Amber Archive Dec 2006: by date

Thursday, 30 November 2006
- AMBER: MM-PBSA problem vanessa wai
Friday, 1 December 2006
- Re: AMBER: How to apply a force to some atom in a residues? a a
- AMBER: How to keep an hydrogen bond during an implicit MD calculation? a a
- AMBER: Ions analysis with hbond, How can I specify an input for hbond to probe ions interactions? j j
- Re: AMBER: How to keep an hydrogen bond during an implicit MD calculation? j j
- AMBER: about the std of computational alanine scanning tongli
- AMBER: question on protein folding simulation Noriaki Okimoto
- AMBER: sander error about fortran Shuting Wei
- AMBER: H-bond analysis (Ptraj) input file Esther Brugger
- Re: AMBER: amber9 parralel compiling Nikola Trbovic
- Re: AMBER: H-bond analysis (Ptraj) input file Thomas Cheatham
- Re: AMBER: Ions analysis with hbond, How can I specify an input for hbond to probe ions interactions? Thomas Cheatham
- Re: AMBER: H-bond analysis (Ptraj) Thomas Cheatham
- RE: AMBER: question on protein folding simulation Yong Duan
- Re: AMBER: H-bond analysis (Ptraj) Esther Brugger
- Re: AMBER: amber9 parralel compiling Scott Brozell
- Re: AMBER: question on protein folding simulation Fenghui Fan
- Re: AMBER: Ions analysis with hbond, How can I specify an input for hbond to probe ions interactions? j j
- AMBER: dihedral calculation problem Esther Brugger
- Re: AMBER: MM-PBSA problem Varsha Goyal
- RE: AMBER: MM-PBSA problem Ray Luo
- Re: AMBER: Ions analysis with hbond, How can I specify an input for hbond to probe ions interactions? Thomas Cheatham
- AMBER: Making sure that Amber jobs use Infiniband? Michael John Hanby
- Re: AMBER: Making sure that Amber jobs use Infiniband? David A. Case
- Re: AMBER: sander error about fortran Scott Brozell
Saturday, 2 December 2006
- Re: AMBER: MM-PBSA problem vanessa wai
- Re: AMBER: MM-PBSA problem vanessa wai
- AMBER: LogP Cenk Andac
- AMBER: problem at the start of heating up (using extra-point) Rachel
- RE: AMBER: MM-PBSA problem Ray Luo
- AMBER: LEaP not recognising Phosphate group in TYR bertrand russell
- Re: AMBER: problem at the start of heating up (using extra-point) Cenk Andac
- Re: AMBER: LEaP not recognising Phosphate group in TYR David A. Case
Sunday, 3 December 2006
- AMBER: Problem with specifying NOSHAKEMASK Gobind Singh Bisht
- Re: AMBER: Problem with specifying NOSHAKEMASK Carlos Simmerling
- AMBER: bugfix mahdi fathi
- Re: AMBER: Problem with specifying NOSHAKEMASK Gobind Singh Bisht
- Re: AMBER: bugfix Ye Mei
- Re: AMBER: Problem with specifying NOSHAKEMASK David A. Case
- Re: AMBER: problem at the start of heating up (using extra-point) David A. Case
- Re: AMBER: MM-PBSA problem vanessa wai
- AMBER: About the creation of 1-4 pairs in AMBER program J. Zhang
- AMBER: The VDW correctioin J. Zhang
- Re: AMBER: question on protein folding simulation Noriaki Okimoto
- Re: AMBER: question on protein folding simulation Noriaki Okimoto
- Re: AMBER: Problem with specifying NOSHAKEMASK Gobind Singh Bisht
Monday, 4 December 2006
- AMBER: xleap problems anna.schrey.gmx.de
- Re: AMBER: question on protein folding simulation Carlos Simmerling
- Re: AMBER: Ions analysis with hbond, How can I specify an input for hbond to probe ions interactions? j j
- Re: AMBER: xleap problems Cenk Andac
- AMBER: how to include EXTRA POINTS in AMBER8 Rachel
- Re: AMBER: how to include EXTRA POINTS in AMBER8 David A. Case
- Re: AMBER: xleap problems David A. Case
- Re: AMBER: Problem with specifying NOSHAKEMASK David A. Case
- AMBER: Is there anyway to recover the LISTOUT obtained after running a md with nmr restrictions j j
- Re: AMBER: how to include EXTRA POINTS in AMBER8 Rachel
- Re: AMBER: sander error about fortran Shuting Wei
- Re: AMBER: phantom sander8 in dmesg Lachele Foley (Lists)
- Re: AMBER: Is there anyway to recover the LISTOUT obtained after running a md with nmr restrictions David A. Case
- Re: AMBER: how to include EXTRA POINTS in AMBER8 Rachel
- Re: AMBER: question on protein folding simulation Gustavo Seabra
- AMBER: ptraj vector corrplane bug Myunggi Yi
- Re: AMBER: sander error about fortran Scott Brozell
- Re: AMBER: Is there anyway to recover the LISTOUT obtained after running a md with nmr restrictions j j
- AMBER: Zn2+ and Ca2+ ions explicitly treated in MMPB/GB/SA Piotr Cieplak
- AMBER: AMBER parallel run bombs Rahaman, Asif
- Re: AMBER: question on protein folding simulation Fenghui Fan
- Re: AMBER: AMBER parallel run bombs Michael Crowley
- Re: AMBER: Problem with specifying NOSHAKEMASK Gobind Singh Bisht
Tuesday, 5 December 2006
- AMBER: MD with restraint (nmropt=1) a a
- AMBER: A BUG report, "ptraj corrplane" Myunggi Yi
- RE: AMBER: MM-PBSA problem Ray Luo
- RE: AMBER: question on protein folding simulation Yong Duan
- Re: AMBER: MD with restraint (nmropt=1) David A. Case
- Re: AMBER: MM-PBSA problem vanessa wai
- Re: AMBER: MD with restraint (nmropt=1) a a
Wednesday, 6 December 2006
- AMBER: nonplanarity of NH2 groups laura zanet
- Re: AMBER: MD with restraint (nmropt=1) David A. Case
- AMBER: perturbed and unperturbed charges Rachel
- Re: AMBER: perturbed and unperturbed charges David A. Case
- AMBER: parameter definitions Ed Pate
- Re: AMBER: parameter definitions David A. Case
- AMBER: setBox with buffer in leap Steven Winfield
- AMBER: Amber9 failure to compile parallel on Rocks 4.2.1 system Michael John Hanby
- RE: AMBER: Amber9 failure to compile parallel on Rocks 4.2.1 system Ross Walker
- AMBER: ibelly not work JunJun Liu
- RE: AMBER: ibelly not work Ross Walker
- AMBER: setBox with buffer in leap Steven Winfield
- AMBER: How could I simulate lipid membrane with AMBER9.0? 曹冉
- AMBER: What's going wrong when I use antechamber dealing with lipid molecular? 曹冉
- Re: AMBER: How could I simulate lipid membrane with AMBER9.0? Fenghui Fan
- Re: AMBER: What's going wrong when I use antechamber dealing with lipid molecular? Fenghui Fan
- Re: AMBER: MD with restraint (nmropt=1) a a
- Re: AMBER: MD with restraint (nmropt=1) Thomas Cheatham
- Re: AMBER: how to include EXTRA POINTS in AMBER8 David A. Case
Thursday, 7 December 2006
- AMBER: PMEMD scaling Tiziano Tuccinardi
- Re: AMBER: LEaP not recognising Phosphate group in TYR bertrand russell
- AMBER: Installing Amber 9 on Mac Pro Burkhard Heil
- Re: AMBER: question on protein folding simulation Noriaki Okimoto
- RE: AMBER: ibelly not work Andy Purkiss-Trew
- Re: AMBER: Installing Amber 9 on Mac Pro Mathy Froeyen
- Re: AMBER: PMEMD scaling Robert Duke
- Re: AMBER: LEaP not recognising Phosphate group in TYR David A. Case
- RE: AMBER: Problem about dummy atoms when running antechamber Junmei Wang
- Re: AMBER: nonplanarity of NH2 groups FyD
- Re: AMBER: nonplanarity of NH2 groups Jiri Sponer
- AMBER: DRMS setting for Nmode calculation Shuting Wei
- AMBER: MD with positional and NMR restraints Mike Summers
- Re: AMBER: MD with positional and NMR restraints David A. Case
- Re: AMBER: MD with positional and NMR restraints Mike Summers
- Re: AMBER: MD with positional and NMR restraints David A. Case
- AMBER: Simulating proteins with calcium ion Qing Zhang
- Re: AMBER: problem of the REMD with nmr constraints wenfei Li
- Re: AMBER: How could I simulate lipid membrane with AMBER9.0? 曹冉
- Re: AMBER: Simulating proteins with calcium ion Fenghui Fan
- AMBER: Error message in methane solvent system Atsutoshi Okabe
- Re: AMBER: Simulating proteins with calcium ion Thomas Cheatham
Friday, 8 December 2006
- AMBER: atome type error Steve Seibold
- RE: AMBER: atome type error Ross Walker
- AMBER: Atom Type problem Steve Seibold
- AMBER: Atom Type problem Steve Seibold
- RE: AMBER: Atom Type problem Ross Walker
- Re: AMBER: Error message in methane solvent system David A. Case
- RE: AMBER: Atom Type problem Steve Seibold
- AMBER: Compiling Amber 9 on SGI with gcc Shin, John Y CONTRACTOR WRAIR-Wash DC
- AMBER: RDC refinement Lee, Young-Tae
- AMBER: description of prep file Piotr Cieplak
- Re: AMBER: description of prep file David A. Case
- AMBER: dihedral angle problem Esther Brugger
- Re: AMBER: dihedral angle problem David A. Case
- Re: AMBER: RDC refinement David A. Case
- Re: AMBER: Simulating proteins with calcium ion Qing Zhang
- Re: AMBER: dihedral angle problem Esther Brugger
- Re: AMBER: dihedral angle problem David A. Case
- Re: AMBER: Compiling Amber 9 on SGI with gcc Scott Brozell
Saturday, 9 December 2006
- Re: AMBER: Compiling Amber 9 on SGI with gcc David A. Case
Sunday, 10 December 2006
- AMBER: Amber9 Parallel compiled with -lam, how to run test.parallel? Michael John Hanby
- Re: AMBER: Amber9 Parallel compiled with -lam, how to run test.parallel? David A. Case
- Re: AMBER: A BUG report, "ptraj corrplane" Myunggi Yi
- RE: AMBER: Amber9 Parallel compiled with -lam, how to run test.parallel? Michael John Hanby
Monday, 11 December 2006
- AMBER: General Question about Abmer Sanya Kryklia
- Re: AMBER: General Question about Abmer M. L. Dodson
- AMBER: addition of subroutine in pmemd module kakali sen
- AMBER: Atoms overlapping Nitin Bhardwaj
- Re: AMBER: Atoms overlapping David A. Case
- Re: AMBER: Atoms overlapping Nitin Bhardwaj
- AMBER: Building Parameters Steve Seibold
- Re: AMBER: Atoms overlapping Thomas Steinbrecher
- AMBER: Coodinates not being unique Nitin Bhardwaj
- Re: AMBER: Installing Amber 9 on Mac Pro Mengjuei Hsieh
- AMBER: QM/MD energy conservation Evan Kelly
- Re: AMBER: setBox with buffer in leap Scott Brozell
- AMBER: LEaP problem bertrand russell
- Re: AMBER: LEaP problem Bill Ross
- Re: AMBER: LEaP problem Fenghui Fan
Tuesday, 12 December 2006
- AMBER: ERROR: The PDB file is not in the working directory saurabh agrawal
- Re: AMBER: ERROR: The PDB file is not in the working directory FyD
- Re: AMBER: QM/MD energy conservation Gustavo Seabra
- Re: AMBER: setBox with buffer in leap David A. Case
- Re: AMBER: Simulating proteins with calcium ion Karen Callahan
- AMBER: RDF problem Esther Brugger
- Re: AMBER: Simulating proteins with calcium ion Bill Ross
- Re: AMBER: Simulating proteins with calcium ion 张勇
- Re: AMBER: How to run QM/MM simulation of DNA duplex bound with platinum moietes Chengwen Chen
Wednesday, 13 December 2006
- AMBER: floating point assist faults on IA64 PMEMD 9 Jarrod Smith
- AMBER: Unit 5 Error on OPEN: md.in Rachel
- Re: AMBER: floating point assist faults on IA64 PMEMD 9 Robert Duke
- Re: AMBER: floating point assist faults on IA64 PMEMD 9 Jarrod Smith
- Re: AMBER: floating point assist faults on IA64 PMEMD 9 Jarrod Smith
- Re: AMBER: floating point assist faults on IA64 PMEMD 9 Robert Duke
- Re: AMBER: floating point assist faults on IA64 PMEMD 9 Jarrod Smith
- AMBER: amber 9 installation problem Ed Pate
- AMBER: coordinate out of bounds Miguel Ferreira
- AMBER: ISTRNG or SALT in MM_PBSA Qizhi Cui
- Re: AMBER: ERROR: The PDB file is not in the working directory saurabh agrawal
Thursday, 14 December 2006
- AMBER: Free energy perturbation in SANDER Yumi Nukusina
- Re: AMBER: RESP charges of iron-porphyrin system Shin Tokumoto
- Re: AMBER: Free energy perturbation in SANDER Sergey Samsonov
- Re: AMBER: coordinate out of bounds j j
- AMBER: parallel computation time vs serial computation time Cenk Andac
- Re: AMBER: ERROR: The PDB file is not in the working directory saurabh agrawal
- Re: AMBER: parallel computation time vs serial computation time Robert Duke
- AMBER: Free energy perturbation in SANDER Chris Moth
- AMBER: sander: cannot execute binary file Kailee
- AMBER: Test Message Please Ignore Ross Walker
- AMBER: Test Message Please Ignore. Ross Walker
- AMBER: Can't compile PMEMD Michael John Hanby
- RE: AMBER: sander: cannot execute binary file Michael John Hanby
- Re: AMBER: Can't compile PMEMD Robert Duke
- RE: AMBER: sander: cannot execute binary file Ross Walker
- RE: AMBER: Can't compile PMEMD Michael John Hanby
- Re: AMBER: Can't compile PMEMD Robert Duke
Friday, 15 December 2006
- Re: AMBER: ERROR: The PDB file is not in the working directory FyD
- AMBER: rdparm venditti2.unisi.it
- Re: AMBER: sander: cannot execute binary file Kailee
- Re: AMBER: sander: cannot execute binary file David A. Case
- AMBER: AMBER - leap - problems with impose command Piotr Cieplak
- AMBER: Is there a way to simulate a box of pure water with amber Li Su
- RE: AMBER: Is there a way to simulate a box of pure water with amber Ross Walker
- Re: AMBER: Is there a way to simulate a box of pure water with amber Bill Ross
- AMBER: Solvating a bilayer Matthew Tessier
- AMBER: Error in sysdepend.c? Shin, John Y CONTRACTOR WRAIR-Wash DC
- Re: AMBER: Error in sysdepend.c? David A. Case
- Re: AMBER: AMBER - leap - problems with impose command FyD
- Re: AMBER: AMBER - leap - problems with impose command Piotr Cieplak
Saturday, 16 December 2006
- AMBER: Volume of ucell too big Atsutoshi Okabe
- AMBER: How to make a movie with .crd files in VMD? bertrand russell
- Re: AMBER: How to make a movie with .crd files in VMD? Carlos Simmerling
- Re: AMBER: AMBER - leap - problems with impose command Ilyas Yildirim
- Re: AMBER: How to make a movie with .crd files in VMD? bertrand russell
- Re: AMBER: Unit 5 Error on OPEN: md.in Rachel
- Re: AMBER: Unit 5 Error on OPEN: md.in Chris Moth
- Re: AMBER: Unit 5 Error on OPEN: md.in Chris Moth
- Re: AMBER: How to make a movie with .crd files in VMD? Nicolas Lux Fawzi
- Re: AMBER: How to make a movie with .crd files in VMD? Chris Moth
- Re: AMBER: Volume of ucell too big Nicolas Lux Fawzi
- Re: AMBER: How to make a movie with .crd files in VMD? Carlos Simmerling
- Re: AMBER: rdparm Thomas Cheatham
- Re: AMBER: AMBER - leap - problems with impose command Piotr Cieplak
Sunday, 17 December 2006
- Re: AMBER: AMBER - leap - problems with impose command Ilyas Yildirim
- AMBER: Amber 9 Leap install error A Box
- Re: AMBER: Amber 9 Leap install error David A. Case
- Re: AMBER: Is there a way to simulate a box of pure water with amber Sergey Samsonov
Monday, 18 December 2006
- AMBER: (no subject) lily ferreira
- AMBER: MM-PBSA Shozeb Haider
- Re: AMBER: MM-PBSA Angelo
- Re: AMBER: sander: cannot execute binary file Kailee
- Re: AMBER: sander: cannot execute binary file Kailee
- RE: AMBER: sander: cannot execute binary file Ross Walker
- RE: AMBER: Error in sysdepend.c? Shin, John Y CONTRACTOR WRAIR-Wash DC
- AMBER: RESP charge fitting for HFIP Mingfeng Yang
- AMBER: sander ntc=2 ntf=1 Nicolas Lux Fawzi
- Re: AMBER: RESP charge fitting for HFIP Raviprasad Aduri
- Re: AMBER: RESP charge fitting for HFIP Mingfeng Yang
- Re: AMBER: RESP charge fitting for HFIP FyD
Tuesday, 19 December 2006
- Re: AMBER: sander ntc=2 ntf=1 Carlos Simmerling
- AMBER: Frozen at Minimization Steve Seibold
- Re: AMBER: Frozen at Minimization Chris Moth
- Re: AMBER: rdparm Tim Meyer
- Re: AMBER: sander: cannot execute binary file Kailee
- AMBER: Parallelization method Jordi Camps
- Re: AMBER: Parallelization method Robert Duke
- Re: AMBER: Parallelization method Scott Brozell
- RE: AMBER: Error in sysdepend.c? Scott Brozell
- RE: AMBER: Error in sysdepend.c? Shin, John Y CONTRACTOR WRAIR-Wash DC
- AMBER: Renumber residues in LEAP Akshay Patny
- AMBER: charge problem in MM-PBSA linfu
- AMBER: mixing GAFF and CHARMM Ravinder Abrol
- Re: AMBER: RESP charge fitting for HFIP FyD
Wednesday, 20 December 2006
- AMBER: Installation help - SGI Altix 350 bertrand russell
- AMBER: Amber9 - openmpi? bertrand russell
- Re: AMBER: Amber9 - openmpi? Robert Duke
- AMBER: MM_PBSA lily ferreira
- AMBER: MM_PBSA lily ferreira
- AMBER: RED - help with installation / config Seth Lilavivat
- Re: AMBER: Installation help - SGI Altix 350 Gustavo Seabra
- Re: AMBER: Amber9 - openmpi? Gustavo Seabra
- AMBER: RESP procedure for DMPC monomer Akshay Patny
- RE: AMBER: Installation help - SGI Altix 350 Ross Walker
- Re:AMBER: mixing GAFF and CHARMM 曹冉
- Re: AMBER: mixing GAFF and CHARMM Ravinder Abrol
- RE: AMBER: mixing GAFF and CHARMM Akshay Patny
- Re: AMBER: RESP charge fitting for HFIP Mingfeng Yang
- Re: AMBER: mixing GAFF and CHARMM Christophe Guilbert
- Re: AMBER: RESP procedure for DMPC monomer linfu
- Re: AMBER: mixing GAFF and CHARMM Ravinder Abrol
- Re: AMBER: Installation help - SGI Altix 350 bertrand russell
- Re: AMBER: Amber9 - openmpi? bertrand russell
- RE: AMBER: Installation help - SGI Altix 350 Ross Walker
- Re: AMBER: Installation help - SGI Altix 350 bertrand russell
- RE: AMBER: Installation help - SGI Altix 350 Ross Walker
Thursday, 21 December 2006
- Re: AMBER: RED - help with installation / config FyD
- AMBER: Amber Input file from "qout", "resp.dat" saurabh agrawal
- Re: AMBER: Amber Input file from "qout", "resp.dat" FyD
- AMBER: Replica exchange rate in REMD Seongeun Yang
- AMBER: tetrolic acid Russell Glavey
- AMBER: xleap, generating prep file Seth Lilavivat
- AMBER: EXTRA_PTS: frtype 2 Should not be here Kailee
- AMBER: Sander--NMR refinement Esther Brugger
- Re: AMBER: Installation help - SGI Altix 350 bertrand russell
- AMBER: Compiling Amber8 with Sun HPC ClusterTools 5 Software Muhammad Naim Mohmad Rouyan
Friday, 22 December 2006
- AMBER: Nucgen Problem puneet kacker
- Re: AMBER: Nucgen Problem Navnit Kumar Mishra
- Re: AMBER: Nucgen Problem Bill Ross
- Re: AMBER: Simulating proteins with calcium ion Qing Zhang
- AMBER: Problem with LEaP FyD
- Re: AMBER: Simulating proteins with calcium ion Bill Ross
- Re: AMBER: Simulating proteins with calcium ion Qing Zhang
- Re: AMBER: Simulating proteins with calcium ion Qing Zhang
- Re: AMBER: Simulating proteins with calcium ion Bill Ross
- Re: AMBER: Simulating proteins with calcium ion 张勇
- Re: AMBER: Installation help - SGI Altix 350 Gustavo Seabra
- Re: AMBER: Simulating proteins with calcium ion Qing Zhang
Saturday, 23 December 2006
- Re: AMBER: Compiling Amber8 with Sun HPC ClusterTools 5 Software David A. Case
Monday, 25 December 2006
- Re: AMBER: Renumber residues in LEAP David A. Case
- Re: AMBER: MM_PBSA David A. Case
- Re: AMBER: EXTRA_PTS: frtype 2 Should not be here David A. Case
- AMBER: A problem with mm_pbsa vic.mail.nankai.edu.cn
Tuesday, 26 December 2006
- Re: AMBER: Installation help - SGI Altix 350 bertrand russell
- AMBER: .crd file bertrand russell
- Re: AMBER: .crd file Fenghui Fan
- AMBER: bad connectivity Seth Lilavivat
- Re: AMBER: bad connectivity Fenghui Fan
- AMBER: bad connectivity - more detail Seth Lilavivat
- Re: AMBER: Sander--NMR refinement David A. Case
- AMBER: G5 OSX serial compile error Kevin Kelliher
- Re: AMBER: Installation help - SGI Altix 350 David A. Case
- Re: AMBER: bad connectivity - more detail Fenghui Fan
- Re: AMBER: bad connectivity - more detail Fenghui Fan
- AMBER: Error compiling amber on parallel (MPICH) Muhammad Naim Mohmad Rouyan
Wednesday, 27 December 2006
- Re: AMBER: bad connectivity - more detail Seth Lilavivat
- Re: AMBER: Error compiling amber on parallel (MPICH) David A. Case
- AMBER: recompiling bondtype.C Seth Lilavivat
- Re: AMBER: bad connectivity - more detail David A. Case
- Re: AMBER: bad connectivity - more detail Seth Lilavivat
- Re: AMBER: recompiling bondtype.C David A. Case
- Re: AMBER: bad connectivity - more detail David A. Case
- Re: AMBER: bad connectivity - more detail Seth Lilavivat
- AMBER: PMEMD and OpenMPI, anyone have config options? Michael John Hanby
- AMBER: chirality.c line 121 Seth Lilavivat
- Re: AMBER: chirality.c line 121 David A. Case
- AMBER: PCA analysis Jardas sucuriba
Thursday, 28 December 2006
- Re: AMBER: G5 OSX serial compile error Mathy Froeyen
- AMBER: tree name generated by tleap is different from the input PREP parameter file xiaoqin huang
- AMBER: problems trying to modify Amber8 Ed Pate
- AMBER: problems with Calcium ions treatment in GB run Piotr Cieplak
- AMBER: tree name generated by tleap is different from the input PREP parameter file xiaoqin huang
- AMBER: AMBER complile problem Chengwen Chen
- Re: AMBER: AMBER complile problem David A. Case
- Re: AMBER: problems with Calcium ions treatment in GB run David A. Case
Friday, 29 December 2006
- Re: AMBER: bad connectivity - more detail David A. Case
- AMBER: Simulated Annealing problem... sai vikram
- Re: AMBER: Simulated Annealing problem... David A. Case
- Re: AMBER: tree name generated by tleap is different from the input PREP parameter file Bill Ross
- AMBER: RE: protein simulation using AMBER Ross Walker
Saturday, 30 December 2006
- Re: AMBER: Simulated Annealing problem... sai vikram

Last message date: Sun Dec 31 2006 - 06:07:50 PST
Archived on: Mon Jan 13 2025 - 05:53:30 PST

Amber Archive Dec 2006 by date