Amber Archive Nov 2011: by date

Monday, 31 October 2011
- [AMBER] cutoff in amber cuda Neha Gandhi
Tuesday, 1 November 2011
- Re: [AMBER] Problems with AmberTools compilation under Debian James Starlight
- Re: [AMBER] iron sulphur cluster parametrization FyD
- Re: [AMBER] parameters for anchor-modified glycopeptides Urszula Uciechowska
- [AMBER] Measurement of distance between residues forming Hydrogen bond Aditya Padhi
- Re: [AMBER] distribution of selected water Bruno Rodrigues
- Re: [AMBER] iron sulphur cluster parametrization Francesco Oteri
- [AMBER] Problems with XLEAP James Starlight
- Re: [AMBER] Problems with XLEAP Pavan Giovanni
- Re: [AMBER] Problems with XLEAP James Starlight
- Re: [AMBER] iron sulphur cluster parametrization FyD
- Re: [AMBER] iron sulphur cluster parametrization Ilyas Yildirim
- Re: [AMBER] Problems with XLEAP Pavan Giovanni
- Re: [AMBER] parameters for anchor-modified glycopeptides FyD
- Re: [AMBER] iron sulphur cluster parametrization Francesco Oteri
- Re: [AMBER] molecule out box and correct hbond analysis Bruno Rodrigues
- Re: [AMBER] Problems with XLEAP James Starlight
- Re: [AMBER] Problems with AmberTools compilation under Debian David A Case
- Re: [AMBER] iron sulphur cluster parametrization Francesco Oteri
- Re: [AMBER] Problems with AmberTools compilation under Debian James Starlight
- Re: [AMBER] how to load atom type for divalent ions in leaprc.ff10? David A Case
- Re: [AMBER] Issue with running sander with SHAKE David A Case
- Re: [AMBER] Problems with XLEAP James Starlight
- Re: [AMBER] parameters for anchor-modified glycopeptides Urszula Uciechowska
- Re: [AMBER] iron sulphur cluster parametrization FyD
- Re: [AMBER] cutoff in amber cuda Jason Swails
- Re: [AMBER] parameters for anchor-modified glycopeptides FyD
- Re: [AMBER] Measurement of distance between residues forming Hydrogen bond Jason Swails
- Re: [AMBER] distribution of selected water Jason Swails
- Re: [AMBER] Problems with XLEAP David A Case
- Re: [AMBER] Measurement of distance between residues forming Hydrogen bond Daniel Roe
- Re: [AMBER] distribution of selected water Bruno Rodrigues
- Re: [AMBER] distribution of selected water Jason Swails
- Re: [AMBER] distribution of selected water Daniel Roe
- Re: [AMBER] Problems with XLEAP James Starlight
- Re: [AMBER] distribution of selected water Bruno Rodrigues
- Re: [AMBER] parameters for anchor-modified glycopeptides Urszula Uciechowska
- Re: [AMBER] how to load atom type for divalent ions in leaprc.ff10? Victor Ma
- Re: [AMBER] how to load atom type for divalent ions in leaprc.ff10? David A Case
- Re: [AMBER] distribution of selected water Daniel Roe
- Re: [AMBER] Problems with XLEAP David A Case
- Re: [AMBER] cutoff in amber cuda Ross Walker
- [AMBER] RMSD of one atom Esam Tolba
- Re: [AMBER] RMSD of one atom Adrian Roitberg
- Re: [AMBER] Issue with running sander with SHAKE Breuer, Marian
- Re: [AMBER] RMSD of one atom Thomas Cheatham III
- Re: [AMBER] how to load atom type for divalent ions in leaprc.ff10? Victor Ma
- [AMBER] PB Bomb in pb_atmlist(): maxnba too short manikanthan bhavaraju
- Re: [AMBER] PB Bomb in pb_atmlist(): maxnba too short manikanthan bhavaraju
- [AMBER] AmberTools 1.5 build fails due to undefined symbols in libnetcdf.a Jan-Philip Gehrcke
- Re: [AMBER] AmberTools 1.5 build fails due to undefined symbols in libnetcdf.a Jan-Philip Gehrcke
- Re: [AMBER] AmberTools 1.5 build fails due to undefined symbols in libnetcdf.a Ross Walker
- Re: [AMBER] Issue with running sander with SHAKE Jason Swails
- Re: [AMBER] Issue with running sander with SHAKE Breuer, Marian
- Re: [AMBER] AmberTools 1.5 build fails due to undefined symbols in libnetcdf.a Jan-Philip Gehrcke
- Re: [AMBER] AmberTools 1.5 build fails due to undefined symbols in libnetcdf.a Jason Swails
- Re: [AMBER] PB Bomb in pb_atmlist(): maxnba too short Ray Luo, Ph.D.
- Re: [AMBER] PB Bomb in pb_atmlist(): maxnba too short manikanthan bhavaraju
- Re: [AMBER] PB Bomb in pb_atmlist(): maxnba too short Ray Luo, Ph.D.
- Re: [AMBER] PB Bomb in pb_atmlist(): maxnba too short manikanthan bhavaraju
- Re: [AMBER] Issue with running sander with SHAKE case
- Re: [AMBER] AmberTools 1.5 build fails due to undefined symbols in libnetcdf.a Daniel Roe
- Re: [AMBER] PB Bomb in pb_atmlist(): maxnba too short Ray Luo, Ph.D.
- Re: [AMBER] Issue with running sander with SHAKE Jason Swails
Wednesday, 2 November 2011
- Re: [AMBER] parameters for anchor-modified glycopeptides FyD
- [AMBER] Minimization in sander Anglea A.
- Re: [AMBER] please help me pancham lal gupta
- Re: [AMBER] AmberTools 1.5 build fails due to undefined symbols in libnetcdf.a Jan-Philip Gehrcke
- Re: [AMBER] Problems with XLEAP James Starlight
- Re: [AMBER] Minimization in sander David A Case
- Re: [AMBER] please help me David A Case
- Re: [AMBER] parameters for anchor-modified glycopeptides Urszula Uciechowska
- Re: [AMBER] Minimization in sander Anglea A.
- [AMBER] Softcore TI. Peter Winn
- Re: [AMBER] parameters for anchor-modified glycopeptides FyD
- Re: [AMBER] Problems with XLEAP David A Case
- Re: [AMBER] Minimization in sander David A Case
- Re: [AMBER] Softcore TI. steinbrt.rci.rutgers.edu
- Re: [AMBER] Softcore TI. Ross Walker
- Re: [AMBER] Softcore TI. Peter Winn
- Re: [AMBER] AmberTools 1.5 build fails due to undefined symbols in libnetcdf.a Jan-Philip Gehrcke
- Re: [AMBER] AmberTools 1.5 build fails due to undefined symbols in libnetcdf.a Jason Swails
- [AMBER] test_amber_cuda.sh requires small fix Jan-Philip Gehrcke
- Re: [AMBER] AmberTools 1.5 build fails due to undefined symbols in libnetcdf.a Jan-Philip Gehrcke
- Re: [AMBER] Softcore TI. steinbrt.rci.rutgers.edu
- [AMBER] sander simulated annealing Charles Johnson
- Re: [AMBER] sander simulated annealing Brian Radak
- Re: [AMBER] sander simulated annealing Charles Johnson
- [AMBER] post MD energy calculations peker milas
- Re: [AMBER] sander simulated annealing Brian Radak
- Re: [AMBER] sander simulated annealing David A Case
- Re: [AMBER] post MD energy calculations David A Case
- Re: [AMBER] test_amber_cuda.sh requires small fix Jason Swails
- Re: [AMBER] post MD energy calculations peker milas
- Re: [AMBER] test_amber_cuda.sh requires small fix Ross Walker
- [AMBER] Creating i-motif (cruciform DNA) using NAB?? raghav singh
- Re: [AMBER] test_amber_cuda.sh requires small fix Jan-Philip Gehrcke
- Re: [AMBER] test_amber_cuda.sh requires small fix Jason Swails
- Re: [AMBER] 1JFF Antechamber, LEaP problems Matthew D Antalek
- Re: [AMBER] 1JFF Antechamber, LEaP problems Jason Swails
- Re: [AMBER] 1JFF Antechamber, LEaP problems Matthew D Antalek
- Re: [AMBER] 1JFF Antechamber, LEaP problems Matthew D Antalek
- [AMBER] using AmberTools on Desmond trajectories Ozen, Aysegul
- Re: [AMBER] using AmberTools on Desmond trajectories Thomas Cheatham III
- Re: [AMBER] PB Bomb in pb_atmlist(): maxnba too short Ray Luo, Ph.D.
- Re: [AMBER] using AmberTools on Desmond trajectories Bill Ross
- Re: [AMBER] test_amber_cuda.sh requires small fix case
- Re: [AMBER] 1JFF Antechamber, LEaP problems case
- Re: [AMBER] 1JFF Antechamber, LEaP problems case
- [AMBER] Some questions in cluster output qiao xue
Thursday, 3 November 2011
- Re: [AMBER] 1JFF Antechamber, LEaP problems FyD
- Re: [AMBER] safemem.o error while compiling Ambertools 1.5 Andrew Voronkov
- Re: [AMBER] Softcore TI. now with data! steinbrt.rci.rutgers.edu
- Re: [AMBER] Minimization in sander Anglea A.
- Re: [AMBER] Minimization in sander David A Case
- [AMBER] problems in reading molecule in tleap/xleap Urszula Uciechowska
- Re: [AMBER] safemem.o error while compiling Ambertools 1.5 Josmar R. da Rocha
- Re: [AMBER] AmberTools 1.5 build fails due to undefined symbols in libnetcdf.a Jan-Philip Gehrcke
- [AMBER] sander error Charles Johnson
- Re: [AMBER] AmberTools 1.5 build fails due to undefined symbols in libnetcdf.a Daniel Roe
- Re: [AMBER] AmberTools 1.5 build fails due to undefined symbols in libnetcdf.a Jason Swails
- Re: [AMBER] sander error Ben Roberts
- [AMBER] Minimization problems. same box different water model Brian Radak
- Re: [AMBER] sander error Charles Johnson
- Re: [AMBER] sander error Ben Roberts
- Re: [AMBER] sander error Charles Johnson
- Re: [AMBER] Minimization problems. same box different water model David A Case
- Re: [AMBER] sander error Ben Roberts
- Re: [AMBER] sander error Charles Johnson
- Re: [AMBER] sander error Ben Roberts
- Re: [AMBER] problems in reading molecule in tleap/xleap David A Case
- Re: [AMBER] sander error David A Case
- Re: [AMBER] sander error Charles Johnson
- Re: [AMBER] Minimization problems. same box different water model Brian Radak
- [AMBER] Two LMOD questions Sarah Edwards
- Re: [AMBER] Two LMOD questions Daniel Roe
- Re: [AMBER] sander error Ben Roberts
Friday, 4 November 2011
- Re: [AMBER] problems in reading molecule in tleap/xleap Urszula Uciechowska
- Re: [AMBER] parameters for anchor-modified glycopeptides Urszula Uciechowska
- [AMBER] bashrc problems Andrew Voronkov
- Re: [AMBER] parameters for anchor-modified glycopeptides FyD
- Re: [AMBER] bashrc problems Jan-Philip Gehrcke
- Re: [AMBER] AmberTools 1.5 build fails due to undefined symbols in libnetcdf.a Jan-Philip Gehrcke
- Re: [AMBER] bashrc problems James Starlight
- Re: [AMBER] bashrc problems Jan-Philip Gehrcke
- Re: [AMBER] bashrc problems James Starlight
- Re: [AMBER] Minimization problems. same box different water model David A Case
- Re: [AMBER] problems in reading molecule in tleap/xleap David A Case
- Re: [AMBER] Two LMOD questions David A Case
- [AMBER] Installation of MMPBSA.MPI should be clarified Jan-Philip Gehrcke
- [AMBER] directional pressure variation Giovanni Pavan
- Re: [AMBER] Installation of MMPBSA.MPI should be clarified Jason Swails
- [AMBER] MMPBSA.py: DELTA section missing in FINAL_DECOMP_MMPBSA.dat for dec_verbose=3 Jan-Philip Gehrcke
- Re: [AMBER] Issue with running sander with SHAKE Breuer, Marian
- Re: [AMBER] Issue with running sander with SHAKE David A Case
- Re: [AMBER] sander error David A Case
- Re: [AMBER] bashrc problems Ross Walker
- [AMBER] Segmentation fault in ptraj clustering Seungyeul Yoo
- Re: [AMBER] MMPBSA.py: DELTA section missing in FINAL_DECOMP_MMPBSA.dat for dec_verbose=3 Jason Swails
- Re: [AMBER] MMPBSA.py: DELTA section missing in FINAL_DECOMP_MMPBSA.dat for dec_verbose=3 Jan-Philip Gehrcke
- Re: [AMBER] MMPBSA.py: DELTA section missing in FINAL_DECOMP_MMPBSA.dat for dec_verbose=3 Jason Swails
- Re: [AMBER] Two LMOD questions Sarah Edwards
- [AMBER] crashed run and time estimate Yao Yao
- [AMBER] Visualization of Cluster analysis results wrong string
- Re: [AMBER] crashed run and time estimate Ross Walker
Saturday, 5 November 2011
- Re: [AMBER] problems in reading molecule in tleap/xleap FyD
- [AMBER] About RESP fitting gunajyoti das
- Re: [AMBER] About RESP fitting case
- [AMBER] Some questions of cluster analysis qiao xue
- [AMBER] mm_pbsa error Esam Tolba
- [AMBER] anisotropic NPT simulation Giovanni Pavan
- Re: [AMBER] mm_pbsa error Ray Luo, Ph.D.
- Re: [AMBER] Issue with running sander with SHAKE Breuer, Marian
- Re: [AMBER] anisotropic NPT simulation Benjamin D Madej
Sunday, 6 November 2011
- Re: [AMBER] About RESP fitting FyD
- Re: [AMBER] bashrc problems Andrew Voronkov
- [AMBER] 256 CPUs restriction in AmberMD? Garo Garabedyan
- Re: [AMBER] Some questions of cluster analysis Thomas Cheatham
- [AMBER] How to keep Graphene sheet fixed during MD simulation. hai wei
- Re: [AMBER] 256 CPUs restriction in AmberMD? case
- Re: [AMBER] How to keep Graphene sheet fixed during MD simulation. case
- Re: [AMBER] 1JFF Antechamber, LEaP problems Matthew D Antalek
- Re: [AMBER] How to keep Graphene sheet fixed during MD simulation. hai wei
- [AMBER] About Mn2+ parameters in amber 刘吉元
- Re: [AMBER] How to keep Graphene sheet fixed during MD simulation. hai wei
- Re: [AMBER] How to keep Graphene sheet fixed during MD simulation. hai wei
- [AMBER] Installation of amber11 on the latest Ubuntu 64bit Qinghua Liao
Monday, 7 November 2011
- [AMBER] problem of installation of amber 11 on ubuntu Qinghua Liao
- Re: [AMBER] parameters for anchor-modified glycopeptides Urszula Uciechowska
- Re: [AMBER] Problems with XLEAP James Starlight
- [AMBER] Installation of amber11 on the latest Ubuntu 64bit Qinghua Liao
- [AMBER] problem of installation of amber 11 on ubuntu Qinghua Liao
- Re: [AMBER] Installation of amber11 on the latest Ubuntu 64bit Jason Swails
- Re: [AMBER] How to keep Graphene sheet fixed during MD simulation. Jason Swails
- Re: [AMBER] Problems with XLEAP Jason Swails
- Re: [AMBER] problem of installation of amber 11 on ubuntu Jason Swails
- Re: [AMBER] Installation of amber11 on the latest Ubuntu 64bit Jan-Philip Gehrcke
- Re: [AMBER] How to keep Graphene sheet fixed during MD simulation. David A Case
- Re: [AMBER] How to keep Graphene sheet fixed during MD simulation. David A Case
- Re: [AMBER] parameters for anchor-modified glycopeptides FyD
- Re: [AMBER] problem of installation of amber 11 on ubuntu Qinghua Liao
- Re: [AMBER] Installation of amber11 on the latest Ubuntu 64bit David A Case
- Re: [AMBER] Installation of amber11 on the latest Ubuntu 64bit Qinghua Liao
- Re: [AMBER] problem of installation of amber 11 on ubuntu David A Case
- Re: [AMBER] Installation of amber11 on the latest Ubuntu 64bit Qinghua Liao
- Re: [AMBER] problem of installation of amber 11 on ubuntu Qinghua Liao
- Re: [AMBER] 1JFF Antechamber, LEaP problems FyD
- Re: [AMBER] Installation of amber11 on the latest Ubuntu 64bit Qinghua Liao
- Re: [AMBER] Installation of amber11 on the latest Ubuntu 64bit Jason Swails
- Re: [AMBER] Installation of amber11 on the latest Ubuntu 64bit Jan-Philip Gehrcke
- Re: [AMBER] problem of installation of amber 11 on ubuntu Jason Swails
- [AMBER] Protein structure heating into a mess Xiaozhou Li
- [AMBER] addles "old coordinate file not specified" Jennifer Brookes
- Re: [AMBER] Protein structure heating into a mess DEBOSTUTI GHOSHDASTIDAR
- Re: [AMBER] Protein structure heating into a mess DEBOSTUTI GHOSHDASTIDAR
- Re: [AMBER] addles "old coordinate file not specified" Carlos Simmerling
- Re: [AMBER] Protein structure heating into a mess Xiaozhou Li
- Re: [AMBER] addles "old coordinate file not specified" Jennifer Brookes
- Re: [AMBER] addles "old coordinate file not specified" Carlos Simmerling
- [AMBER] About defining of a modified cytosine which is covalently bonded to the sulfer of cysteine Jin Yang
- Re: [AMBER] parameters for anchor-modified glycopeptides Bill Ross
- Re: [AMBER] addles "old coordinate file not specified" Jennifer Brookes
- Re: [AMBER] Installation of amber11 on the latest Ubuntu 64bit Qinghua Liao
- [AMBER] separate build and install dirs? Michael Sternberg
- Re: [AMBER] separate build and install dirs? Ben Roberts
- Re: [AMBER] How to keep Graphene sheet fixed during MD simulation. hai wei
- [AMBER] AMBER Survey C2075 Winners Ross Walker
- Re: [AMBER] How to keep Graphene sheet fixed during MD simulation. Jason Swails
- Re: [AMBER] How to keep Graphene sheet fixed during MD simulation. hai wei
- [AMBER] AMBER9 in GPU Vijay Manickam Achari
- Re: [AMBER] AMBER9 in GPU Jason Swails
- [AMBER] entropy calculation Sangita Kachhap
- Re: [AMBER] entropy calculation Jason Swails
- [AMBER] Recent mails Marc Baaden
- [AMBER] apologies for an error Marc Baaden
Tuesday, 8 November 2011
- Re: [AMBER] parameters for anchor-modified glycopeptides FyD
- Re: [AMBER] entropy calculation Sangita Kachhap
- Re: [AMBER] About defining of a modified cytosine which is covalently bonded to the sulfer of cysteine FyD
- Re: [AMBER] problems in reading molecule in tleap/xleap FyD
- Re: [AMBER] entropy calculation Bill Miller III
- Re: [AMBER] entropy calculation Sangita Kachhap
- [AMBER] MN2+ ion protein can't be dealed with MCPB 刘吉元
- Re: [AMBER] problems in reading molecule in tleap/xleap FyD
- Re: [AMBER] addles "old coordinate file not specified" Carlos Simmerling
- Re: [AMBER] addles "old coordinate file not specified" Jenny C Brookes
- Re: [AMBER] addles "old coordinate file not specified" Bill Ross
- [AMBER] Membrane building madhumita das
- Re: [AMBER] addles "old coordinate file not specified" Carlos Simmerling
- Re: [AMBER] how to load atom type for divalent ions in leaprc.ff10? Victor Ma
- [AMBER] problem in solvation Senthil Natesan
- Re: [AMBER] problem in solvation Jan-Philip Gehrcke
- Re: [AMBER] addles "old coordinate file not specified" Jennifer Brookes
- Re: [AMBER] addles "old coordinate file not specified" Jenny C Brookes
- Re: [AMBER] problem in solvation Senthil Natesan
- Re: [AMBER] problem in solvation Brian Radak
- Re: [AMBER] problem in solvation Senthil Natesan
- Re: [AMBER] problem in solvation Brian Radak
- [AMBER] AmberTools1.5 install problems on Mac OS X 10.7.2 Frank Barry
- Re: [AMBER] problem in solvation Bill Ross
- Re: [AMBER] AmberTools1.5 install problems on Mac OS X 10.7.2 Jason Swails
- Re: [AMBER] problem in solvation Senthil Natesan
- Re: [AMBER] problem in solvation Bill Ross
- Re: [AMBER] problem in solvation Bill Ross
- Re: [AMBER] problem in solvation Bill Ross
- Re: [AMBER] addles "old coordinate file not specified" Bill Ross
- Re: [AMBER] AmberTools1.5 install problems on Mac OS X 10.7.2 Frank Barry
- [AMBER] Questions about LEaP: atom connect and delete hydrogen Tales Yuan
- Re: [AMBER] AmberTools1.5 install problems on Mac OS X 10.7.2 Jason Swails
- Re: [AMBER] Questions about LEaP: atom connect and delete hydrogen Jason Swails
- Re: [AMBER] how to load atom type for divalent ions in leaprc.ff10? Jason Swails
- [AMBER] calculate residue wise SASA Xiao Chen
- Re: [AMBER] calculate residue wise SASA Daniel Roe
Wednesday, 9 November 2011
- [AMBER] problem with pmemd.cuda Giovanni Pavan
- Re: [AMBER] calculate residue wise SASA Xiao Chen
- [AMBER] AMBER Shesh Nath
- Re: [AMBER] problem in solvation Jan-Philip Gehrcke
- Re: [AMBER] problem in solvation Senthil Natesan
- Re: [AMBER] Questions about LEaP: atom connect and delete hydrogen Tales Yuan
- Re: [AMBER] addles "old coordinate file not specified" Carlos Simmerling
- Re: [AMBER] problem in solvation Bill Ross
- Re: [AMBER] addles "old coordinate file not specified" Jennifer Brookes
- Re: [AMBER] addles "old coordinate file not specified" Carlos Simmerling
- [AMBER] Different print behavior for mdcrd and ncsu modules Brian Radak
- Re: [AMBER] problems in reading molecule in tleap/xleap David A Case
- Re: [AMBER] addles "old coordinate file not specified" David A Case
- [AMBER] PLUMED release 1.3 available Massimiliano Bonomi
- Re: [AMBER] Membrane building David A Case
- Re: [AMBER] problem in solvation David A Case
- Re: [AMBER] problem in solvation Jan-Philip Gehrcke
- Re: [AMBER] problem in solvation Jan-Philip Gehrcke
- Re: [AMBER] addles "old coordinate file not specified" Jenny C Brookes
- Re: [AMBER] problem in solvation Bill Ross
- Re: [AMBER] calculate residue wise SASA Jason Swails
- Re: [AMBER] addles "old coordinate file not specified" Jan-Philip Gehrcke
- Re: [AMBER] addles "old coordinate file not specified" Bill Ross
- Re: [AMBER] problem in solvation Bill Ross
- Re: [AMBER] problem with pmemd.cuda Ross Walker
- Re: [AMBER] separate build and install dirs? Michael Sternberg
- Re: [AMBER] separate build and install dirs? Bill Ross
- [AMBER] help with antechamber jun kit
- Re: [AMBER] problem with pmemd.cuda Pavan Giovanni
- Re: [AMBER] problem in solvation Senthil Natesan
- Re: [AMBER] problem in solvation Senthil Natesan
- Re: [AMBER] separate build and install dirs? Michael Sternberg
- Re: [AMBER] problem with pmemd.cuda Scott Le Grand
- Re: [AMBER] problem in solvation David A Case
- Re: [AMBER] problem in solvation Jason Swails
- Re: [AMBER] problem in solvation Senthil Natesan
- Re: [AMBER] problem in solvation Bill Ross
- Re: [AMBER] addles "old coordinate file not specified" Jennifer Brookes
- Re: [AMBER] problem with pmemd.cuda Scott Le Grand
- [AMBER] Passing the free-format flag to files in sander and nmode case
- Re: [AMBER] help with antechamber case
- Re: [AMBER] Passing the free-format flag to files in sander and nmode Jason Swails
- Re: [AMBER] Nudged Elastic Band (NEB) with torque PBS system c00jsw00.nchc.narl.org.tw
Thursday, 10 November 2011
- Re: [AMBER] Passing the free-format flag to files in sander and nmode Michael Sternberg
- [AMBER] R: problem with pmemd.cuda Giovanni Pavan
- Re: [AMBER] nmropt modes for GPU accelerated pmemd 11 Andre Serobian
- Re: [AMBER] Passing the free-format flag to files in sander and nmode case
- [AMBER] problem of generating prmtop and inpcrd files of a small molecule attached with several amino acids Qinghua Liao
- Re: [AMBER] R: problem with pmemd.cuda case
- Re: [AMBER] Nudged Elastic Band (NEB) with torque PBS system Daniel Roe
- Re: [AMBER] problems in reading linrary/tleap case
- Re: [AMBER] MN2+ ion protein can't be dealed with MCPB case
- Re: [AMBER] Passing the free-format flag to files in sander and nmode Jason Swails
- Re: [AMBER] nmropt modes for GPU accelerated pmemd 11 Ross Walker
- Re: [AMBER] About defining of a modified cytosine which is covalently bonded to the sulfer of cysteine Jin Yang
- [AMBER] Xleap pdb editing James Starlight
- Re: [AMBER] Xleap pdb editing David A Case
- Re: [AMBER] problem of generating prmtop and inpcrd files of a small molecule attached with several amino acids David A Case
- Re: [AMBER] Different print behavior for mdcrd and ncsu modules David A Case
- [AMBER] any fix so that I can compile AmberTools with gfortran 4.6.1? Jose Borreguero
- Re: [AMBER] problems in reading linrary/tleap FyD
- Re: [AMBER] Xleap pdb editing James Starlight
- Re: [AMBER] Xleap pdb editing David A Case
- Re: [AMBER] problem of generating prmtop and inpcrd files of a small molecule attached with several amino acids Qinghua Liao
- [AMBER] leap cannot read MOL2 file that it has written before: small fix suggested Jan-Philip Gehrcke
- Re: [AMBER] Xleap pdb editing James Starlight
- Re: [AMBER] leap cannot read MOL2 file that it has written before: small fix suggested M. L. Dodson
- [AMBER] ZAFF parametrization problem , parameters not saved, could not find bond parameters Andrew Voronkov
- Re: [AMBER] leap cannot read MOL2 file that it has written before: small fix suggested M. L. Dodson
- Re: [AMBER] Xleap pdb editing David A Case
- Re: [AMBER] leap cannot read MOL2 file that it has written before: small fix suggested M. L. Dodson
- Re: [AMBER] leap cannot read MOL2 file that it has written before: small fix suggested Jan-Philip Gehrcke
- Re: [AMBER] leap cannot read MOL2 file that it has written before: small fix suggested Jan-Philip Gehrcke
- Re: [AMBER] nmropt modes for GPU accelerated pmemd 11 serobian.a.student.unsw.edu.au
- Re: [AMBER] R: problem with pmemd.cuda Scott Le Grand
- Re: [AMBER] leap cannot read MOL2 file that it has written before: small fix suggested M. L. Dodson
- Re: [AMBER] R: problem with pmemd.cuda Ross Walker
Friday, 11 November 2011
- Re: [AMBER] leap cannot read MOL2 file that it has written before: small fix suggested Jan-Philip Gehrcke
- Re: [AMBER] problem of generating prmtop and inpcrd files of a small molecule attached with several amino acids Qinghua Liao
- [AMBER] AMBER 11 (Problem with the input format) Fernando Blanco
- Re: [AMBER] problem of generating prmtop and inpcrd files of a small molecule attached with several amino acids case
- Re: [AMBER] AMBER 11 (Problem with the input format) case
- Re: [AMBER] AMBER 11 (Problem with the input format) Fernando Blanco
- Re: [AMBER] AMBER 11 (Problem with the input format) Fernando Blanco
- Re: [AMBER] leap cannot read MOL2 file that it has written before: small fix suggested M. L. Dodson
- Re: [AMBER] global build; was: Passing the free-format flag to files in sander and nmode Michael Sternberg
- [AMBER] MKL: lib dir name changed for 64bit version Michael Sternberg
- Re: [AMBER] Passing the free-format flag to files in sander and nmode Michael Sternberg
- [AMBER] Phi/psi to free energies Lekpa Duukori
- Re: [AMBER] AMBER 11 (Problem with the input format) Jason Swails
- Re: [AMBER] R: problem with pmemd.cuda Pavan Giovanni
- [AMBER] bad atom type: Br Hector A. Baldoni
- [AMBER] Problems of generating prmtop and inpcrd files for ligand-receptor with two Mg2+ ions --please help Crystal.CHIA-YU Ku
- Re: [AMBER] Problems of generating prmtop and inpcrd files for ligand-receptor with two Mg2+ ions --please help case
- [AMBER] comparison failures in the Amber11 and AT15 test bin wang
- [AMBER] question about MMPBSA.py Sidney Elmer
- Re: [AMBER] Problems of generating prmtop and inpcrd files for ligand-receptor with two Mg2+ ions --please help Crystal.CHIA-YU Ku
- Re: [AMBER] question about MMPBSA.py Jason Swails
- Re: [AMBER] bad atom type: Br Jason Swails
- Re: [AMBER] comparison failures in the Amber11 and AT15 test Jason Swails
- Re: [AMBER] Problems of generating prmtop and inpcrd files for ligand-receptor with two Mg2+ ions --please help case
- [AMBER] msd subrata paul
Saturday, 12 November 2011
- [AMBER] mpirun leila karami
- [AMBER] mpirun leila karami
- [AMBER] Discrepancy of GBSA results Anglea A.
- Re: [AMBER] Discrepancy of GBSA results Carlos Simmerling
- Re: [AMBER] Discrepancy of GBSA results Adrian Roitberg
- Re: [AMBER] mpirun Jason Swails
- Re: [AMBER] mpirun case
- Re: [AMBER] mpirun case
- [AMBER] building a polymer and running antechamber on it Changwoo Do
- [AMBER] Calculate charges using better method/basis set? Ismail, Mohd F.
- [AMBER] MMPBSA - running dynamics Fernando Blanco
Sunday, 13 November 2011
- [AMBER] MN2+ ion protein can't be dealed with MCPB 刘吉元
- Re: [AMBER] bad atom type: Br Baldoni Hector Armando
- [AMBER] how to use ptraj to convert trajectory files? Yun Shi
- [AMBER] Ca(2+) LJ parameters Dr. Vitaly V. Chaban
- Re: [AMBER] how to use ptraj to convert trajectory files? Jan-Philip Gehrcke
- Re: [AMBER] Calculate charges using better method/basis set? Dr. Vitaly V. Chaban
- Re: [AMBER] Calculate charges using better method/basis set? Adrian Roitberg
- Re: [AMBER] Calculate charges using better method/basis set? Dr. Vitaly V. Chaban
- [AMBER] 16 microsecond MD run David Condon
- Re: [AMBER] Ca(2+) LJ parameters case
- Re: [AMBER] Ca(2+) LJ parameters ros
- Re: [AMBER] bashrc problems Ben Roberts
- [AMBER] MCPB settings file 刘吉元
- [AMBER] Compiling trouble of AmberTools with intel compiler v12.1.0. K. Uebayashi
Monday, 14 November 2011
- Re: [AMBER] msd Bruno Rodrigues
- [AMBER] Pre-equilibrium of REMD simulations ÏéÇ« ¿×
- Re: [AMBER] Pre-equilibrium of REMD simulations Carlos Simmerling
- Re: [AMBER] MCPB settings file Ben Roberts
- Re: [AMBER] Calculate charges using better method/basis set? Ismail, Mohd F.
- Re: [AMBER] Calculate charges using better method/basis set? Ross Walker
- Re: [AMBER] Calculate charges using better method/basis set? Dr. Vitaly V. Chaban
- Re: [AMBER] Calculate charges using better method/basis set? Dr. Vitaly V. Chaban
- Re: [AMBER] Calculate charges using better method/basis set? Adrian Roitberg
- Re: [AMBER] Calculate charges using better method/basis set? Ross Walker
- Re: [AMBER] Calculate charges using better method/basis set? Brian Radak
- [AMBER] "force field" vs. "potential" Jan-Philip Gehrcke
- Re: [AMBER] comparison failures in the Amber11 and AT15 test bin wang
- Re: [AMBER] "force field" vs. "potential" Dr. Vitaly V. Chaban
- Re: [AMBER] "force field" vs. "potential" Ross Walker
- Re: [AMBER] Problems of generating prmtop and inpcrd files for ligand-receptor with two Mg2+ ions --please help Crystal.CHIA-YU Ku
- [AMBER] problems of MMPBSA.py.MPI Qinghua Liao
- Re: [AMBER] Problems of generating prmtop and inpcrd files for ligand-receptor with two Mg2+ ions --please help case
- Re: [AMBER] Problems of generating prmtop and inpcrd files for ligand-receptor with two Mg2+ ions --please help Crystal.CHIA-YU Ku
- Re: [AMBER] problems of MMPBSA.py.MPI Jason Swails
- Re: [AMBER] MCPB settings file Ben Roberts
- [AMBER] QMMM SCC-DFTB: ERROR ON EWEVGE (Eigenvalue solver) Emmanuel Baribefe Naziga
- Re: [AMBER] Problems of generating prmtop and inpcrd files for ligand-receptor with two Mg2+ ions --please help Crystal.CHIA-YU Ku
- [AMBER] How MCPB add ligand with a small molecule in *_siderchain.bcl 刘吉元
- [AMBER] Building non standard DNA residue Buddhadev Maiti
- Re: [AMBER] mpirun Sudeep Narayan Banerjee
- Re: [AMBER] problems of MMPBSA.py.MPI Qinghua Liao
Tuesday, 15 November 2011
- [AMBER] Installing AMBER9 in SGI_ALTIX-XE1300 - need some help Vijay Manickam Achari
- [AMBER] dummny atoms in .prep file Andrew Voronkov
- Re: [AMBER] "force field" vs. "potential" Jan-Philip Gehrcke
- Re: [AMBER] leap cannot read MOL2 file that it has written before: small fix suggested Jan-Philip Gehrcke
- Re: [AMBER] Building non standard DNA residue FyD
- Re: [AMBER] building a polymer and running antechamber on it FyD
- Re: [AMBER] leap cannot read MOL2 file that it has written before: small fix suggested David A Case
- Re: [AMBER] Installing AMBER9 in SGI_ALTIX-XE1300 - need some help David A Case
- Re: [AMBER] Problems of generating prmtop and inpcrd files for ligand-receptor with two Mg2+ ions --please help David A Case
- Re: [AMBER] Problems of generating prmtop and inpcrd files for ligand-receptor with two Mg2+ ions --please help David A Case
- [AMBER] ambertools 1.5 compiling ERROR: Return type mismatch of function 'cgalf' at (1) (REAL(8)/REAL(4)) Jose Borreguero
- Re: [AMBER] QMMM SCC-DFTB: ERROR ON EWEVGE (Eigenvalue solver) Brian Radak
- Re: [AMBER] "force field" vs. "potential" Brian Radak
- [AMBER] Minimization of only certain atoms David Condon
- Re: [AMBER] Compiling trouble of AmberTools with intel compiler v12.1.0. Mark Williamson
- [AMBER] [SOLVED] Compiling trouble of AmberTools with intel compiler v12.1.0. Jose Borreguero
- Re: [AMBER] ambertools 1.5 compiling ERROR: Return type mismatch of function 'cgalf' at (1) (REAL(8)/REAL(4)) David A Case
- Re: [AMBER] ambertools 1.5 compiling ERROR: Return type mismatch of function 'cgalf' at (1) (REAL(8)/REAL(4)) Jose Borreguero
- Re: [AMBER] QMMM SCC-DFTB: ERROR ON EWEVGE (Eigenvalue solver) Emmanuel Baribefe Naziga
- Re: [AMBER] QMMM SCC-DFTB: ERROR ON EWEVGE (Eigenvalue solver) Adrian Roitberg
- Re: [AMBER] QMMM SCC-DFTB: ERROR ON EWEVGE (Eigenvalue solver) Emmanuel Baribefe Naziga
- Re: [AMBER] Minimization of only certain atoms Brian Radak
- Re: [AMBER] QMMM SCC-DFTB: ERROR ON EWEVGE (Eigenvalue solver) Brian Radak
- Re: [AMBER] QMMM SCC-DFTB: ERROR ON EWEVGE (Eigenvalue solver) Emmanuel Baribefe Naziga
- Re: [AMBER] QMMM SCC-DFTB: ERROR ON EWEVGE (Eigenvalue solver) Gustavo Seabra
- Re: [AMBER] Problems of generating prmtop and inpcrd files for ligand-receptor with two Mg2+ ions --please help Irene Newhouse
- [AMBER] Charge method Changwoo Do
- Re: [AMBER] Charge method Dr. Vitaly V. Chaban
- Re: [AMBER] Charge method Dr. Vitaly V. Chaban
- Re: [AMBER] Problems of generating prmtop and inpcrd files for ligand-receptor with two Mg2+ ions --please help Crystal.CHIA-YU Ku
- Re: [AMBER] Charge method Changwoo Do
- Re: [AMBER] Problems of generating prmtop and inpcrd files for ligand-receptor with two Mg2+ ions --please help Crystal.CHIA-YU Ku
- Re: [AMBER] Minimization of only certain atoms Jason Swails
- Re: [AMBER] Problems of generating prmtop and inpcrd files for ligand-receptor with two Mg2+ ions --please help case
- Re: [AMBER] Problems of generating prmtop and inpcrd files for ligand-receptor with two Mg2+ ions --please help case
- Re: [AMBER] Charge method Dr. Vitaly V. Chaban
Wednesday, 16 November 2011
- Re: [AMBER] Installing AMBER9 in SGI_ALTIX-XE1300 - need some help Vijay Manickam Achari
- [AMBER] problem in leap Qinghua Liao
- [AMBER] MMPBSA - ptraj for RMSD Fernando Blanco
- [AMBER] mpirun leila karami
- [AMBER] compilation openmpi FAIL for AMBER9 Vijay Manickam Achari
- Re: [AMBER] MMPBSA - ptraj for RMSD Daniel Roe
- [AMBER] Compilation fail of amberTools 1.2 for amber10 support Jose Borreguero
- Re: [AMBER] Installing AMBER9 in SGI_ALTIX-XE1300 - need some help David A Case
- Re: [AMBER] problem in leap David A Case
- Re: [AMBER] mpirun David A Case
- Re: [AMBER] Minimization of only certain atoms David Condon
- Re: [AMBER] Compilation fail of amberTools 1.2 for amber10 support David A Case
- Re: [AMBER] Calculate charges using better method/basis set? Ismail, Mohd F.
- Re: [AMBER] Calculate charges using better method/basis set? Karl N. Kirschner
- [AMBER] [SOLVED] Re: Compilation fail of amberTools 1.2 for amber10 support Jose Borreguero
- [AMBER] H-Bond problem najmul arfin
- [AMBER] pulling the ligand in different directions Sai Kumar Ramadugu
- Re: [AMBER] Calculate charges using better method/basis set? Ismail, Mohd F.
- Re: [AMBER] Problems of generating prmtop and inpcrd files for ligand-receptor with two Mg2+ ions --please help Crystal.CHIA-YU Ku
- Re: [AMBER] dummny atoms in .prep file Jason Swails
- Re: [AMBER] problem in leap Qinghua Liao
- [AMBER] Parameters for Ionic liquids in AMBER Ganesh Kamath
- Re: [AMBER] Parameters for Ionic liquids in AMBER Jones de Andrade
- Re: [AMBER] Problems of generating prmtop and inpcrd files for ligand-receptor with two Mg2+ ions --please help David A Case
- Re: [AMBER] Parameters for Ionic liquids in AMBER Ganesh Kamath
- Re: [AMBER] H-Bond problem David A Case
- [AMBER] ncsu_pmd and ncsu_smd Sai Kumar Ramadugu
- Re: [AMBER] Parameters for Ionic liquids in AMBER case
- Re: [AMBER] Compiling trouble of AmberTools with intel compiler v12.1.0. K. Uebayashi
Thursday, 17 November 2011
- [AMBER] how to calculate interaction surface in time Tomáš Kučera
- [AMBER] question to R.E.D server Urszula Uciechowska
- [AMBER] Got a mistake with 3H68_OH_large.bcl 刘吉元
- Re: [AMBER] ncsu_pmd and ncsu_smd Brian Radak
- Re: [AMBER] question to R.E.D server intra\\sa175950
- Re: [AMBER] Problems of generating prmtop and inpcrd files for ligand-receptor with two Mg2+ ions --please help David A Case
- [AMBER] Spherical Coordinates & Pulling Ligand Sai Kumar Ramadugu
- Re: [AMBER] Phi/psi to free energies Ben Roberts
- [AMBER] Differentially restraining backbone and sidechain atoms from Chamber generated prmtop Joshua Adelman
- Re: [AMBER] large.bcl bug in MCPB Ben Roberts
- Re: [AMBER] Got a mistake with 3H68_OH_large.bcl Ben Roberts
- Re: [AMBER] How MCPB add ligand with a small molecule in *_siderchain.bcl Ben Roberts
- Re: [AMBER] Problems of generating prmtop and inpcrd files for ligand-receptor with two Mg2+ ions --please help Crystal.CHIA-YU Ku
- [AMBER] compiling pmemd in amber9 Vijay Manickam Achari
- [AMBER] Select cuda ID device in PMEMD Gonzalo Jimenez
- Re: [AMBER] Problems of generating prmtop and inpcrd files for ligand-receptor with two Mg2+ ions --please help David A. Case
- Re: [AMBER] compiling pmemd in amber9 David A. Case
- Re: [AMBER] Select cuda ID device in PMEMD Gonzalo Jimenez
- Re: [AMBER] Select cuda ID device in PMEMD Jason Swails
- Re: [AMBER] Select cuda ID device in PMEMD Gonzalo Jimenez
- Re: [AMBER] Select cuda ID device in PMEMD Ross Walker
- Re: [AMBER] Select cuda ID device in PMEMD Ross Walker
- Re: [AMBER] MCPB settings file JiYuan Liu
- Re: [AMBER] How MCPB add ligand with a small molecule in*_siderchain.bcl JiYuan Liu
- Re: [AMBER] Select cuda ID device in PMEMD Gonzalo Jimenez
- Re: [AMBER] Select cuda ID device in PMEMD Gonzalo Jimenez
- [AMBER] Can't get the correct gaussian input name after runed *_sidechain.bcl in MCPB JiYuan Liu
Friday, 18 November 2011
- Re: [AMBER] Differentially restraining backbone and sidechain atoms from Chamber generated prmtop Mark Williamson
- [AMBER] bonds problem in leap Qinghua Liao
- [AMBER] Segmentation fault - LeAP - Ring structure Volker Lesch
- Re: [AMBER] Differentially restraining backbone and sidechain atoms from Chamber generated prmtop Joshua Adelman
- [AMBER] problems with MCBP parametrization Andrew Voronkov
- Re: [AMBER] Segmentation fault - LeAP - Ring structure David A Case
- Re: [AMBER] Segmentation fault - LeAP - Ring structure Jason Swails
- Re: [AMBER] Problems of generating prmtop and inpcrd files for ligand-receptor with two Mg2+ ions --please help FyD
- [AMBER] 2 traj approach using MMPBSA.py ? Marek Maly
- Re: [AMBER] MCPB settings file Ben Roberts
- Re: [AMBER] Can't get the correct gaussian input name after runed *_sidechain.bcl in MCPB Martin Peters
- Re: [AMBER] problems with MCBP parametrization Martin Peters
- [AMBER] how to add new groups to all_amino94.in Li, Yawen (MU-Student)
- Re: [AMBER] Select cuda ID device in PMEMD Ross Walker
- [AMBER] generating frcmod files Soma Ghosh
- Re: [AMBER] Differentially restraining backbone and sidechain atoms from Chamber generated prmtop Jason Swails
- Re: [AMBER] compiling pmemd in amber9 Ross Walker
- Re: [AMBER] problems with MCBP parametrization Yang, Yue
- Re: [AMBER] Problems of generating prmtop and inpcrd files for ligand-receptor with two Mg2+ ions --please help Crystal.CHIA-YU Ku
- [AMBER] atom type requested that does not appear in the prep file arikcohen
- Re: [AMBER] atom type requested that does not appear in the prep file Bill Ross
- Re: [AMBER] atom type requested that does not appear in the prep file arikcohen
- Re: [AMBER] Problems of generating prmtop and inpcrd files for ligand-receptor with two Mg2+ ions --please help Crystal.CHIA-YU Ku
- Re: [AMBER] generating frcmod files David A. Case
- Re: [AMBER] Problems of generating prmtop and inpcrd files for ligand-receptor with two Mg2+ ions --please help David A. Case
- Re: [AMBER] Segmentation fault - LeAP - Ring structure David A. Case
Saturday, 19 November 2011
- Re: [AMBER] how to add new groups to all_amino94.in FyD
- Re: [AMBER] Membrane building madhumita das
- Re: [AMBER] Membrane building Vlad Cojocaru
- [AMBER] Order parameter subrata paul
- Re: [AMBER] Order parameter David A. Case
- Re: [AMBER] Membrane building Benjamin Madej
- Re: [AMBER] how to add new groups to all_amino94.in Jason Swails
- Re: [AMBER] How MCPB add ligand with a small molecule in*_siderchain.bcl JiYuan Liu
Sunday, 20 November 2011
- [AMBER] binding energy calculated by mm_pbsa.pl Qinghua Liao
- Re: [AMBER] MCPB settings file JiYuan Liu
- Re: [AMBER] binding energy calculated by mm_pbsa.pl Ray Luo, Ph.D.
- Re: [AMBER] binding energy calculated by mm_pbsa.pl Qinghua Liao
- Re: [AMBER] how to add new groups to all_amino94.in FyD
- Re: [AMBER] how to add new groups to all_amino94.in M. L. Dodson
- Re: [AMBER] how to add new groups to all_amino94.in M. L. Dodson
- [AMBER] polymer blend Changwoo Do
- Re: [AMBER] help with antechamber jun kit
- Re: [AMBER] how to add new groups to all_amino94.in Jason Swails
- Re: [AMBER] how to add new groups to all_amino94.in M. L. Dodson
- [AMBER] how to speed up nmode calculation using MMPBSA.MPI? Josmar R. da Rocha
- Re: [AMBER] Can't get the correct gaussian input name after runed*_sidechain.bcl in MCPB JiYuan Liu
- Re: [AMBER] how to speed up nmode calculation using MMPBSA.MPI? Jason Swails
Monday, 21 November 2011
- Re: [AMBER] how to add new groups to all_amino94.in FyD
- [AMBER] dynamics of isotopically labelled proteins vaibhav dixit
- Re: [AMBER] Can't get the correct gaussian input name after runed*_sidechain.bcl in MCPB Martin Peters
- Re: [AMBER] 2 traj approach using MMPBSA.py ? Marek Maly
- [AMBER] Stability of water force fields Bruno Rodrigues
- Re: [AMBER] Can't get the correct gaussian input name afterruned*_sidechain.bcl in MCPB JiYuan Liu
- Re: [AMBER] How MCPB add ligand with a small molecule in*_siderchain.bcl JiYuan Liu
- Re: [AMBER] dynamics of isotopically labelled proteins Jason Swails
- [AMBER] installation of amberTools on lion fails Jorgen Simonsen
- Re: [AMBER] installation of amberTools on lion fails Jason Swails
- Re: [AMBER] installation of amberTools on lion fails Gustavo Seabra
- Re: [AMBER] dynamics of isotopically labelled proteins vaibhav dixit
- Re: [AMBER] installation of amberTools on lion fails Jorgen Simonsen
- Re: [AMBER] installation of amberTools on lion fails Jason Swails
- Re: [AMBER] installation of amberTools on lion fails Jason Swails
- Re: [AMBER] problems with MCBP parametrization Andrew Voronkov
- Re: [AMBER] installation of amberTools on lion fails Gustavo Seabra
- Re: [AMBER] dynamics of isotopically labelled proteins Francesco Paesani
- Re: [AMBER] dynamics of isotopically labelled proteins vaibhav dixit
- Re: [AMBER] help with antechamber David A Case
- Re: [AMBER] Stability of water force fields David A Case
- Re: [AMBER] Stability of water force fields Bruno Rodrigues
- Re: [AMBER] binding energy calculated by mm_pbsa.pl Ray Luo, Ph.D.
- Re: [AMBER] installation of amberTools on lion fails Jorgen Simonsen
- Re: [AMBER] installation of amberTools on lion fails Jason Swails
- Re: [AMBER] installation of amberTools on lion fails Jason Swails
- Re: [AMBER] installation of amberTools on lion fails Jorgen Simonsen
- Re: [AMBER] installation of amberTools on lion fails Jason Swails
- [AMBER] amber99sb in AMBER vs amber99sb in GROMACS or NAMD Thomas Evangelidis
- Re: [AMBER] installation of amberTools on lion fails Jorgen Simonsen
- Re: [AMBER] installation of amberTools on lion fails Jason Swails
- Re: [AMBER] installation of amberTools on lion fails Jorgen Simonsen
- Re: [AMBER] amber99sb in AMBER vs amber99sb in GROMACS or NAMD George M Giambasu
- Re: [AMBER] installation of amberTools on lion fails Jason Swails
- Re: [AMBER] Problems of generating prmtop and inpcrd files for ligand-receptor with two Mg2+ ions --please help Crystal.CHIA-YU Ku
- Re: [AMBER] How MCPB add ligand with a small molecule in*_siderchain.bcl JiYuan Liu
- [AMBER] How to repair defect RNA residues? Crystal.CHIA-YU Ku
- [AMBER] How to use strip mask and receptor mask in the new mmpbsa.py? bin wang
- Re: [AMBER] binding energy calculated by mm_pbsa.pl Qinghua Liao
Tuesday, 22 November 2011
- [AMBER] mpirun leila karami
- Re: [AMBER] amber99sb in AMBER vs amber99sb in GROMACS or NAMD Oliver Grant
- [AMBER] clustering analysis in ptraj takes too long time liu junjun
- [AMBER] AmberTools 1.5 compilation: Error importing cpinutil.py python modules! cpinutil will not work Vlad Cojocaru
- [AMBER] frcmod file for metal-amino acid complex Soma Ghosh
- Re: [AMBER] How to repair defect RNA residues? Jason Swails
- Re: [AMBER] How to use strip mask and receptor mask in the new mmpbsa.py? Jason Swails
- Re: [AMBER] mpirun Jason Swails
- Re: [AMBER] AmberTools 1.5 compilation: Error importing cpinutil.py python modules! cpinutil will not work Jason Swails
- Re: [AMBER] frcmod file for metal-amino acid complex Jason Swails
- Re: [AMBER] how to speed up nmode calculation using MMPBSA.MPI? Josmar R. da Rocha
- Re: [AMBER] clustering analysis in ptraj takes too long time Alex Rodriguez
- Re: [AMBER] frcmod file for metal-amino acid complex David A Case
- Re: [AMBER] Stability of water force fields David A Case
- Re: [AMBER] Stability of water force fields Jiri Sponer
- Re: [AMBER] clustering analysis in ptraj takes too long time liu junjun
- Re: [AMBER] AmberTools 1.5 compilation: Error importing cpinutil.py python modules! cpinutil will not work Vlad Cojocaru
- [AMBER] Error on PCA Elisabeth Widjajakusuma
- [AMBER] how to obtain NOEs from MD trajectory ? Jose Borreguero
- Re: [AMBER] AmberTools 1.5 compilation: Error importing cpinutil.py python modules! cpinutil will not work Vlad Cojocaru
- Re: [AMBER] How MCPB add ligand with a small molecule in*_siderchain.bcl JiYuan Liu
- Re: [AMBER] MCPB settings file JiYuan Liu
- Re: [AMBER] AmberTools 1.5 compilation: Error importing cpinutil.py python modules! cpinutil will not work Jason Swails
- Re: [AMBER] how to obtain NOEs from MD trajectory ? David A Case
- Re: [AMBER] Error on PCA David A Case
- Re: [AMBER] AmberTools 1.5 compilation: Error importing cpinutil.py python modules! cpinutil will not work Vlad Cojocaru
- Re: [AMBER] Error on PCA Elisabeth Widjajakusuma
- [AMBER] makeDIST_RST error Charles Johnson
- Re: [AMBER] clustering analysis in ptraj takes too long time Daniel Roe
- Re: [AMBER] AmberTools 1.5 compilation: Error importing cpinutil.py python modules! cpinutil will not work Jason Swails
- Re: [AMBER] AmberTools 1.5 compilation: Error importing cpinutil.py python modules! cpinutil will not work Vlad Cojocaru
- Re: [AMBER] AmberTools 1.5 compilation: Error importing cpinutil.py python modules! cpinutil will not work Vlad Cojocaru
- Re: [AMBER] makeDIST_RST error David A Case
- [AMBER] compilation of Amber Tools 1.5 with GCC 4.6.2 with "-nopython" Vlad Cojocaru
- Re: [AMBER] compilation of Amber Tools 1.5 with GCC 4.6.2 with "-nopython" Tyler Luchko
- Re: [AMBER] help with antechamber jun kit
- Re: [AMBER] compilation of Amber Tools 1.5 with GCC 4.6.2 with "-nopython" Vlad Cojocaru
- Re: [AMBER] How to repair defect RNA residues? Crystal.CHIA-YU Ku
- [AMBER] How to fix the installation problem of mopac Crystal.CHIA-YU Ku
- Re: [AMBER] help with antechamber jun kit
- Re: [AMBER] Can't get the correct gaussian input name afterruned*_sidechain.bcl in MCPB Ben Roberts
- Re: [AMBER] How MCPB add ligand with a small molecule in*_siderchain.bcl Ben Roberts
- Re: [AMBER] How MCPB add ligand with a small molecule in*_siderchain.bcl Ben Roberts
- Re: [AMBER] How MCPB add ligand with a small molecule in*_siderchain.bcl Ben Roberts
- Re: [AMBER] MCPB settings file Ben Roberts
- Re: [AMBER] How MCPB add ligand with a small moleculein*_siderchain.bcl JiYuan Liu
Wednesday, 23 November 2011
- [AMBER] ICST-Amber Install co nguyentruong
- Re: [AMBER] ICST-Amber Install co nguyentruong
- [AMBER] MD of a Ca2+ dependent interaction Juan Carlos
- [AMBER] parameters in mm/pbsa calculations Qinghua Liao
- Re: [AMBER] parameters in mm/pbsa calculations Bill Miller III
- Re: [AMBER] How to fix the installation problem of mopac David A Case
- Re: [AMBER] parameters in mm/pbsa calculations Qinghua Liao
- Re: [AMBER] parameters in mm/pbsa calculations Bill Miller III
- Re: [AMBER] parameters in mm/pbsa calculations Qinghua Liao
- [AMBER] alpha helix structure consist of Alanine Tong Zhu
- Re: [AMBER] help with antechamber jun kit
- Re: [AMBER] How to repair defect RNA residues? Jason Swails
- [AMBER] BUG in NAB file nabgrm.y Chris Whittleston
- Re: [AMBER] alpha helix structure consist of Alanine Carlos Simmerling
- Re: [AMBER] How MCPB add ligand with a small moleculein*_siderchain.bcl JiYuan Liu
- Re: [AMBER] parameters in mm/pbsa calculations Ray Luo, Ph.D.
- Re: [AMBER] alpha helix structure consist of Alanine Bill Ross
- [AMBER] CCYX not recognized by ff03 in tleap Raik Grünberg
- Re: [AMBER] CCYX not recognized by ff03 in tleap Jason Swails
- Re: [AMBER] How to fix the installation problem of mopac Crystal.CHIA-YU Ku
- Re: [AMBER] How to repair defect RNA residues? Crystal.CHIA-YU Ku
- Re: [AMBER] CCYX not recognized by ff03 in tleap Raik Grünberg
- Re: [AMBER] CCYX not recognized by ff03 in tleap Jason Swails
- Re: [AMBER] ICST-Amber Install Jason Swails
Thursday, 24 November 2011
- [AMBER] combination of CHAMBER prmtop and pmemd.cuda is causing serious instability Marc van der Kamp
- Re: [AMBER] combination of CHAMBER prmtop and pmemd.cuda is causing serious instability Marc van der Kamp
- Re: [AMBER] ICST-Amber Install co nguyentruong
- Re: [AMBER] combination of CHAMBER prmtop and pmemd.cuda is causing serious instability Mark Williamson
- Re: [AMBER] How to fix the installation problem of mopac case
- Re: [AMBER] CCYX not recognized by ff03 in tleap Raik Grünberg
- Re: [AMBER] BUG in NAB file nabgrm.y case
- Re: [AMBER] help with antechamber jun kit
- Re: [AMBER] ICST-Amber Install Jason Swails
- Re: [AMBER] combination of CHAMBER prmtop and pmemd.cuda is causing serious instability Marc van der Kamp
- Re: [AMBER] How to repair defect RNA residues? case
- Re: [AMBER] ICST-Amber Install co nguyentruong
- [AMBER] Fwd: problems with MCBP parametrization Andrew Voronkov
- [AMBER] q4md-forcefieldtools.org announcement FyD
- [AMBER] General Amber FF Parameters Caglar Bayar
- Re: [AMBER] General Amber FF Parameters Bill Ross
- Re: [AMBER] General Amber FF Parameters Jason Swails
- [AMBER] 2-d PMF calculation with REMD caobb0214
- Re: [AMBER] 2-d PMF calculation with REMD Daniel Sindhikara
- [AMBER] Problem running Ptraj with CHARMM psf and dcd trajectory file Puspita Halder
Friday, 25 November 2011
- [AMBER] Parameters for heme C Konrad Hinsen
- Re: [AMBER] BUG in NAB file nabgrm.y Chris Whittleston
- [AMBER] Sander kanika sharma
- [AMBER] MMPBSA M. Reza Ganjalikhany
- Re: [AMBER] Sander case
- [AMBER] question on antechamber generating parameters for a charged ligand fn1.rice.edu
- Re: [AMBER] question on antechamber generating parameters for a charged ligand Dmitry Nilov
- Re: [AMBER] question on antechamber generating parameters for a charged ligand fn1.rice.edu
- Re: [AMBER] question on antechamber generating parameters for a charged ligand ros
- Re: [AMBER] Fwd: problems with MCBP parametrization Ben Roberts
- Re: [AMBER] question on antechamber generating parameters for a charged ligand Dmitry Nilov
- Re: [AMBER] How MCPB add ligand with a small moleculein*_siderchain.bcl Ben Roberts
- Re: [AMBER] question on antechamber generating parameters for a charged ligand fn1.rice.edu
- Re: [AMBER] question on antechamber generating parameters for a charged ligand fn1.rice.edu
- Re: [AMBER] question on antechamber generating parameters for a charged ligand Dmitry Nilov
- [AMBER] top2mol2 charges output in mol2 Jio M
- Re: [AMBER] MMPBSA Jason Swails
- Re: [AMBER] question on antechamber generating parameters for a charged ligand case
- Re: [AMBER] top2mol2 charges output in mol2 case
- Re: [AMBER] 2-d PMF calculation with REMD Yong Duan
- Re: [AMBER] top2mol2 charges output in mol2 Jio M
- Re: [AMBER] MMPBSA M. Reza Ganjalikhany
Saturday, 26 November 2011
- Re: [AMBER] Issue with running sander with SHAKE Andrew Voronkov
- Re: [AMBER] Issue with running sander with SHAKE Andrew Voronkov
- [AMBER] ANTECHAMBER: fatal error George Tzotzos
- [AMBER] cutoff distance again Yun Shi
- Re: [AMBER] ANTECHAMBER: fatal error George Tzotzos
- [AMBER] Fwd: Issue with running sander with SHAKE Andrew Voronkov
- Re: [AMBER] Fwd: Issue with running sander with SHAKE Yong Duan
- Re: [AMBER] ANTECHAMBER: fatal error Yong Duan
- Re: [AMBER] ANTECHAMBER: fatal error George Tzotzos
- Re: [AMBER] question on antechamber generating parameters for a charged ligand Dean Cuebas
- Re: [AMBER] question on antechamber generating parameters for a charged ligand fn1.rice.edu
- [AMBER] Using nrespa with NPT Sasha Perkins
- Re: [AMBER] Using nrespa with NPT Bill Ross
Sunday, 27 November 2011
- Re: [AMBER] Fwd: Issue with running sander with SHAKE Andrew Voronkov
- Re: [AMBER] Using nrespa with NPT Jason Swails
- [AMBER] running of the sander in background in parallel state leila karami
- Re: [AMBER] help with antechamber jun kit
- Re: [AMBER] Using nrespa with NPT Sasha Perkins
- [AMBER] how to prepare 4:4:1 methanol–chloroform–water mixture rameshwar prajapati
- Re: [AMBER] Fwd: Issue with running sander with SHAKE Yong Duan
- Re: [AMBER] Fwd: Issue with running sander with SHAKE Andrew Voronkov
- [AMBER] adding a phosphate group to a protein Petit, Chad
- [AMBER] Calculation of free energy of solvation M. Reza Ganjalikhany
- Re: [AMBER] Calculation of free energy of solvation Jason Swails
- [AMBER] fwd: top2mol2 charges output in mol2: no reply Jio M
- [AMBER] MCPB execution error Soma Ghosh
Monday, 28 November 2011
- Re: [AMBER] adding a phosphate group to a protein Marc van der Kamp
- [AMBER] R: how to prepare 4:4:1 methanol-chloroform-water mixture Giovanni Pavan
- [AMBER] antechamber solvent Алексей Раевский
- [AMBER] NVIDIA GPU Event at Imperial College London Gould, Ian R
- Re: [AMBER] R: how to prepare 4:4:1 methanol-chloroform-water mixture rameshwar prajapati
- Re: [AMBER] How MCPB add ligand with a smallmoleculein*_siderchain.bcl JiYuan Liu
- [AMBER] glibc error while running Xleap Vlad Cojocaru
- [AMBER] pdb file with a covalently linked nerve agent Urszula Uciechowska
- [AMBER] Restarting an MD run Beale, John
- Re: [AMBER] Restarting an MD run Jason Swails
- Re: [AMBER] Restarting an MD run Carlos Simmerling
- Re: [AMBER] cutoff distance again David A Case
- Re: [AMBER] antechamber solvent David A Case
- Re: [AMBER] top2mol2 charges output in mol2 David A Case
- Re: [AMBER] antechamber solvent Алексей Раевский
- Re: [AMBER] How MCPB add ligand with a smallmoleculein*_siderchain.bcl Ben Roberts
- Re: [AMBER] Problem running Ptraj with CHARMM psf and dcd trajectory file Daniel Roe
- Re: [AMBER] How MCPB add ligand with asmallmoleculein*_siderchain.bcl JiYuan Liu
- Re: [AMBER] help with antechamber David A Case
- Re: [AMBER] pdb file with a covalently linked nerve agent David A Case
- Re: [AMBER] running of the sander in background in parallel state Ross Walker
- Re: [AMBER] running of the sander in background in parallel state Brian Radak
- Re: [AMBER] How MCPB add ligand with asmallmoleculein*_siderchain.bcl Ben Roberts
- [AMBER] mdrun continuation Yao Yao
- Re: [AMBER] How MCPB add ligand withasmallmoleculein*_siderchain.bcl JiYuan Liu
- [AMBER] REMD umbrella sampling caobb0214
- [AMBER] atom types error Urszula Uciechowska
Tuesday, 29 November 2011
- Re: [AMBER] REMD umbrella sampling Daniel Sindhikara
- Re: [AMBER] top2mol2 charges output in mol2 Jio M
- Re: [AMBER] atom types error FyD
- Re: [AMBER] REMD umbrella sampling Adrian Roitberg
- Re: [AMBER] mdrun continuation David A Case
- [AMBER] ptraj atomic fluctuation analysis Asmita Gupta
- [AMBER] sp3d hybridization Lee Lior
- Re: [AMBER] sp3d hybridization Jason Swails
- [AMBER] leap problem: TER cards disappearing thomas.fox.boehringer-ingelheim.com
- [AMBER] MCPB execution error (repeat mail) Soma Ghosh
- Re: [AMBER] Issue with running sander with SHAKE David A Case
- Re: [AMBER] ANTECHAMBER: fatal error David A Case
- Re: [AMBER] glibc error while running Xleap David A Case
- [AMBER] amber - TUTORIAL A9 Atila Petrosian
- Re: [AMBER] glibc error while running Xleap Vlad Cojocaru
- Re: [AMBER] combination of CHAMBER prmtop and pmemd.cuda is causing serious instability Marc van der Kamp
- Re: [AMBER] How MCPB add ligand withasmallmoleculein*_siderchain.bcl Ben Roberts
- Re: [AMBER] glibc error while running Xleap David A Case
- [AMBER] cis conformation of amino acid Yun Shi
- Re: [AMBER] leap problem: TER cards disappearing David A Case
- Re: [AMBER] How MCPB add ligand withasmallmoleculein*_siderchain.bcl JiYuan Liu
- Re: [AMBER] Sufficient CPU cores/GPU ratio ? Jodi Ann Hadden
- Re: [AMBER] combination of CHAMBER prmtop and pmemd.cuda is causing serious instability Scott Le Grand
- Re: [AMBER] ptraj atomic fluctuation analysis Thomas Cheatham III
- Re: [AMBER] combination of CHAMBER prmtop and pmemd.cuda is causing serious instability Scott Le Grand
- Re: [AMBER] cis conformation of amino acid David A Case
- Re: [AMBER] combination of CHAMBER prmtop and pmemd.cuda is causing serious instability Ross Walker
- Re: [AMBER] Issue with running sander with SHAKE Andrew Voronkov
- [AMBER] chlorine naming question and parametrization Andrew Voronkov
- Re: [AMBER] Issue with running sander with SHAKE David A Case
- Re: [AMBER] How to use strip mask and receptor mask in the new mmpbsa.py? bin wang
- Re: [AMBER] Sufficient CPU cores/GPU ratio ? Scott Le Grand
- Re: [AMBER] Sufficient CPU cores/GPU ratio ? Marek Maly
- Re: [AMBER] Problem running Ptraj with CHARMM psf and dcd trajectory file Puspita Halder
- [AMBER] antechamber error kureeckal ramesh
Wednesday, 30 November 2011
- Re: [AMBER] glibc error while running Xleap Vlad Cojocaru
- Re: [AMBER] glibc error while running Xleap Vlad Cojocaru
- Re: [AMBER] amber - TUTORIAL A9 steinbrt.rci.rutgers.edu
- Re: [AMBER] antechamber error David A Case
- Re: [AMBER] glibc error while running Xleap David A Case
- [AMBER] error by running MMPBSa Urszula Uciechowska
- Re: [AMBER] combination of CHAMBER prmtop and pmemd.cuda is causing serious instability Marc van der Kamp
- Re: [AMBER] amber - TUTORIAL A9 Atila Petrosian
- Re: [AMBER] error by running MMPBSa Jason Swails
- Re: [AMBER] error by running MMPBSa Urszula Uciechowska
- Re: [AMBER] amber - TUTORIAL A9 steinbrt.rci.rutgers.edu
- Re: [AMBER] glibc error while running Xleap Vlad Cojocaru
- [AMBER] Fwd: error by running MMPBSa Ray Luo, Ph.D.
- Re: [AMBER] combination of CHAMBER prmtop and pmemd.cuda is causing serious instability Marc van der Kamp
- Re: [AMBER] combination of CHAMBER prmtop and pmemd.cuda is causing serious instability Marc van der Kamp
- [AMBER] D-N-Sulfate-glucosamine net charge Massimiliano Porrini
- [AMBER] ATOM TYPES for MODIFIED dCTP Jana Sefcikova 1
- Re: [AMBER] D-N-Sulfate-glucosamine net charge Matthew Tessier
- Re: [AMBER] Sufficient CPU cores/GPU ratio ? filip fratev
- Re: [AMBER] Sufficient CPU cores/GPU ratio ? Ross Walker
- Re: [AMBER] Sufficient CPU cores/GPU ratio ? Marek Maly
- [AMBER] CUDA NaN error occuring at "wrapping first mol" Bill Sinko
- [AMBER] Fwd: error by running MMPBSa Ray Luo, Ph.D.
- Re: [AMBER] Fwd: error by running MMPBSa Qin Cai
- Re: [AMBER] CUDA NaN error occuring at "wrapping first mol" Ross Walker
- Re: [AMBER] CUDA NaN error occuring at "wrapping first mol" Ross Walker
- Re: [AMBER] error in MD simulation Ross Walker
- Re: [AMBER] combination of CHAMBER prmtop and pmemd.cuda is causing serious instability Scott Le Grand
- Re: [AMBER] error in MD simulation Yong Duan

Last message date: Wed Nov 30 2011 - 23:00:03 PST
Archived on: Fri Apr 19 2024 - 05:54:13 PDT

Amber Archive Nov 2011 by date