
- AMBER: Serial "make" failure with xleap Francesco Pietra
- AMBER: Fwd: Serial "make" failure with xleap Francesco Pietra
- Re: AMBER: Serial "make" failure with xleap David A. Case
- Re: AMBER: Serial "make" failure with xleap Francesco Pietra
- AMBER: Serial "make" failure Francesco Pietra
- AMBER: make serial failure for xleap Francesco Pietra
- Re: AMBER: Sander Error Colby C
- Re: AMBER: make serial failure for xleap M. L. Dodson
- Re: AMBER: make serial failure for xleap David A. Case
- Re: AMBER: Sander Error Carlos Simmerling
- RE: AMBER: Sander Error Ross Walker
Saturday, 30 June 2007
- Re: AMBER: make serial failure for xleap Francesco Pietra
- Fwd: Re: AMBER: make serial failure for xleap Francesco Pietra
- AMBER: amber7 and xleap Saiful Islam
- Fwd: Re: AMBER: make test serial Francesco Pietra
- Re: AMBER: Problem with leaprc yen li
- Re: Fwd: Re: AMBER: make test serial David A. Case
- Re: AMBER: Problem with leaprc David A. Case
- Re: Fwd: Re: AMBER: make test serial Francesco Pietra
- Re: AMBER: Problem with leaprc Francesco Pietra
- Re: Fwd: Re: AMBER: make test serial M. L. Dodson
- RE: Fwd: Re: AMBER: make test serial Ross Walker
- AMBER: MM-PBSA POPC/TIP3P/GPCR/LIGAND Jojart Balazs
- Re: AMBER: amber7 and xleap David A. Case

Last message date: Sun Jul 01 2007 - 06:07:55 PDT
Archived on: Wed Dec 25 2024 - 05:53:38 PST

Amber Archive Jun 2007 by date