Amber Archive Nov 2009: by date

Saturday, 31 October 2009
- [AMBER] Different results for different computers cyk5056
- Re: [AMBER] pairwise per-residue decomposition manoj singh
Sunday, 1 November 2009
- [AMBER] retinal lib file, params? Mark M Huntress
- [AMBER] Re: RESP with -a and witout -a flag Jio M
- [AMBER] Is it taking too much time nicholus bhattacharjee
- Re: [AMBER] Is it taking too much time manoj singh
Monday, 2 November 2009
- Re: [AMBER] retinal lib file, params? Simon Becker
- Re: [AMBER] Is it taking too much time nicholus bhattacharjee
- [AMBER] MPI process terminated unexpectedly after cluster upgrade Dmitri Nilov
- Re: [AMBER] MPI process terminated unexpectedly after cluster upgrade Jason Swails
- Re: [AMBER] MPI process terminated unexpectedly after cluster upgrade Dmitri Nilov
- Re: [AMBER] Is it taking too much time manoj singh
- [AMBER] amber 10 test failures... peker milas
- Re: [AMBER] Is it taking too much time Nicolas SAPAY
- Re: [AMBER] Is it taking too much time nicholus bhattacharjee
- Re: [AMBER] Is it taking too much time Nicolas SAPAY
- Re: [AMBER] Gaussian log file error Ben Roberts
- Re: [AMBER] Gaussian log file error Junmei Wang
- Re: [AMBER] Re: RESP with -a and witout -a flag Junmei Wang
- Re: [AMBER] MPI process terminated unexpectedly after cluster upgrade Jason Swails
- [AMBER] 60 giga output file .mdcrd file Silvia Carlotto
- Re: [AMBER] 60 giga output file .mdcrd file Peter Schmidtke
- [AMBER] Is it possible to simulate transmembrane protein with GB model ? cgji
- RE: [AMBER] 60 giga output file .mdcrd file Ross Walker
- RE: [AMBER] amber 10 test failures... Ross Walker
- [AMBER] RE: question Ross Walker
- RE: [AMBER] MPI process terminated unexpectedly after cluster upgrade Ross Walker
- RE: [AMBER] Is it taking too much time Ross Walker
- Re: [AMBER] amber 10 test failures... Mark Williamson
- Re: [AMBER] amber 10 test failures... Jason Swails
- [AMBER] sander.APBS install problem Rilei Yu
- Re: [AMBER] sander.APBS install problem Robert Konecny
- Re: [AMBER] Is it taking too much time nicholus bhattacharjee
- Re: [AMBER] Is it taking too much time nicholus bhattacharjee
- Re: [AMBER] Some queries about pH simulation nicholus bhattacharjee
Tuesday, 3 November 2009
- Re: [AMBER] Is it taking too much time Nicolas Sapay
- Re: [AMBER] 60 giga output file .mdcrd file Silvia Carlotto
- Re: [AMBER] 60 giga output file .mdcrd file Fernando Martín García
- Re: [AMBER] Some queries about pH simulation case
- Re: [AMBER] MPI process terminated unexpectedly after cluster upgrade Dmitri Nilov
- Re: [AMBER] 60 giga output file .mdcrd file Jason Swails
- Re: [AMBER] MPI process terminated unexpectedly after cluster upgrade Dmitri Nilov
- Re: [AMBER] amber 10 test failures... peker milas
- Re: [AMBER] MPI process terminated unexpectedly after cluster upgrade Jason Swails
- RE: [AMBER] 60 giga output file .mdcrd file Richard Owczarzy
- [AMBER] Phosphorylated Threonine Beale, John
- Re: [AMBER] 60 giga output file .mdcrd file Silvia Carlotto
- Re: [AMBER] Phosphorylated Threonine FyD
- [AMBER] AMBER: segmentation fault when running parmchk Alexander Boncheff
- [AMBER] error in reading namelist cntrl Giuseppe De Marco
- [AMBER] Re: question Marek Maly
- Re: [AMBER] AMBER: segmentation fault when running parmchk Jason Swails
- Re: [AMBER] AMBER: segmentation fault when running parmchk Alexander Boncheff
- RE: [AMBER] error in reading namelist cntrl Ross Walker
- RE: [AMBER] 60 giga output file .mdcrd file Ross Walker
- RE: [AMBER] MPI process terminated unexpectedly after cluster upgrade Ross Walker
- Re: [AMBER] AMBER: segmentation fault when running parmchk Bill Ross
- [AMBER] Antechamber and Parmchk problems cyk5056
- [AMBER] amber parameter file creation and usage Donald Keidel
- Re: [AMBER] amber parameter file creation and usage Jason Swails
- [AMBER] errors on leap for a RNA+Adenine pdb structure zgong.hust
- [AMBER] Re: RESP with -a and witout -a flag Jio M
Wednesday, 4 November 2009
- Re: [AMBER] errors on leap for a RNA+Adenine pdb structure case
- Re: [AMBER] 60 giga output file .mdcrd file case
- Re: Re: [AMBER] errors on leap for a RNA+Adenine pdb structure zgong.hust
- Re: [AMBER] errors on leap for a RNA+Adenine pdb structure FyD
- [AMBER] total number of hydrogen bonds of the system as a function of time Markus Kaukonen
- Re: [AMBER] total number of hydrogen bonds of the system as a function of time Jason Swails
- [AMBER] errors on leap for a RNA+Adenine pdb structure with antechamber zgong.hust
- Re: [AMBER] Antechamber and Parmchk problems case
- Re: [AMBER] errors on leap for a RNA+Adenine pdb structure with antechamber FyD
- Re: [AMBER] AMBER: segmentation fault when running parmchk Alexander Boncheff
- Re: [AMBER] AMBER: segmentation fault when running parmchk Mark Williamson
- [AMBER] pmemd vs sander.MPI Taufik Al-Sarraj
- Re: [AMBER] amber parameter file creation and usage Donald Keidel
- RE: [AMBER] pmemd vs sander.MPI Ross Walker
- Re: [AMBER] AMBER: segmentation fault when running parmchk Bill Ross
- [AMBER] HB for each snapshot Marcin Krol
- Re: [AMBER] Antechamber and Parmchk problems Junmei Wang
- Re: [AMBER] AMBER: segmentation fault when running parmchk Junmei Wang
- Re: [AMBER] HB for each snapshot Jason Swails
- Re: Re: [AMBER] Antechamber and Parmchk problems cyk5056
- Re: Re: [AMBER] Antechamber and Parmchk problems cyk5056
- Re: Re: [AMBER] Antechamber and Parmchk problems Junmei Wang
- Re: Re: [AMBER] errors on leap for a RNA+Adenine pdb structure withantechamber zgong.hust
- Re: [AMBER] RE: question rrd
- Re: [AMBER] errors on leap for a RNA+Adenine pdb structure withantechamber FyD
Thursday, 5 November 2009
- Re: [AMBER] RE: question steinbrt.rci.rutgers.edu
- Re: [AMBER] HB for each snapshot Nicolas Sapay
- [AMBER] Phosphothreonine Beale, John
- [AMBER] Calculaiton stop ? xuemeiwang1103
- Re: [AMBER] Phosphothreonine Anselm Horn
- Re: [AMBER] RE: question Marek Maly
- Re: [AMBER] pmemd vs sander.MPI Marek Maly
- Re: [AMBER] pmemd vs sander.MPI Robert Duke
- Re: [AMBER] MPI process terminated unexpectedly after cluster upgrade Dmitri Nilov
- Re: [AMBER] MPI process terminated unexpectedly after cluster upgrade Jason Swails
- Re: [AMBER] MPI process terminated unexpectedly after cluster upgrade Dmitri Nilov
- Re: [AMBER] MPI process terminated unexpectedly after cluster upgrade Dmitri Nilov
- RE: [AMBER] MPI process terminated unexpectedly after cluster upgrade Ross Walker
- [AMBER] zeros in excluded atom list in topology file Peter Schmidtke
- Re: [AMBER] pmemd vs sander.MPI Marek Maly
- [AMBER] Segmentation Fault Beale, John
- Re: [AMBER] pmemd vs sander.MPI Robert Duke
- RE: [AMBER] pmemd vs sander.MPI Ross Walker
- RE: [AMBER] Segmentation Fault Ross Walker
- Re: [AMBER] pmemd vs sander.MPI Marek Maly
- Re: [AMBER] pmemd vs sander.MPI Marek Maly
- Re: Re: Re: [AMBER] Antechamber and Parmchk problems cyk5056
- [AMBER] RESP using antechamber with Se atom Donald Keidel
- Re: Re: Re: [AMBER] Antechamber and Parmchk problems Junmei Wang
- [AMBER] ff fitting ? Marek Maly
- Re: [AMBER] RESP using antechamber with Se atom Junmei Wang
- RE: [AMBER] pmemd vs sander.MPI Ross Walker
- Re: [AMBER] pmemd vs sander.MPI Marek Maly
- Re: [AMBER] RE: question rrd
- Re: [AMBER] zeros in excluded atom list in topology file Carlos Simmerling
- [AMBER] varying positional restraints with PMEMD Julian Garrec
- Re: [AMBER] RESP using antechamber with Se atom subarna thakur
- [AMBER] error in kclust of MMTB_tool set kureeckal ramesh
Friday, 6 November 2009
- Re: [AMBER] zeros in excluded atom list in topology file Peter Schmidtke
- [AMBER] amber9 compilation Myunggi Yi
- [AMBER] amber 9 compilation Myunggi Yi
- Re: [AMBER] amber9 compilation David Watson
- Re: [AMBER] amber9 compilation Myunggi Yi
- Re: [AMBER] amber9 compilation David Watson
- Re: [AMBER] RESP using antechamber with Se atom Eric Pettersen
- [AMBER] -np not 2^x a problem w/ sander??? Dean Cuebas
- [AMBER] -np not 2^x a problem w/ sander??? update Dean Cuebas
- Re: [AMBER] zeros in excluded atom list in topology file case
- Re: [AMBER] zeros in excluded atom list in topology file Peter Schmidtke
- Re: [AMBER] zeros in excluded atom list in topology file Bill Ross
- [AMBER] unable to find mopac charges in mopac.out Richard Tseng
- Re: [AMBER] unable to find mopac charges in mopac.out Bill Ross
- RE: [AMBER] -np not 2^x a problem w/ sander??? Ross Walker
- [AMBER] ptraj script for H bond for protein (explicit ) kureeckal ramesh
Saturday, 7 November 2009
- [AMBER] Low frequency Raman spectra babak minoofar
- Re: [AMBER] unable to find mopac charges in mopac.out case
- [AMBER] the problem of nucgen.dat liangchen88.ucla.edu
- Re: [AMBER] the problem of nucgen.dat case
- Re: [AMBER] Low frequency Raman spectra case
- [AMBER] linux version for Amber10 liangchen88.ucla.edu
- Re: [AMBER] linux version for Amber10 Peter Schmidtke
- RE: [AMBER] -np not 2^x a problem w/ sander??? update Ross Walker
- [AMBER] build up solvate box Huikuan Chao
- [AMBER] sleap fastbld error Oliver Kuhn
- [AMBER] sleap fastbld error is not an error Oliver Kuhn
- Re: [AMBER]Amber10 + g95 Sudeep Narayan Banerjee
- Re: [AMBER] linux version for Amber10 Sudeep Narayan Banerjee
- Re: [AMBER] linux version for Amber10 Jason Swails
- Re: [AMBER]Amber10 + g95 Abhishek Banerjee
- Re: [AMBER] the problem of nucgen.dat liangchen88.ucla.edu
- Re: [AMBER] linux version for Amber10 liangchen88.ucla.edu
- [AMBER] LJ parameters for HO and HW manoj singh
- Re: [AMBER] LJ parameters for HO and HW Jason Swails
- Re: [AMBER] LJ parameters for HO and HW manoj singh
Sunday, 8 November 2009
- [AMBER] solvent Jio M
- [AMBER] MM_PBSA enquiries s. Bill
- Re: [AMBER] LJ parameters for HO and HW Jason Swails
- Re: [AMBER] MM_PBSA enquiries manoj singh
- Re: [AMBER] the problem of nucgen.dat case
- [AMBER] pmemd failure Francesco Pietra
- Re: [AMBER] pmemd failure Robert Duke
- [AMBER] Gly -> Ala mutation manoj singh
- Re: [AMBER] varying positional restraints with PMEMD case
- Re: [AMBER] ff fitting ? case
- Re: [AMBER] Gly -> Ala mutation Jason Swails
- Re: [AMBER] pmemd failure Francesco Pietra
- Re: [AMBER] Gly -> Ala mutation manoj singh
- Re: [AMBER] Gly -> Ala mutation Jason Swails
- Re: [AMBER] Gly -> Ala mutation manoj singh
- [AMBER] error in kclust of MMTB_tool set kureeckal ramesh
- [AMBER] analyzeMatrix: cannot find a match in the matrixInfoStack Naser Alijabbari
- [AMBER] conversion of kelvin to kcal/mol aneesh cna
- Re: [AMBER] conversion of kelvin to kcal/mol manoj singh
- Re: [AMBER] conversion of kelvin to kcal/mol aneesh cna
Monday, 9 November 2009
- Re: [AMBER] LJ parameters for HO and HW steinbrt.rci.rutgers.edu
- [AMBER] sander.mpi. mdfil: Error unknown flag: sander Andrew Voronkov
- Re: [AMBER] ff fitting ? Marek Maly
- [AMBER] Task is running on supercomputer without any output Andrew Voronkov
- Re: [AMBER] Task is running on supercomputer without any output michael bane
- Re: [AMBER] sander.mpi. mdfil: Error unknown flag: sander case
- Re: [AMBER] Gly -> Ala mutation Carlos Simmerling
- Re: [AMBER] Gly -> Ala mutation manoj singh
- Re: [AMBER] Gly -> Ala mutation Adrian Roitberg
- Re: [AMBER] Gly -> Ala mutation manoj singh
- Re: [AMBER] unable to find mopac charges in mopac.out Richard Tseng
- Re: [AMBER] unable to find mopac charges in mopac.out case
- [AMBER] PCA analysis with ptraj Alessandro Contini
- Re: [AMBER] LJ parameters for HO and HW Bill Ross
- [AMBER] AmberTools 1.2 Installation on Ubuntu 9.10 Karmic Koala Wallace Kunin
- Re: [AMBER] unable to find mopac charges in mopac.out Richard Tseng
- Re: [AMBER] AmberTools 1.2 Installation on Ubuntu 9.10 Karmic Koala David Watson
- [AMBER] Getting minimized .pdb file without non-polar hydrogens Francesco Pietra
- Re: [AMBER] AmberTools 1.2 Installation on Ubuntu 9.10 Karmic Koala case
- Re: [AMBER] AmberTools 1.2 Installation on Ubuntu 9.10 Karmic Koala Mark Williamson
- Re: [AMBER] AmberTools 1.2 Installation on Ubuntu 9.10 Karmic Koala case
- Re: [AMBER] AmberTools 1.2 Installation on Ubuntu 9.10 Karmic Koala Wallace Kunin
- [AMBER] rectangular box with PME problem Ivan Gladich
- Re: [AMBER] AmberTools 1.2 Installation on Ubuntu 9.10 Karmic Koala David Watson
- Re: [AMBER] AmberTools 1.2 Installation on Ubuntu 9.10 Karmic Koala David Watson
Tuesday, 10 November 2009
- RE: [AMBER] PCA analysis with ptraj hannes.loeffler.stfc.ac.uk
- [AMBER] three trials to create topologies with sleap and tleap Oliver Kuhn
- RE: [AMBER] PCA analysis with ptraj Alessandro Contini
- [AMBER] error in kclust of MMTB_tool set kureeckal ramesh
- [AMBER] MMTSB tool set PDF kureeckal ramesh
- [AMBER] matrixinfoStack Naser Alijabbari
- Re: [AMBER] AmberTools 1.2 Installation on Ubuntu 9.10 Karmic Koala Wallace Kunin
- Re: [AMBER] AmberTools 1.2 Installation on Ubuntu 9.10 Karmic Koala case
- [AMBER] error reading namelist cntrl Shaikh Abdul R S Ramaju
Wednesday, 11 November 2009
- [AMBER] coarse-grained MD Francesco Pietra
- [AMBER] Creating new residue with tleap. rrd
- Re: [AMBER] Creating new residue with tleap. case
- Re: [AMBER] error reading namelist cntrl Jason Swails
- Re: [AMBER] AmberTools 1.2 Installation on Ubuntu 9.10 Karmic Koala Wallace Kunin
- [AMBER] Increase Temperature to 550 K Chih-Ying Lin
- [AMBER] High-temperature simulation ? Chih-Ying Lin
- Re: [AMBER] AmberTools 1.2 Installation on Ubuntu 9.10 Karmic Koala Giorgio Maccari
- Re: [AMBER] AmberTools 1.2 Installation on Ubuntu 9.10 Karmic Koala David Watson
- Re: [AMBER] High-temperature simulation ? Carlos Simmerling
- Re: [AMBER] Increase Temperature to 550 K Carlos Simmerling
- Re: [AMBER] AmberTools 1.2 Installation on Ubuntu 9.10 Karmic Koala Bill Ross
- Re: [AMBER] Increase Temperature to 550 K Chih-Ying Lin
- Re: [AMBER] Increase Temperature to 550 K Carlos Simmerling
- [AMBER] Lisp library for amber analysis? Eric Shamay
- Re: [AMBER] AmberTools 1.2 Installation on Ubuntu 9.10 Karmic Koala Wallace Kunin
- Re: [AMBER] AmberTools 1.2 Installation on Ubuntu 9.10 Karmic Koala Jason Swails
- Re: [AMBER] AmberTools 1.2 Installation on Ubuntu 9.10 Karmic Koala case
- Re: [AMBER] Increase Temperature to 550 K FyD
Thursday, 12 November 2009
- Re: [AMBER] AmberTools 1.2 Installation on Ubuntu 9.10 Karmic Koala Wallace Kunin
- RE: [AMBER] AmberTools 1.2 Installation on Ubuntu 9.10 Karmic Koala Ross Walker
- [AMBER] reg. GBA balaji nagarajan
- Re: [AMBER] Increase Temperature to 550 K case
- Re: [AMBER] reg. GBA case
- [AMBER] MD snapshots of most probable protein conformations in Amber Andrew Voronkov
- Re: [AMBER] Task is running on supercomputer without any output Andrew Voronkov
- Re: [AMBER] MD snapshots of most probable protein conformations in Amber Adrian Roitberg
- Re: [AMBER] Increase Temperature to 550 K Carlos Simmerling
- [AMBER] MM_PBSA energy per residue Hemant Kumar
- Re: [AMBER] AmberTools 1.2 Installation on Ubuntu 9.10 Karmic Koala Wallace Kunin
- [AMBER] slope Jio M
- [AMBER] R.E.D. resp error s. Bill
- Re: [AMBER] Increase Temperature to 550 K Chih-Ying Lin
- Re: [AMBER] Increase Temperature to 550 K Carlos Simmerling
- Re: [AMBER] Increase Temperature to 550 K Chih-Ying Lin
- Re: [AMBER] R.E.D. resp error FyD
Friday, 13 November 2009
- [AMBER] R.E.D. too small charges Andrei Neamtu
- Re: [AMBER] Increase Temperature to 550 K FyD
- Re: [AMBER] R.E.D. too small charges FyD
- [AMBER] enquiry regarding parameter file to be used bharat lakhani
- Re: [AMBER] Increase Temperature to 550 K Carlos Simmerling
- Re: [AMBER] enquiry regarding parameter file to be used Carlos Simmerling
- [AMBER] matrixInfoStack Naser Alijabbari
- [AMBER] request sculiujl
- [AMBER] the different RMSD? qiaoyan
- Re: [AMBER] the different RMSD? Thomas Cheatham
- Re: Re: [AMBER] the different RMSD? qiaoyan
- [AMBER] is rst file the last structure? qiaoyan
- Re: [AMBER] enquiry regarding parameter file to be used bharat lakhani
Saturday, 14 November 2009
- [AMBER] Hydrogen bond analysis for protein dna complex using ptraj shamoon siddiqui
- Re: [AMBER] Hydrogen bond analysis for protein dna complex using ptraj Carlos Simmerling
- Re: [AMBER] Hydrogen bond analysis for protein dna complex using ptraj shamoon siddiqui
- Re: Re: [AMBER] the different RMSD? Thomas Cheatham
- Re: [AMBER] Hydrogen bond analysis for protein dna complex using ptraj Thomas Cheatham
- Re: [AMBER] is rst file the last structure? Jason Swails
- Re: Re: Re: [AMBER] the different RMSD? qiaoyan
Sunday, 15 November 2009
- Re: [AMBER] is rst file the last structure? case
- [AMBER] How to split mdcrd files shamoon siddiqui
- Re: [AMBER] How to split mdcrd files Carlos Simmerling
- Re: [AMBER] How to split mdcrd files Jason Swails
- Re: [AMBER] How to split mdcrd files Carlos Simmerling
- [AMBER] slope {no reply} Jio M
- Re: [AMBER] slope {no reply} Carlos Simmerling
- Re: [AMBER] How to split mdcrd files Thomas Cheatham
- Re: [AMBER] slope Jio M
- [AMBER] Etot positive Jio M
Monday, 16 November 2009
- Re: [AMBER] slope Carlos Simmerling
- Re: [AMBER] Etot positive Carlos Simmerling
- Re: [AMBER] enquiry regarding parameter file to be used Carlos Simmerling
- [AMBER] Segmentation fault in antechamber albert albert
- Re: [AMBER] Segmentation fault in antechamber case
- Re: [AMBER] Segmentation fault in antechamber albert albert
- [AMBER] Installing AMBER 10 on Ubuntu 9.10 Karmic Koala Wallace Kunin
- Re: [AMBER] Installing AMBER 10 on Ubuntu 9.10 Karmic Koala Mark Williamson
- Re: [AMBER] slope {no reply} Bill Ross
- Re: [AMBER] Segmentation fault in antechamber Mark Williamson
- Re: [AMBER] Installing AMBER 10 on Ubuntu 9.10 Karmic Koala Wallace Kunin
- Re: [AMBER] Installing AMBER 10 on Ubuntu 9.10 Karmic Koala Mark Williamson
- RE: [AMBER] Etot positive Ross Walker
- Re: [AMBER] slope Jio M
- [AMBER] Re:Etot positive Jio M
- Re: [AMBER] slope {no reply} Jio M
- [AMBER] compilation problem of amber9 sculiujl
- [AMBER] compilation problem of amber sculiujl
Tuesday, 17 November 2009
- [AMBER] which is the best intel complier for amber 10? jacky zhao
- Re: [AMBER]Amber10 + g95 jacky zhao
- [AMBER] About zinc parameters ? xuemeiwang1103
- Re: [AMBER] About zinc parameters ? steinbrt.rci.rutgers.edu
- Re: [AMBER] slope Carlos Simmerling
- Re: [AMBER] slope {no reply} Carlos Simmerling
- Re: [AMBER] compilation problem of amber Jason Swails
- Re: [AMBER] compilation problem of amber9 Jason Swails
- Re: [AMBER] About zinc parameters ? Jason Swails
- Re: [AMBER] Installing AMBER 10 on Ubuntu 9.10 Karmic Koala Wallace Kunin
- [AMBER] non standart residue library creation with tleap (Zn atom) Andrew Voronkov
- Re: [AMBER] non standart residue library creation with tleap (Zn atom) Jason Swails
- RE: [AMBER] non standart residue library creation with tleap (Zn atom) intra\\sa175950
- Re: [AMBER] non standart residue library creation with tleap (Zn atom) Andrew Voronkov
- [AMBER] tleap maximum coordination exceeded Jack Shultz
- Re: [AMBER] Segmentation fault in antechamber albert albert
- Re: [AMBER] Installing AMBER 10 on Ubuntu 9.10 Karmic Koala case
- Re: [AMBER] About zinc parameters ? Sally Pias
- Re: [AMBER] slope {no reply} Bill Ross
- Re: [AMBER] non standart residue library creation with tleap (Zn atom) Jason Swails
- [AMBER] MSD of ligand?? Chih-Ying Lin
- Re: [AMBER] slope {no reply} Jio M
- Re: [AMBER] non standart residue library creation with tleap (Zn atom) FyD
- Re: [AMBER] tleap maximum coordination exceeded FyD
- Re: [AMBER] tleap maximum coordination exceeded case
- [AMBER] combining parameter files of ligand and enzyme Amire-Brahimi Benjamin
- Re: [AMBER] slope {no reply} Carlos Simmerling
- Re: [AMBER] slope {no reply} Bill Ross
- Re: [AMBER] tleap maximum coordination exceeded Jack Shultz
- [AMBER] have a question jacky zhao
- Re: [AMBER] have a question Bill Ross
- [AMBER] the different RMSD? qiaoyan
- Re: [AMBER] tleap maximum coordination exceeded Jack Shultz
- Re: [AMBER] Segmentation fault in antechamber case
- [AMBER] How to change the input matrix for "analyze matrix" instruction? cyk5056
- [AMBER] Can I get an average trajectory? cyk5056
- Re: [AMBER] tleap maximum coordination exceeded case
- Re: [AMBER] slope {no reply} Jio M
- 回复： [AMBER] the different RMSD? Rilei Yu
- Re: [AMBER] combining parameter files of ligand and enzyme FyD
Wednesday, 18 November 2009
- [AMBER] GB and Atom Type Alexander Seifert
- Re: [AMBER] Can I get an average trajectory? Carlos Simmerling
- [AMBER] Asking help for parallel installation of Amber9 nicholus bhattacharjee
- Re: [AMBER] Asking help for parallel installation of Amber9 David Watson
- Re: [AMBER] Asking help for parallel installation of Amber9 nicholus bhattacharjee
- Re: [AMBER] MD snapshots of most probable protein conformations in Amber Andrew Voronkov
- Re: [AMBER] non standart residue library creation with tleap (Zn atom) Andrew Voronkov
- Re: [AMBER] Asking help for parallel installation of Amber9 David Watson
- [AMBER] read substrate into leap sculiujl
- Re: [AMBER] MD snapshots of most probable protein conformations in Amber Renata KWIECIEN
- Re: [AMBER] MD snapshots of most probable protein conformations in Amber Carlos Simmerling
- Re: [AMBER] Installing AMBER 10 on Ubuntu 9.10 Karmic Koala Wallace Kunin
- Re: [AMBER] non standart residue library creation with tleap (Zn atom) FyD
- Re: [AMBER] MD snapshots of most probable protein conformations in Amber Andrew Voronkov
- Re: [AMBER] MD snapshots of most probable protein conformations in Amber Andrew Voronkov
- Re: Re: [AMBER] Can I get an average trajectory? cyk5056
- Re:[AMBER] How to change the input matrix for "analyze matrix" instruction? 陈一侃
- [AMBER] about divcon Alan
- Re: [AMBER] about divcon case
- Re: [AMBER] about divcon Alan
- Re: [AMBER] MD snapshots of most probable protein conformations in Amber Carlos Simmerling
- Re: [AMBER] Asking help for parallel installation of Amber9 Bill Ross
- Re: [AMBER] Asking help for parallel installation of Amber9 David Watson
- Re: [AMBER] read substrate into leap Jason Swails
- Re: [AMBER] Installing AMBER 10 on Ubuntu 9.10 Karmic Koala Jason Swails
- Re: [AMBER] about divcon Jason Swails
- [AMBER] The decreasing MSD of ligand?? Chih-Ying Lin
- [AMBER] Is the integral value from RDF the same as average number of atoms? Gustaf Olsson (go22bi.student.hik.se)
- Re:Re: [AMBER] read substrate into leap sculiujl
- Re: Re: [AMBER] read substrate into leap Jason Swails
- Re:Re: [AMBER] read substrate into leap Bill Ross
- Re: [AMBER] GB and Atom Type Sally Pias
- Re: [AMBER] slope {no reply} Sally Pias
Thursday, 19 November 2009
- Re: [AMBER] slope {no reply} Jio M
- [AMBER] AmberTools 1.3 has a likely release date? Alan
- [AMBER] implicit_run_error balaji nagarajan
- [AMBER] The MSD and periodic boundary condition Chih-Ying Lin
- Re: [AMBER] The MSD and periodic boundary condition Jason Swails
- [AMBER] errors on leap for a RNA + Non-Standard molecule pdb structure Yunjie Zhao
- Re: [AMBER] enquiry regarding parameter file to be used bharat lakhani
Friday, 20 November 2009
- Re: [AMBER] enquiry regarding parameter file to be used Carlos Simmerling
- Re: [AMBER] non standart residue library creation with tleap (Zn atom) Andrew Voronkov
- Re: [AMBER] non standart residue library creation with tleap (Zn atom) case
- Re: [AMBER] non standart residue library creation with tleap (Zn atom) FyD
- Re: [AMBER] AmberTools 1.3 has a likely release date? case
- Re: [AMBER] implicit_run_error case
- Re: [AMBER] non standart residue library creation with tleap (Zn atom) Andrew Voronkov
- Re: [AMBER] non standart residue library creation with tleap (Zn atom) FyD
- Re: [AMBER] non standart residue library creation with tleap (Zn atom) Andrew Voronkov
- [AMBER] rmsd Taufik Al-Sarraj
- Re: [AMBER] non standart residue library creation with tleap (Zn atom) FyD
Saturday, 21 November 2009
- [AMBER] standard way to upload a lipid bilayer Syed Kashif Zafar
- Re: [AMBER] standard way to upload a lipid bilayer David Watson
- Re: [AMBER] rmsd Thomas Cheatham
- [AMBER] looking for parameters for DHFR substrates and inhibitors... Sidney Elmer
- Re: [AMBER] slope {no reply} Sally Pias
Sunday, 22 November 2009
- [AMBER] NAD - mmpbsa Urszula Uciechowska
- [AMBER] Polarizable simulation of the slab Jan Heyda
Monday, 23 November 2009
- [AMBER] Fortran error in standard simulation Oliver Kuhn
- [AMBER] Fortran error in standard simulation 2 Oliver Kuhn
- [AMBER] Fortran error in standard simulation 3 Oliver Kuhn
- Re: [AMBER] non standart residue library creation with tleap (Zn atom) Andrew Voronkov
- Re: [AMBER] non standart residue library creation with tleap (Zn atom) FyD
- [AMBER] matrixInfoStack Naser Alijabbari
- Re: [AMBER] Segmentation fault in antechamber albert albert
- Re: [AMBER] non standart residue library creation with tleap (Zn atom) Andrew Voronkov
- [AMBER] hbond analysis by ptraj- segmentation fault Jayalakshmi Sridhar
- Re: [AMBER] non standart residue library creation with tleap (Zn atom) FyD
- Re: [AMBER] non standart residue library creation with tleap (Zn atom) Andrew Voronkov
- Re: [AMBER] non standart residue library creation with tleap (Zn atom) FyD
- Re: [AMBER] non standart residue library creation with tleap (Zn atom) FyD
- Re: [AMBER] non standart residue library creation with tleap (Zn atom) Andrew Voronkov
- Re: [AMBER] hbond analysis by ptraj- segmentation fault Daniel Roe
- Re: [AMBER] non standart residue library creation with tleap (Zn atom) FyD
- Re: [AMBER] hbond analysis by ptraj- segmentation fault Daniel Roe
- Re: [AMBER] hbond analysis by ptraj- segmentation fault Jayalakshmi Sridhar
- Re: [AMBER] rmsd Taufik Al-Sarraj
- Re: [AMBER] non standart residue library creation with tleap (Zn atom) FyD
- [AMBER] Regarding Urey-Bradley term in amber calculation aneesh cna
Tuesday, 24 November 2009
- Re: [AMBER] non standart residue library creation with tleap (Zn atom) Andrew Voronkov
- [AMBER] How to get total energy of asystem gunajyoti das
- Re: [AMBER] non standart residue library creation with tleap (Zn atom) FyD
- Re: [AMBER] How to get total energy of asystem steinbrt.rci.rutgers.edu
- Re: [AMBER] non standart residue library creation with tleap (Zn atom) Andrew Voronkov
- Re: [AMBER] How to get total energy of asystem case
- Re: [AMBER] Regarding Urey-Bradley term in amber calculation Jason Swails
- Re: [AMBER] non standart residue library creation with tleap (Zn atom) FyD
- Re: [AMBER] non standart residue library creation with tleap (Zn atom) Andrew Voronkov
- RE: [AMBER] Fortran error in standard simulation Ross Walker
- RE: [AMBER] non standart residue library creation with tleap (Zn atom) Ross Walker
- RE: [AMBER] non standart residue library creation with tleap (Zn atom) Ross Walker
- [AMBER] Hbond analysis output giving no hbonds Jayalakshmi Sridhar
- RE: [AMBER] Regarding Urey-Bradley term in amber calculation Ross Walker
- RE: [AMBER] Hbond analysis output giving no hbonds Thomas Cheatham
- RE: [AMBER] Hbond analysis output giving no hbonds Jayalakshmi Sridhar
- Re: [AMBER] non standart residue library creation with tleap (Zn atom) Bill Ross
- [AMBER] trouble with antechamber Jennifer L. Muzyka
- Re: [AMBER] trouble with antechamber case
- [AMBER] how to use amber to verify the reason for difference in affinity Josmar R. da Rocha
- [AMBER] check MAXPR in locmem.f error on minimization Jodi Hadden
- [AMBER] MM-PBSA NMODE Zhongjie Liang
- [AMBER] i-APBS and apbs Rilei Yu
- Re: [AMBER] i-APBS and apbs Robert Konecny
- Re: [AMBER] i-APBS and apbs Jason Swails
- [AMBER] Not able to compile pmemd with openmpi in Amber9 Kito
- [AMBER] MM-PB/GBSA NMODE Zhongjie Liang
- Re: [AMBER] Not able to compile pmemd with openmpi in Amber9 Jason Swails
- Re: [AMBER] Not able to compile pmemd with openmpi in Amber9 Kito
- Re: Re: [AMBER] Not able to compile pmemd with openmpi in Amber9 Kito
Wednesday, 25 November 2009
- Re: Re: Re: [AMBER] Not able to compile pmemd with openmpi in Amber9 Kito
- Re: [AMBER] i-APBS and apbs Rilei Yu
- Re: [AMBER] check MAXPR in locmem.f error on minimization case
- Re: [AMBER] MM-PBSA NMODE case
- [AMBER] heme (united-atom) Simon Becker
- Re: [AMBER] heme (united-atom) case
- Re: Re: Re: [AMBER] Not able to compile pmemd with openmpi in Amber9 Jason Swails
- [AMBER] Verlet update time in explicit water Replica Exchange MD Da-Wei Li
- Re: [AMBER] Verlet update time in explicit water Replica Exchange MD Carlos Simmerling
- [AMBER] Re: Verlet update time in explicit water Replica Exchange MD Da-Wei Li
- Re: [AMBER] Verlet update time in explicit water Replica Exchange MD Da-Wei Li
- Re: [AMBER] Verlet update time in explicit water Replica Exchange MD Da-Wei Li
- Re: [AMBER] Verlet update time in explicit water Replica Exchange MD Robert Duke
- Re: [AMBER] check MAXPR in locmem.f error on minimization Jodi Hadden
- Re: [AMBER] check MAXPR in locmem.f error on minimization Jason Swails
- Re: [AMBER] Verlet update time in explicit water Replica Exchange MD Da-Wei Li
- RE: Re: Re: [AMBER] Not able to compile pmemd with openmpi in Amber9 Ross Walker
- RE: [AMBER] Verlet update time in explicit water Replica Exchange MD Ross Walker
- Re: Re: Re: [AMBER] Not able to compile pmemd with openmpi in Amber9 case
- Re: Re: Re: [AMBER] Not able to compile pmemd with openmpi in Amber9 Robert Duke
- [AMBER] difference between two inputs Jio M
Thursday, 26 November 2009
- [AMBER] rings getting planar Jio M
- [AMBER] ligand parameterization Nahoum Anthony
- Re: [AMBER] heme (united-atom) Simon Becker
- Re: [AMBER] rings getting planar Jio M
- Re: [AMBER] rings getting planar case
- Re: [AMBER] ligand parameterization case
- Re: [AMBER] ligand parameterization Jason Swails
- [AMBER] Atomic radii assignment for WAT molecules DIMAS SUAREZ RODRIGUEZ
- RE: [AMBER] ligand parameterization Nahoum Anthony
- [AMBER] Polarizable simulation of the slab Jan Heyda
- Re: [AMBER] ligand parameterization Jason Swails
- Re: [AMBER] ligand parameterization Ilyas Yildirim
- [AMBER] MM_PBSA error Jagdeesh C
Friday, 27 November 2009
- [AMBER] Re: MM_PBSA error Jagdeesh C
- Re: [AMBER] Re: MM_PBSA error Mengjuei Hsieh
- Re: [AMBER] Re: MM_PBSA error Jagdeesh C
- Re: [AMBER] Polarizable simulation of the slab case
- Re: [AMBER] check MAXPR in locmem.f error on minimization Robert Duke
- Re: [AMBER] Polarizable simulation of the slab Jan Heyda
- Re: [AMBER] difference between two inputs case
- Re: [AMBER] Polarizable simulation of the slab case
- Re: [AMBER] Polarizable simulation of the slab Jan Heyda
- Re: [AMBER] Polarizable simulation of the slab Robert Duke
- [AMBER] Regarding rigid bond aneesh cna
- Re: [AMBER] Regarding rigid bond Carlos Simmerling
- [AMBER] LYS-ASP s. Bill
- Re: [AMBER] LYS-ASP Jason Swails
- Re: [AMBER] LYS-ASP case
Saturday, 28 November 2009
- Re: [AMBER] Re: MM_PBSA error Ray Luo
- Re: [AMBER] Atomic radii assignment for WAT molecules Ray Luo
- [AMBER] where to get leaprc.ff99sb? Jack Shultz
- Re: [AMBER] where to get leaprc.ff99sb? Jason Swails
- Re: [AMBER] where to get leaprc.ff99sb? Jack Shultz
- [AMBER] Scripting tleap Jack Shultz
- Re: [AMBER] Scripting tleap Tom Joseph
- Re: [AMBER] where to get leaprc.ff99sb? Jason Swails
- Re: [AMBER] Scripting tleap Jack Shultz
Sunday, 29 November 2009
- [AMBER] How to compile and recompile ptraj? cyk5056
- [AMBER] Re: How to compile and recompile ptraj? cyk5056
- Re: [AMBER] Re: How to compile and recompile ptraj? case
- Re: [AMBER] how to use amber to verify the reason for difference in affinity case
- [AMBER] how to use GLYCAM04 for carbonhydrate in amber9? sculiujl
- [AMBER] reagarding Dihedral PCA jani sahil
- [AMBER] regarding Dihedral PCA jani sahil
- [AMBER] distance-dependent dielectric constant minimization Rilei Yu
Monday, 30 November 2009
- Re: [AMBER] how to use GLYCAM04 for carbonhydrate in amber9? Karl Kirschner
- [AMBER] trajout problem Anna Reymer
- Re: [AMBER] trajout problem Carlos Simmerling
- [AMBER] problem with FAD in tleap M. Shahid
- Re: [AMBER] MD snapshots of most probable protein conformations in Amber Andrew Voronkov
- RE: [AMBER] trajout problem Anna Reymer
- Re: [AMBER] distance-dependent dielectric constant minimization case
- Re: [AMBER] problem with FAD in tleap FyD
- Re: [AMBER] problem with FAD in tleap case
- Re: [AMBER] heme (united-atom) case
- Re: [AMBER] trajout problem Carlos Simmerling
- RE: [AMBER] trouble with antechamber Jennifer L. Muzyka
- Re: [AMBER] trouble with antechamber case
- Re: [AMBER] problem with FAD in tleap M. Shahid
- Re: [AMBER] problem with FAD in tleap case
- Re: [AMBER] problem with FAD in tleap M. Shahid
- [AMBER] Output Does Not Match in Tutorial B1 Wallace Kunin
- Re: [AMBER] Output Does Not Match in Tutorial B1 case
- Re: [AMBER] trajout problem Sally Pias
- Re: [AMBER] Output Does Not Match in Tutorial B1 Bill Ross
- Re: [AMBER] Output Does Not Match in Tutorial B1 Wallace Kunin
- Re: [AMBER] problem with FAD in tleap FyD
- Re: [AMBER] problem with FAD in tleap FyD
- Re: [AMBER] Output Does Not Match in Tutorial B1 case
- [AMBER] fillratio Qinghua Liao
- Re: [AMBER] fillratio Ray Luo
- Re: [AMBER] fillratio Qinghua Liao

Last message date: Mon Nov 30 2009 - 22:30:02 PST
Archived on: Fri Apr 19 2024 - 05:53:42 PDT

Amber Archive Nov 2009 by date