Amber Archive Sep 2010: by date

Tuesday, 31 August 2010
- [AMBER] PB warning in pb_miccg 宋德寿
- [AMBER] PB warning in pb_miccg 宋德寿
- Re: [AMBER] Residue name problem in PTRAJ Fredrick Devadoss
Wednesday, 1 September 2010
- [AMBER] hydrogen bond analysis Ehsan Habibi
- Re: [AMBER] hydrogen bond analysis Daniel Roe
- Re: [AMBER] PB warning in pb_miccg Bill Miller III
- Re: [AMBER] Installing Amber9 on Ubuntu platform Arun Gupta
- Re: [AMBER] Installing Amber9 on Ubuntu platform Jason Swails
- Re: [AMBER] MD and LES Carlos Simmerling
- [AMBER] ERROR in MM-PBSA Siddharth Rastogi
- Re: [AMBER] ERROR in MM-PBSA Dwight McGee
- Re: [AMBER] PB warning in pb_miccg Ray Luo
- [AMBER] Trivial VMD question Computational Chemist
- Re: [AMBER] Trivial VMD question steinbrt.rci.rutgers.edu
- Re: [AMBER] Antechamber issue P Bhattacharya
- [AMBER] mm_pbsa fails xue wang
- [AMBER] visualizing the output from PTRAJ -Cluster Senthil Natesan
- Re: [AMBER] Antechamber issue David A. Case
- Re: [AMBER] mm_pbsa fails Ray Luo
- Re: [AMBER] visualizing the output from PTRAJ -Cluster Jianyin Shao
- Re: [AMBER] visualizing the output from PTRAJ -Cluster Senthil Natesan
- Re: [AMBER] ERROR in MM-PBSA Jason Swails
- Re: [AMBER] Trivial VMD question Jason Swails
- Re: [AMBER] ERROR in MM-PBSA Siddharth Rastogi
- Re: [AMBER] ERROR in MM-PBSA Jason Swails
- [AMBER] PB warning in pb_miccg 宋德寿
- [AMBER] PB warning in pb_miccg 宋德寿
- Re: [AMBER] Cut-off distance "in Closest" command of ptraj Amor San Juan
Thursday, 2 September 2010
- Re: [AMBER] MMPBSA.py: minimization issue with nmode Nicolas SAPAY
- [AMBER] Amber10 tests and benchmark verification failures across compilers Rasale, Anupama
- Re: [AMBER] Cut-off distance "in Closest" command of ptraj Carlos Simmerling
- [AMBER] installation of Ambertools Rebeca García Fandiño
- Re: [AMBER] how we increase the number of sugar molecule in a system subrata paul
- [AMBER] how to add Zn into a protein structure. Chinh Su Tran To
- Re: [AMBER] installation of Ambertools Jason Swails
- Re: [AMBER] Amber10 tests and benchmark verification failures across compilers Jason Swails
- [AMBER] 'cluster' option of ptraj: Is it possible to directly feed a file with rmsd values as input? Arvind
- Re: [AMBER] how we increase the number of sugar molecule in a system Lachele Foley (Lists)
- [AMBER] Is there any Amber training programm in Europe? albert
- [AMBER] eV to kcal/mol conversion factor Ben Roberts
- Re: [AMBER] eV to kcal/mol conversion factor Adrian Roitberg
- Re: [AMBER] phenylalanine amide FyD
- Re: [AMBER] ERROR in MM-PBSA Siddharth Rastogi
- Re: [AMBER] visualizing the output from PTRAJ -Cluster Jianyin Shao
- [AMBER] Symposium on Accelerating Biology jani vinod
- Re: [AMBER] Symposium on Accelerating Biology Indrajit Deb
- [AMBER] QUESTION ON AMBER WORKSHOP or SYMPOSIUM Indrajit Deb
- Re: [AMBER] Symposium on Accelerating Biology vhakkim boy
- Re: [AMBER] Symposium on Accelerating Biology Kshatresh Dutta Dubey
Friday, 3 September 2010
- [AMBER] explicitly set the ig variable for ntt=3 colvin
- Re: [AMBER] explicitly set the ig variable for ntt=3 hirdesh kumar
- Re: [AMBER] Is there any Amber training programm in Europe? Ross Walker
- [AMBER] Heating up the sytem hirdesh kumar
- [AMBER] Hbond Analysis Mannan
- Re: [AMBER] phenylalanine amide Francesco Pietra
- Re: [AMBER] Heating up the sytem Sangita Kachhap
- Re: [AMBER] Hbond Analysis Daniel Roe
- Re: [AMBER] explicitly set the ig variable for ntt=3 Jason Swails
- Re: [AMBER] about the tutorials Carlos Simmerling
- Re: [AMBER] Hbond Analysis Mannan
- [AMBER] extended conjugated systems - possible? Hannes Loeffler
- Re: [AMBER] eV to kcal/mol conversion factor Ben Roberts
- Re: [AMBER] eV to kcal/mol conversion factor Gustavo Seabra
- [AMBER] cis/trans transition Jorgen Simonsen
- Re: [AMBER] cis/trans transition Carlos Simmerling
- [AMBER] printing rdc violations Eliana Asciutto
- Re: [AMBER] 'cluster' option of ptraj: Is it possible to directly feed a file with rmsd values as input? Jianyin Shao
- Re: [AMBER] 'cluster' option of ptraj: Is it possible to directly feed a file with rmsd values as input? Bill Ross
- Re: [AMBER] phenylalanine amide FyD
- Re: [AMBER] 'cluster' option of ptraj: Is it possible to directly feed a file with rmsd values as input? Jianyin Shao
- [AMBER] how to set charge and radius of my own custom ion Anbang Li
- Re: [AMBER] how to set charge and radius of my own custom ion Bill Ross
- Re: [AMBER] how to set charge and radius of my own custom ion Bill Ross
- Re: [AMBER] ERROR in MM-PBSA Siddharth Rastogi
- Re: [AMBER] ERROR in MM-PBSA Bill Ross
- [AMBER] ptraj-problem Rilei Yu
- Re: [AMBER] how to set charge and radius of my own custom ion Anbang Li
- [AMBER] Nvidia driver bug for GTX400 series gpu's Sergio R Aragon
- Re: [AMBER] how to set charge and radius of my own custom ion Bill Ross
- Re: [AMBER] how to set charge and radius of my own custom ion Jason Swails
Saturday, 4 September 2010
- [AMBER] mm_pbsa nmode error Sangita Kachhap
- Re: [AMBER] mm_pbsa nmode error Bill Miller III
- Re: [AMBER] mm_pbsa nmode error Sangita Kachhap
- Re: [AMBER] ptraj-problem Jason Swails
- Re: [AMBER] eV to kcal/mol conversion factor case
- Re: [AMBER] how to add Zn into a protein structure. case
- Re: [AMBER] Heating up the sytem Senthil Natesan
- Re: [AMBER] printing rdc violations case
- [AMBER] ERROR in safe_malloc: Error in alloc of -2030981184 bytes Ehsan Habibi
- Re: [AMBER] Nvidia driver bug for GTX400 series gpu's Scott Le Grand
- Re: [AMBER] Nvidia driver bug for GTX400 series gpu's Scott Le Grand
- Re: [AMBER] Nvidia driver bug for GTX400 series gpu's Ross Walker
- Re: [AMBER] Nvidia driver bug for GTX400 series gpu's Scott Le Grand
- Re: [AMBER] ERROR in safe_malloc: Error in alloc of -2030981184 bytes Jason Swails
- Re: [AMBER] ERROR in safe_malloc: Error in alloc of -2030981184 bytes Thomas Cheatham
Sunday, 5 September 2010
- [AMBER] read the traj file to analyzing hbonds Ehsan Habibi
- [AMBER] significance of time-average or representative structures from MD Senthil Natesan
- Re: [AMBER] Nvidia driver bug for GTX400 series gpu's Sergio R Aragon
- [AMBER] builiding an oxide substrate tomba.uni-bremen.de
- [AMBER] pmemd.cuda errors on GTX400 series cards - USER POLL Sasha Buzko
- Re: [AMBER] significance of time-average or representative structures from MD Jason Swails
- Re: [AMBER] Nvidia driver bug for GTX400 series gpu's/update 1 Sergio R Aragon
- [AMBER] Water Box Shape hirdesh kumar
Monday, 6 September 2010
- Re: [AMBER] Water Box Shape Sushil Mishra
- Re: [AMBER] Water Box Shape hirdesh kumar
- [AMBER] which conformation to choose asaki asaki
- Re: [AMBER] read the traj file to analyzing hbonds Daniel Roe
- Re: [AMBER] read the traj file to analyzing hbonds Ehsan Habibi
- [AMBER] problem of GTX480 running pmemd.cuda Yi Xue
- [AMBER] GLYCAM residue naming manoj singh
- Re: [AMBER] GLYCAM residue naming Lachele Foley (Lists)
- Re: [AMBER] significance of time-average or representative structures from MD Senthil Natesan
- Re: [AMBER] problem of GTX480 running pmemd.cuda Sasha Buzko
- Re: [AMBER] problem of GTX480 running pmemd.cuda Yi Xue
- [AMBER] Gamma_ln in REMD Lekpa Duukori
- Re: [AMBER] problem of GTX480 running pmemd.cuda Ross Walker
- Re: [AMBER] problem of GTX480 running pmemd.cuda Yi Xue
- Re: [AMBER] problem of GTX480 running pmemd.cuda Sasha Buzko
- Re: [AMBER] GLYCAM residue naming manoj singh
- [AMBER] Quasiharmonic Analysis Tyler Glembo
Tuesday, 7 September 2010
- [AMBER] NMR multiple structures Baptiste Legrand
- Re: [AMBER] Gamma_ln in REMD Carlos Simmerling
- Re: [AMBER] NMR multiple structures Jason Swails
- Re: [AMBER] Quasiharmonic Analysis case
- Re: [AMBER] NMR multiple structures case
- Re: [AMBER] read the traj file to analyzing hbonds Daniel Roe
- [AMBER] NAMD -trajectory and amber10 mm_pbsa Sangita Kachhap
- Re: [AMBER] NMR multiple structures Baptiste Legrand
- Re: [AMBER] Gamma_ln in REMD Lekpa Duukori
- Re: [AMBER] GLYCAM residue naming Lachele Foley (Lists)
- [AMBER] Query regarding the Hydrogen Bond duration analysis hirdesh kumar
- Re: [AMBER] NMR multiple structures Jason Swails
- Re: [AMBER] NMR multiple structures Baptiste Legrand
- Re: [AMBER] NMR multiple structures case
- Re: [AMBER] About dipoles hong-bin Xie
- [AMBER] $AMBERHOME/test/LES_noPME/Run.LESmd Alan
- Re: [AMBER] NMR multiple structures Bill Ross
- Re: [AMBER] $AMBERHOME/test/LES_noPME/Run.LESmd Jason Swails
- Re: [AMBER] $AMBERHOME/test/LES_noPME/Run.LESmd Alan
- Re: [AMBER] GLYCAM residue naming manoj singh
- Re: [AMBER] GLYCAM residue naming Bill Ross
- Re: [AMBER] GLYCAM residue naming manoj singh
- [AMBER] Confirmation of System equilibration ? hirdesh kumar
- Re: [AMBER] Confirmation of System equilibration ? manikanthan bhavaraju
- Re: [AMBER] Confirmation of System equilibration ? hirdesh kumar
Wednesday, 8 September 2010
- [AMBER] amber7 vs xleap on 64bit machine Rossella Noschese
- Re: [AMBER] Query regarding the Hydrogen Bond duration analysis monica.imtech.res.in
- Re: [AMBER] Query regarding the Hydrogen Bond duration analysis hirdesh kumar
- Re: [AMBER] which conformation to choose FyD
- Re: [AMBER] amber7 vs xleap on 64bit machine Jason Swails
- Re: [AMBER] Confirmation of System equilibration ? Jason Swails
- Re: [AMBER] amber7 vs xleap on 64bit machine case
- [AMBER] Compilation problems for amber9/parallel (aka: How to use g77?) Frank Thommen
- Re: [AMBER] Compilation problems for amber9/parallel (aka: How to use g77?) Jason Swails
- Re: [AMBER] amber7 vs xleap on 64bit machine Rossella Noschese
- Re: [AMBER] amber7 vs xleap on 64bit machine Jason Swails
- Re: [AMBER] Compilation problems for amber9/parallel (aka: How to use g77?) Frank Thommen
- Re: [AMBER] GLYCAM residue naming Lachele Foley (Lists)
- Re: [AMBER] amber7 vs xleap on 64bit machine Frank Thommen
- Re: [AMBER] Compilation problems for amber9/parallel (aka: How to use g77?) peter.stauffert.boehringer-ingelheim.com
- Re: [AMBER] Compilation problems for amber9/parallel (aka: How to use g77?) Frank Thommen
- Re: [AMBER] amber7 vs xleap on 64bit machine Jason Swails
- Re: [AMBER] Compilation problems for amber9/parallel (aka: How to use g77?) Jason Swails
- Re: [AMBER] Compilation problems for amber9/parallel (aka: How to use g77?) Frank Thommen
- Re: [AMBER] amber7 vs xleap on 64bit machine Rossella Noschese
- Re: [AMBER] amber7 vs xleap on 64bit machine case
- Re: [AMBER] amber7 vs xleap on 64bit machine Rossella Noschese
- Re: [AMBER] NMR multiple structures Baptiste Legrand
- Re: [AMBER] amber7 vs xleap on 64bit machine Jason Swails
- Re: [AMBER] NMR multiple structures Bill Ross
- [AMBER] mixing GAFF with CHARMM Alan
- Re: [AMBER] mixing GAFF with CHARMM Ross Walker
- [AMBER] Create a carbon nanotube. moacyr comar
- [AMBER] problem of GTX470 running pmemd.cuda_DPDP/input file access provided Sergio R Aragon
- Re: [AMBER] problem of GTX470 running pmemd.cuda_DPDP/input file access provided Scott Le Grand
- Re: [AMBER] GLYCAM residue naming manoj singh
- Re: [AMBER] amber7 vs xleap on 64bit machine case
- Re: [AMBER] GLYCAM residue naming Lachele Foley (Lists)
- Re: [AMBER] problem of GTX470 running pmemd.cuda_DPDP/input file access provided Sasha Buzko
- Re: [AMBER] GLYCAM residue naming manoj singh
- Re: [AMBER] problem of GTX470 running pmemd.cuda_DPDP/input file access provided Scott Le Grand
- Re: [AMBER] problem of GTX470 running pmemd.cuda_DPDP/input file access provided Ross Walker
- Re: [AMBER] GLYCAM residue naming Lachele Foley (Lists)
- Re: [AMBER] GLYCAM residue naming Lekpa Duukori
- Re: [AMBER] GLYCAM residue naming manoj singh
- Re: [AMBER] mixing GAFF with CHARMM Alan
- Re: [AMBER] problem of GTX470 running pmemd.cuda_DPDP/input file access provided Sasha Buzko
- Re: [AMBER] GLYCAM residue naming Lachele Foley (Lists)
- Re: [AMBER] GLYCAM residue naming Lekpa Duukori
- Re: [AMBER] GLYCAM residue naming manoj singh
- Re: [AMBER] GLYCAM residue naming Bill Ross
- [AMBER] JAC test on GTX 470 started Sergio R Aragon
- Re: [AMBER] GLYCAM residue naming manoj singh
- Re: [AMBER] JAC test on GTX 470 started Scott Le Grand
- Re: [AMBER] GLYCAM residue naming Lachele Foley (Lists)
- Re: [AMBER] amber7 vs xleap on 64bit machine Scott Brozell
- Re: [AMBER] ERROR in MM-PBSA Siddharth Rastogi
- [AMBER] JAC test on GTX 470 error produced Sergio R Aragon
- Re: [AMBER] JAC test on GTX 470 error produced Jason Swails
- [AMBER] Atom selection Rahul Banerjee
- Re: [AMBER] JAC test on GTX 470 error produced/run again w/o changes/need help Sergio R Aragon
- Re: [AMBER] ERROR in MM-PBSA Jason Swails
- Re: [AMBER] JAC test on GTX 470 error produced/run again w/o changes/need help Ross Walker
- Re: [AMBER] GLYCAM residue naming manoj singh
Thursday, 9 September 2010
- [AMBER] pmemd installation colvin
- Re: [AMBER] pmemd installation Per Jr. Greisen
- Re: [AMBER] pmemd installation colvin
- Re: [AMBER] pmemd installation Jason Swails
- [AMBER] Varying restraint values on subsets of a restraint mask in sander/pmemd Matthew Tessier
- [AMBER] Restraints for Glycan in REMD Lekpa Duukori
- Re: [AMBER] Restraints for Glycan in REMD Lachele Foley (Lists)
- Re: [AMBER] pmemd.cuda errors on GTX400 series cards - USER POLL Christophe Deprez
- Re: [AMBER] problem of GTX470 running pmemd.cuda_DPDP/input file access provided Ross Walker
- [AMBER] installation of python script for mm_pbsa Sangita Kachhap
- [AMBER] JAC error reproduced 3 times on GTX 470 Sergio R Aragon
- Re: [AMBER] installation of python script for mm_pbsa Bill Miller III
- Re: [AMBER] Restraints for Glycan in REMD Lekpa Duukori
- [AMBER] mmpbsa problem Lidong Wang
- [AMBER] Building a sequence using a new molecular fragment Millen, Andrea
- [AMBER] AMBER 11 with OpenMPI and Intel Compiler on MacOSX Kazuo Ohta
- Re: [AMBER] Building a sequence using a new molecular fragment FyD
Friday, 10 September 2010
- [AMBER] compilation fails ALL make.parallel tests Daniel Sindhikara
- [AMBER] Complex distorts during pressure adjustment in equilibration Alexander Metz
- Re: [AMBER] compilation fails ALL make.parallel tests case
- Re: [AMBER] Atom selection Senthil Natesan
- Re: [AMBER] JAC error reproduced 3 times on GTX 470 Mark Williamson
- Re: [AMBER] JAC error reproduced 3 times on GTX 470 Scott Le Grand
- [AMBER] GPU memory test program Sergio R Aragon
- Re: [AMBER] Complex distorts during pressure adjustment in equilibration Sergio R Aragon
- [AMBER] PTRAJ residue naming problem. Hoshin Kim
- Re: [AMBER] Complex distorts during pressure adjustment in equilibration Alexander Metz
- Re: [AMBER] PTRAJ residue naming problem. Jason Swails
- Re: [AMBER] GPU memory test program Scott Le Grand
- Re: [AMBER] PTRAJ residue naming problem. Kevin Hauser
- Re: [AMBER] PTRAJ residue naming problem. Bill Ross
- [AMBER] debug run Sergio R Aragon
- [AMBER] Questions on Minimization Jiang Yusheng
- Re: [AMBER] debug run Jason Swails
- Re: [AMBER] Questions on Minimization Jason Swails
- [AMBER] curves question Temiz, Nuri (NIH/NCI) [C]
- [AMBER] sleap error manoj singh
- Re: [AMBER] sleap error Jason Swails
- Re: [AMBER] sleap error manoj singh
- Re: [AMBER] sleap error Jason Swails
- Re: [AMBER] sleap error manoj singh
- Re: [AMBER] debug run Scott Le Grand
- Re: [AMBER] Questions on Minimization Jiang Yusheng
- Re: [AMBER] Questions on Minimization Kevin Hauser
- Re: [AMBER] Questions on Minimization Jason Swails
- Re: [AMBER] Questions on Minimization Jiang Yusheng
- Re: [AMBER] Questions on Minimization Jason Swails
- Re: [AMBER] debug run Sergio R Aragon
- [AMBER] pmemd 11 (parallel) compilation error Paul S. Nerenberg
- Re: [AMBER] Complex distorts during pressure adjustment in equilibr ation. . Don.Bashford.stjude.org
- Re: [AMBER] pmemd 11 (parallel) compilation error Ross Walker
- Re: [AMBER] pmemd 11 (parallel) compilation error Jason Swails
- Re: [AMBER] pmemd 11 (parallel) compilation error Paul S. Nerenberg
- Re: [AMBER] Complex distorts during pressure adjustment in equilibration Thomas Cheatham III
- Re: [AMBER] pmemd 11 (parallel) compilation error Paul S. Nerenberg
- [AMBER] RESP calculation using non-Gaussian software? Ilyas Yildirim
- Re: [AMBER] RESP calculation using non-Gaussian software? Jason Swails
- Re: [AMBER] RESP calculation using non-Gaussian software? FyD
Saturday, 11 September 2010
- [AMBER] How to control the speed of heating? xqkong
- Re: [AMBER] How to control the speed of heating? Daniel Sindhikara
- Re: [AMBER] How to control the speed of heating? xqkong
- Re: [AMBER] How to control the speed of heating? Carlos Simmerling
- Re: [AMBER] How to control the speed of heating? xqkong
- Re: [AMBER] How to control the speed of heating? Carlos Simmerling
- Re: [AMBER] pmemd 11 (parallel) compilation error Ross Walker
- [AMBER] ig value M. Reza Ganjalikhany
- Re: [AMBER] ig value Daniel Sindhikara
- Re: [AMBER] pmemd 11 (parallel) compilation error Paul S. Nerenberg
- Re: [AMBER] How to control the speed of heating? cieplak.cgl.ucsf.edu
- Re: [AMBER] How to control the speed of heating? xqkong
Sunday, 12 September 2010
- Re: [AMBER] compilation fails ALL make.parallel tests Daniel Sindhikara
- [AMBER] MMPBSA.py installation error Sangita Kachhap
- Re: [AMBER] MMPBSA.py installation error Jason Swails
- [AMBER] PMEMD with CUDA support for Windows? Thomas Patko
- Re: [AMBER] MMPBSA.py installation error Sangita Kachhap
- Re: [AMBER] compilation fails ALL make.parallel tests case
- Re: [AMBER] MMPBSA.py installation error Jason Swails
- Re: [AMBER] Memory test con GTX 470 Sergio R Aragon
- [AMBER] memory allocation problem? Seibold, Stephen
- Re: [AMBER] memory allocation problem? Daniel Roe
- Re: [AMBER] PMEMD with CUDA support for Windows? Ross Walker
- Re: [AMBER] memory allocation problem? Seibold, Stephen
- [AMBER] contacts command Andrew Voronkov
- [AMBER] question on diffusion comand in ptraj Andrew Voronkov
- Re: [AMBER] pmemd installation colvin
- Re: [AMBER] pmemd installation Jason Swails
- Re: [AMBER] pmemd installation colvin
- Re: [AMBER] pmemd installation Jason Swails
- Re: [AMBER] Memory test con GTX 470 Scott Le Grand
- Re: [AMBER] 'cluster' option of ptraj: Is it possible to directly feed a file with rmsd values as input? Arvind
- Re: [AMBER] compilation fails ALL make.parallel tests Daniel Sindhikara
Monday, 13 September 2010
- [AMBER] remd coordinate output Jorgen Simonsen
- Re: [AMBER] remd coordinate output Carlos Simmerling
- Re: [AMBER] remd coordinate output Jorgen Simonsen
- Re: [AMBER] remd coordinate output Carlos Simmerling
- Re: [AMBER] remd coordinate output Adrian Roitberg
- Re: [AMBER] remd coordinate output Jorgen Simonsen
- [AMBER] Average distance between two hydrogens over a 1 ns simulation Edward M.
- Re: [AMBER] compilation fails ALL make.parallel tests case
- [AMBER] MD based on 3D-RISM can be really used in AMBER11? kyousuke_tsumura.fujifilm.co.jp
- [AMBER] regarding wham analysis jani vinod
- Re: [AMBER] regarding wham analysis Carlos Simmerling
- Re: [AMBER] Average distance between two hydrogens over a 1 ns simulation Peter Schmidtke
- Re: [AMBER] pmemd installation colvin
- Re: [AMBER] regarding wham analysis jani vinod
- Re: [AMBER] regarding wham analysis Carlos Simmerling
- Re: [AMBER] remd coordinate output Carlos Simmerling
- Re: [AMBER] MD based on 3D-RISM can be really used in AMBER11? case
- [AMBER] ptraj hbond analysis George Tzotzos
- Re: [AMBER] remd coordinate output Jorgen Simonsen
- [AMBER] ptraj image, overlap of molecules Nadine Utz
- Re: [AMBER] ptraj hbond analysis Alexander Metz
- [AMBER] chamber At line 2692 of file _psfprm.f Jorgen Simonsen
- Re: [AMBER] chamber At line 2692 of file _psfprm.f Mark Williamson
- Re: [AMBER] chamber At line 2692 of file _psfprm.f Ross Walker
- [AMBER] Question about Heating and equilibration protocol? M. Reza Ganjalikhany
- Re: [AMBER] Question about Heating and equilibration protocol? case
- Re: [AMBER] Question about Heating and equilibration protocol? manikanthan bhavaraju
- Re: [AMBER] Question about Heating and equilibration protocol? Bill Ross
- Re: [AMBER] Debug pmemd.cuda Sergio R Aragon
- [AMBER] Pressure in bar or atm? Ben Roberts
- Re: [AMBER] Debug pmemd.cuda Scott Le Grand
- Re: [AMBER] how to set clock rate? temperature in a C2050 card? hardware replacement? Sergio R Aragon
- Re: [AMBER] how to set clock rate? temperature in a C2050 card? hardware replacement? Scott Le Grand
- [AMBER] Exactly the same energy output over multiple runs of cuda_SPDP Trevor Gokey
- Re: [AMBER] Exactly the same energy output over multiple runs of cuda_SPDP Ross Walker
- Re: [AMBER] Exactly the same energy output over multiple runs of cuda_SPDP Trevor Gokey
- Re: [AMBER] Exactly the same energy output over multiple runs of cuda_SPDP Scott Le Grand
- [AMBER] LD and SGLD runs (Simulations) shaktis.gbu.ac.in
- Re: [AMBER] LD and SGLD runs (Simulations) Daniel Sindhikara
- Re: [AMBER] regarding wham analysis jani vinod
- Re: [AMBER] regarding wham analysis Daniel Sindhikara
- [AMBER] unit of Bfactor Ashutosh Shandilya
- Re: [AMBER] compilation fails ALL make.parallel tests Daniel Sindhikara
- Re: [AMBER] unit of Bfactor hirdesh kumar
- Re: [AMBER] unit of Bfactor Kshatresh Dutta Dubey
- Re: [AMBER] unit of Bfactor hirdesh kumar
Tuesday, 14 September 2010
- [AMBER] AMBER 10 on OPENMPI CHAMI F.
- Re: [AMBER] LD and SGLD runs (Simulations) Carlos Simmerling
- Re: [AMBER] AMBER 10 on OPENMPI Ye MEI
- [AMBER] Residues with multiple conformations George Tzotzos
- [AMBER] set coordinate axis eduardo.troche.uvigo.es
- Re: [AMBER] Residues with multiple conformations Alexander Metz
- Re: [AMBER] Residues with multiple conformations Sergio R Aragon
- [AMBER] list of atoms with associated total forces ? Marek Maly
- Re: [AMBER] ERROR in MM-PBSA Siddharth Rastogi
- Re: [AMBER] ERROR in MM-PBSA Jason Swails
- Re: [AMBER] set coordinate axis Jason Swails
- [AMBER] units of eigenvalues from pca moitrayee.mbu.iisc.ernet.in
- Re: [AMBER] list of atoms with associated total forces ? Ben Roberts
- Re: [AMBER] list of atoms with associated total forces ? Marek Maly
- [AMBER] mm_pbsa.pl error for per residue decomposition. manoj singh
- Re: [AMBER] mm_pbsa.pl error for per residue decomposition. Jason Swails
- Re: [AMBER] mm_pbsa.pl error for per residue decomposition. manoj singh
- Re: [AMBER] mm_pbsa.pl error for per residue decomposition. Jason Swails
- Re: [AMBER] mm_pbsa.pl error for per residue decomposition. manoj singh
Wednesday, 15 September 2010
- Re: [AMBER] units of eigenvalues from pca case
- Re: [AMBER] Pressure in bar or atm? case
- Re: [AMBER] NMR multiple structures Baptiste Legrand
- Re: [AMBER] NMR multiple structures Jason Swails
- Re: [AMBER] NMR multiple structures Baptiste Legrand
- [AMBER] comparison of PDBs from clustering - representative, average and from rst file Andrew Voronkov
- [AMBER] Domainwise rmsd using ptraj rms moitrayee.mbu.iisc.ernet.in
- [AMBER] Fwd: comparison of PDBs from clustering - representative, average and from rst file Andrew Voronkov
- Re: [AMBER] Domainwise rmsd using ptraj rms Daniel Roe
- Re: [AMBER] comparison of PDBs from clustering - representative, average and from rst file Thomas Cheatham III
- [AMBER] Compaliation of sander.APBS Hemant Kumar
- Re: [AMBER] comparison of PDBs from clustering - representative, average and from rst file Andrew Voronkov
- Re: [AMBER] Domainwise rmsd using ptraj rms moitrayee.mbu.iisc.ernet.in
Thursday, 16 September 2010
- Re: [AMBER] comparison of PDBs from clustering - representative, average and from rst file Andrew Voronkov
- Re: [AMBER] NMR multiple structures Baptiste Legrand
- Re: [AMBER] comparison of PDBs from clustering - representative, average and from rst file Thomas Cheatham III
- Re: [AMBER] list of atomsG4 with amber with associated total forces ? Philippe Pinard
- Re: [AMBER] NMR multiple structures case
- [AMBER] Nudge elastic band, DNA Replica temperature does not go to zero. Abhishek Singh
- [AMBER] Nudge elastic band, DNA Replica temperature does not go to zero. Abhishek Singh
- Re: [AMBER] Nudge elastic band, DNA Replica temperature does not go to zero. Carlos Simmerling
- Re: [AMBER] list of atomsG4 with amber with associated total forces ? Marek Maly
- Re: [AMBER] NMR multiple structures Baptiste Legrand
- [AMBER] pmemd.MPI problem George Tzotzos
- [AMBER] pmemd.MPI problem George Tzotzos
- Re: [AMBER] pmemd.MPI problem Jason Swails
- Re: [AMBER] pmemd.MPI problem Jason Swails
- [AMBER] netCDF support for mmpbsa.py + general question Trevor Gokey
- Re: [AMBER] pmemd.MPI problem George Tzotzos
- Re: [AMBER] netCDF support for mmpbsa.py + general question Jason Swails
- Re: [AMBER] pmemd.MPI problem Jason Swails
- Re: [AMBER] Using AMBER force field for ionic compounds Preshit Dandekar
- [AMBER] Sander/pmemd usage: refc question mdkvia.yahoo.com
- Re: [AMBER] Sander/pmemd usage: refc question Jason Swails
- Re: [AMBER] Sander/pmemd usage: refc question mdkvia.yahoo.com
- Re: [AMBER] Sander/pmemd usage: refc question Scott Le Grand
- Re: [AMBER] Sander/pmemd usage: refc question Jason Swails
- Re: [AMBER] netCDF support for mmpbsa.py + general question Trevor Gokey
- Re: [AMBER] netCDF support for mmpbsa.py + general question Jason Swails
- Re: [AMBER] Sander/pmemd usage: refc question mdkvia.yahoo.com
- Re: [AMBER] Compaliation of sander.APBS Robert Konecny
- [AMBER] ambertools1.4 install problem Anuradha Mittal
- Re: [AMBER] ERROR in MM-PBSA Siddharth Rastogi
- Re: [AMBER] ambertools1.4 install problem Jason Swails
- Re: [AMBER] ERROR in MM-PBSA Jason Swails
- Re: [AMBER] ambertools1.4 install problem Anuradha Mittal
- Re: [AMBER] ambertools1.4 install problem Jason Swails
- Re: [AMBER] ambertools1.4 install problem Anuradha Mittal
- [AMBER] Restraint of atom distance during minimization tong Zhu
Friday, 17 September 2010
- Re: [AMBER] Restraint of atom distance during minimization Jason Swails
- Re: [AMBER] pmemd.MPI problem George Tzotzos
- Re: [AMBER] ambertools1.4 install problem case
- Re: [AMBER] pmemd.MPI problem Ben Roberts
- Re: [AMBER] Using AMBER force field for ionic compounds Preshit Dandekar
- [AMBER] ptraj clustering for long trajetories Senthil Natesan
- Re: [AMBER] ambertools1.4 install problem Anuradha Mittal
- Re: [AMBER] ambertools1.4 install problem manoj singh
- Re: [AMBER] ambertools1.4 install problem case
- Re: [AMBER] ambertools1.4 install problem case
- Re: [AMBER] ambertools1.4 install problem Bill Ross
- Re: [AMBER] mm_pbsa fails xue wang
- Re: [AMBER] mm_pbsa fails Bill Miller III
- [AMBER] Water pdb parameterization Anthony Costa
- Re: [AMBER] mm_pbsa fails xue wang
- Re: [AMBER] Pressure in bar or atm? Ben Roberts
- [AMBER] Nudge elastic band, DNA Replica temperature does not go to zero. Abhishek Singh
- [AMBER] A question regarding mm_pbsa_statistics.pl bin wang
- Re: [AMBER] A question regarding mm_pbsa_statistics.pl Jason Swails
- [AMBER] restraints in pmemd.cuda Sasha Buzko
- Re: [AMBER] restraints in pmemd.cuda Scott Le Grand
- [AMBER] problem of nmode calculation fancy2012
- Re: [AMBER] problem of nmode calculation Jason Swails
- [AMBER] Restrainmask problem xue wang
- Re: [AMBER] Restrainmask problem Jason Swails
Saturday, 18 September 2010
- [AMBER] Regarding atomic charges in parmtop file aneesh cna
- Re: [AMBER] comparison of PDBs from clustering - representative, average and from rst file Andrew Voronkov
- [AMBER] Clarification: nscm and iwrap mdkvia.yahoo.com
- Re: [AMBER] Regarding atomic charges in parmtop file Alessandro Nascimento
- Re: [AMBER] Water pdb parameterization case
- Re: [AMBER] Regarding atomic charges in parmtop file Jason Swails
- Re: [AMBER] restraints in pmemd.cuda Ross Walker
- Re: [AMBER] Water pdb parameterization Anthony Costa
- [AMBER] inconsistency between steered Md and GBSA MEHMET ALI OZTURK
- [AMBER] Blowing array Seibold, Stephen
- Re: [AMBER] inconsistency between steered Md and GBSA Jason Swails
- Re: [AMBER] Nudge elastic band, DNA Replica temperature does not go to zero. Carlos Simmerling
- Re: [AMBER] Blowing array Daniel Roe
- Re: [AMBER] Nudge elastic band, DNA Replica temperature does not go to zero. Abhishek Singh
- Re: [AMBER] Nudge elastic band, DNA Replica temperature does not go to zero. Carlos Simmerling
- Re: [AMBER] Nudge elastic band, DNA Replica temperature does not go to zero. Abhishek Singh
- Re: [AMBER] Nudge elastic band, DNA Replica temperature does not go to zero. Abhishek Singh
- Re: [AMBER] Nudge elastic band, DNA Replica temperature does not go to zero. Carlos Simmerling
- Re: [AMBER] Nudge elastic band, DNA Replica temperature does not go to zero. Abhishek Singh
- Re: [AMBER] Nudge elastic band, DNA Replica temperature does not go to zero. Carlos Simmerling
- [AMBER] Amber11 compile issue Anuradha Mittal
- Re: [AMBER] Amber11 compile issue Jason Swails
- Re: [AMBER] Amber11 compile issue Anuradha Mittal
- Re: [AMBER] Restrainmask problem xue wang
- Re: [AMBER] Restrainmask problem xue wang
- Re: [AMBER] Amber11 compile issue Jason Swails
- Re: [AMBER] Amber11 compile issue Anuradha Mittal
- Re: [AMBER] Amber11 compile issue Ross Walker
- Re: [AMBER] Amber11 compile issue Anuradha Mittal
- Re: [AMBER] Amber11 compile issue Ross Walker
Sunday, 19 September 2010
- Re: [AMBER] ptraj hbond analysis rameshwar prajapati
- [AMBER] a pdb-trajout problems bingbing zhang
- [AMBER] Minimization terminated without any output xue wang
- Re: [AMBER] Amber11 compile issue Anuradha Mittal
- Re: [AMBER] Water pdb parameterization case
- Re: [AMBER] Blowing array case
- Re: [AMBER] Nudge elastic band, DNA Replica temperature does not go to zero. Abhishek Singh
- [AMBER] making bond to water molecule Jorgen Simonsen
- Re: [AMBER] making bond to water molecule Bill Ross
- [AMBER] Error due to ***s in restart file Arvind
- Re: [AMBER] Minimization terminated without any output case
- Re: [AMBER] Error due to ***s in restart file case
- Re: [AMBER] Pressure in bar or atm? case
- [AMBER] Blowing array Seibold, Stephen
- Re: [AMBER] Blowing array Yi Shang
- Re: [AMBER] Blowing array case
- Re: [AMBER] a pdb-trajout problems bingbing zhang
- [AMBER] molecular dynamics simulation-water-box-diffution problem Rilei Yu
- Re: [AMBER] molecular dynamics simulation-water-box-diffution problem Ye MEI
- Re: [AMBER] Regarding atomic charges in parmtop file aneesh cna
Monday, 20 September 2010
- [AMBER] problems with xleap Rossella Noschese
- [AMBER] PTRAJ Hbond analysis George Tzotzos
- Re: [AMBER] problems with xleap Rossella Noschese
- Re: [AMBER] problems with xleap Jason Swails
- Re: [AMBER] Error due to ***s in restart file Arvind
- [AMBER] GRID-enabled web portal for the use of the AMBER Lucio Ferella
- [AMBER] on gas phase energies calculation pxq
- [AMBER] changing mdcrd file to XYZ hong-bin Xie
- Re: [AMBER] GRID-enabled web portal for the use of the AMBER Sergio R Aragon
- Re: [AMBER] changing mdcrd file to XYZ Jason Swails
- Re: [AMBER] changing mdcrd file to XYZ Lekpa Duukori
- Re: [AMBER] changing mdcrd file to XYZ hong-bin Xie
- Re: [AMBER] Building a sequence using a new molecular fragment Millen, Andrea
- Re: [AMBER] mm_pbsa.pl error for per residue decomposition. manoj singh
- Re: [AMBER] A question regarding mm_pbsa_statistics.pl bin wang
- [AMBER] Aromatic C and N atom type problems in Antechamber Gabriel Rocklin
- [AMBER] constraint of bond Jorgen Simonsen
- Re: [AMBER] Minimization terminated without any output xue wang
- Re: [AMBER] Aromatic C and N atom type problems in Antechamber Sasha Buzko
- [AMBER] Running MM-PBSA at different temperatures Khaled Barakat
- Re: [AMBER] A question regarding mm_pbsa_statistics.pl manoj singh
- Re: [AMBER] constraint of bond case
- Re: [AMBER] Minimization terminated without any output case
- Re: [AMBER] Running MM-PBSA at different temperatures manoj singh
- Re: [AMBER] Running MM-PBSA at different temperatures Khaled Barakat
- Re: [AMBER] Running MM-PBSA at different temperatures manoj singh
- Re: [AMBER] Running MM-PBSA at different temperatures Thomas Cheatham
- Re: [AMBER] Running MM-PBSA at different temperatures manoj singh
- [AMBER] how to calculate the interaction energies pxq
- Re: [AMBER] Running MM-PBSA at different temperatures Khaled Barakat
- Re: [AMBER] Running MM-PBSA at different temperatures manoj singh
- Re: [AMBER] Running MM-PBSA at different temperatures manoj singh
- Re: [AMBER] Running MM-PBSA at different temperatures Khaled Barakat
Tuesday, 21 September 2010
- [AMBER] Problems with Amber 8 PMEMD Su Qiu
- Re: [AMBER] problems with xleap Rossella Noschese
- [AMBER] 2D radial distribution function Lekpa Duukori
- [AMBER] Creation of a mol2/pdb initial structure file of a pharmaceutical compound. Baptiste Legrand
- [AMBER] MM_PBSA fillratio error/ compiling mm_pbsa.pl Oliver Grant
- Re: [AMBER] 2D radial distribution function Daniel Sindhikara
- Re: [AMBER] MM_PBSA fillratio error/ compiling mm_pbsa.pl Bill Miller III
- Re: [AMBER] 2D radial distribution function Lekpa Duukori
- Re: [AMBER] Problems with Amber 8 PMEMD case
- Re: [AMBER] problems with xleap case
- Re: [AMBER] Creation of a mol2/pdb initial structure file of a pharmaceutical compound. case
- Re: [AMBER] MM_PBSA fillratio error/ compiling mm_pbsa.pl Oliver Grant
- Re: [AMBER] 2D radial distribution function Daniel Sindhikara
- Re: [AMBER] Creation of a mol2/pdb initial structure file of a pharmaceutical compound. Baptiste Legrand
- [AMBER] How to calculate total potential energy for protein chain only? Liu, Jingyuan
- Re: [AMBER] Blowing array Daniel Roe
- Re: [AMBER] 2D radial distribution function Lekpa Duukori
- Re: [AMBER] Blowing array Seibold, Stephen
- Re: [AMBER] a pdb-trajout problems Daniel Roe
- [AMBER] error in MMPBSA calculation Chanchal
- Re: [AMBER] Running MM-PBSA at different temperatures Jason Swails
- [AMBER] How to calculate total potential energy for protein chain only? Liu, Jingyuan
- [AMBER] MM-PBSA analysis on a protein ligand complex with 32000 atoms marta.gomes.fc.up.pt
- [AMBER] How to calculate total potential energy for protein chain only? Liu, Jingyuan
- Re: [AMBER] Water pdb parameterization Anthony Costa
- Re: [AMBER] Creation of a mol2/pdb initial structure file of a pharmaceutical compound. case
- Re: [AMBER] MM-PBSA analysis on a protein ligand complex with 32000 atoms Dwight McGee
- [AMBER] problems compiling amber10 Jeffrey Sanders
- [AMBER] hydrogen-deuterium exchange: iso program or papers that outline methods Sidney Elmer
- Re: [AMBER] error in MMPBSA calculation Bill Miller III
- Re: [AMBER] problems compiling amber10 case
- Re: [AMBER] How to calculate total potential energy for protein chain only? Bill Ross
- Re: [AMBER] problems compiling amber10 Jeffrey Sanders
- Re: [AMBER] Water pdb parameterization case
- Re: [AMBER] hydrogen-deuterium exchange: iso program or papers that outline methods case
- Re: [AMBER] error in MMPBSA calculation Chanchal
- Re: [AMBER] a pdb-trajout problems bingbing zhang
- Re: [AMBER] How to calculate total potential energy for protein chain only? steinbrt.rci.rutgers.edu
- Re: [AMBER] How to calculate total potential energy for protein chain only? hirdesh kumar
- Re: [AMBER] How to calculate total potential energy for protein chain only? Jason Swails
- Re: [AMBER] How to calculate total potential energy for protein chain only? steinbrt.rci.rutgers.edu
- Re: [AMBER] a pdb-trajout problems Trevor Gokey
- Re: [AMBER] Error due to ***s in restart file Trevor Gokey
- Re: [AMBER] molecular dynamics simulation-water-box-diffution problem Trevor Gokey
- Re: [AMBER] molecular dynamics simulation-water-box-diffution problem hirdesh kumar
- Re: [AMBER] molecular dynamics simulation-water-box-diffution problem Ross Walker
Wednesday, 22 September 2010
- Re: [AMBER] molecular dynamics simulation-water-box-diffution problem Trevor Gokey
- Re: [AMBER] Creation of a mol2/pdb initial structure file of a pharmaceutical compound. Trevor Gokey
- [AMBER] pmemd performance colvin
- [AMBER] Confirmation of stabilisation of protein at equilibrium step shweta
- Re: [AMBER] Confirmation of stabilisation of protein at equilibrium step steinbrt.rci.rutgers.edu
- [AMBER] Query regarding Hydrogen Bond Duration map hirdesh kumar
- Re: [AMBER] molecular dynamics simulation-water-box-diffution problem hirdesh kumar
- Re: [AMBER] chamber At line 2692 of file _psfprm.f Jorgen Simonsen
- Re: [AMBER] pmemd performance case
- Re: [AMBER] pmemd performance Gustavo Seabra
- Re: [AMBER] pmemd performance michael bane
- Re: [AMBER] Blowing array Seibold, Stephen
- Re: [AMBER] A question regarding mm_pbsa_statistics.pl bin wang
- Re: [AMBER] How to calculate total potential energy for protein chain only? Liu, Jingyuan
- Re: [AMBER] Creation of a mol2/pdb initial structure file of a pharmaceutical compound. Baptiste Legrand
- Re: [AMBER] A question regarding mm_pbsa_statistics.pl Alexander Metz
- [AMBER] MM_PBSA stopped at the last step zhihong ke
- Re: [AMBER] Creation of a mol2/pdb initial structure file of a pharmaceutical compound. Andreas Goetz
- Re: [AMBER] error in MMPBSA calculation Chanchal
- Re: [AMBER] error in MMPBSA calculation Jason Swails
- [AMBER] MD on an array of small molecules Joe Bozell
- Re: [AMBER] Error due to ***s in restart file Arvind
- Re: [AMBER] Water pdb parameterization Anthony Costa
- Re: [AMBER] MD on an array of small molecules case
- Re: [AMBER] Water pdb parameterization case
- Re: [AMBER] Water pdb parameterization Anthony Costa
- Re: [AMBER] error in MMPBSA calculation Chanchal
- Re: [AMBER] How to calculate total potential energy for protein chain only? steinbrt.rci.rutgers.edu
Thursday, 23 September 2010
- [AMBER] Minimum Energy Conformational Structures of Saccharides in Solution Sushil Mishra
- Re: [AMBER] MM_PBSA stopped at the last step Oliver Grant
- [AMBER] AmberTools 1.4 installation problem Shradha Chopra Phd2009,BIC
- Re: [AMBER] AmberTools 1.4 installation problem Jason Swails
- Re: [AMBER] AmberTools 1.4 installation problem case
- [AMBER] FW: MD on an array of small molecules Bozell, Joseph John
- Re: [AMBER] AmberTools 1.4 installation problem Jason Swails
- Re: [AMBER] FW: MD on an array of small molecules M. L. Dodson
- [AMBER] PMEMD 10 on OpenMPI with Intel compiler issues CHAMI F.
- Re: [AMBER] PMEMD 10 on OpenMPI with Intel compiler issues Jason Swails
- Re: [AMBER] error in MMPBSA calculation Chanchal
- Re: [AMBER] error in MMPBSA calculation Jason Swails
- Re: [AMBER] PMEMD 10 on OpenMPI with Intel compiler issues case
- [AMBER] MD for large proteins Laura Perissinotti
- [AMBER] Shake errors Justine Shaw
- [AMBER] amber11 installation error Sangita Kachhap
- Re: [AMBER] amber11 installation error case
- Re: [AMBER] MD for large proteins Jason Swails
- Re: [AMBER] amber11 installation error Sangita Kachhap
- Re: [AMBER] amber11 installation error Paul S. Nerenberg
- Re: [AMBER] amber11 installation error Sangita Kachhap
- Re: [AMBER] amber11 installation error Paul S. Nerenberg
- [AMBER] mm_pbsa.pl frozen, hanging, stopped at end. Oliver Grant
- Re: [AMBER] Shake errors Bill Ross
- [AMBER] problem with AMOEBA force field Igor Sizov
- Re: [AMBER] problem with AMOEBA force field case
- Re: [AMBER] Shake errors case
- Re: [AMBER] MD for large proteins case
- [AMBER] 10-12 hbond terms Philippe Pinard
- Re: [AMBER] error in MMPBSA calculation Chanchal
- Re: [AMBER] error in MMPBSA calculation Bill Miller III
- Re: [AMBER] ERROR in MM-PBSA Siddharth Rastogi
- Re: [AMBER] Minimum Energy Conformational Structures of Saccharides in Solution Lachele Foley (Lists)
- Re: [AMBER] ERROR in MM-PBSA Jason Swails
- [AMBER] Disulphide Bond Cleavage hirdesh kumar
- Re: [AMBER] amber11 installation error Sangita Kachhap
- Re: [AMBER] Minimum Energy Conformational Structures of Saccharides in Solution Sushil Mishra
- Re: [AMBER] amber11 installation error Paul S. Nerenberg
- Re: [AMBER] amber11 installation error Jason Swails
- Re: [AMBER] Disulphide Bond Cleavage Jason Swails
- [AMBER] ERROR: The unperturbed charge of the unit: 0.010000 is not integral Bongkeun Kim
- Re: [AMBER] Disulphide Bond Cleavage hirdesh kumar
- [AMBER] AMBER 11: Line minimizer aborted: step at lower bound Amor San Juan
- [AMBER] Analysis of MD simulation Ashutosh Shandilya
- Re: [AMBER] AMBER 11: Line minimizer aborted: step at lower bound hirdesh kumar
Friday, 24 September 2010
- Re: [AMBER] error in MMPBSA calculation Chanchal
- Re: [AMBER] AMBER 11: Line minimizer aborted: step at lower bound Amor San Juan
- Re: [AMBER] amber11 installation error Sangita Kachhap
- Re: [AMBER] Disulphide Bond Cleavage Aditya Padhi
- [AMBER] Extracting backbone dihedral angles Harald Lanig
- Re: [AMBER] Disulphide Bond Cleavage case
- Re: [AMBER] amber11 installation error case
- Re: [AMBER] AMBER 11: Line minimizer aborted: step at lower bound case
- Re: [AMBER] ERROR: The unperturbed charge of the unit: 0.010000 is not integral James Maier
- [AMBER] Neutralization of the system by Na+ or Cl- ions are needed or not for constant pH MD simulation nicholus bhattacharjee
- Re: [AMBER] Neutralization of the system by Na+ or Cl- ions are needed or not for constant pH MD simulation Carlos Simmerling
- Re: [AMBER] Neutralization of the system by Na+ or Cl- ions are needed or not for constant pH MD simulation case
- Re: [AMBER] Extracting backbone dihedral angles Jason Swails
- Re: [AMBER] FW: MD on an array of small molecules Bozell, Joseph John
- Re: [AMBER] 10-12 hbond terms case
- Re: [AMBER] FW: MD on an array of small molecules Jason Swails
- [AMBER] chamber At line 2692 of file _psfprm.f Jorgen Simonsen
- Re: [AMBER] ERROR: The unperturbed charge of the unit: 0.010000 is not integral FyD
- Re: [AMBER] chamber At line 2692 of file _psfprm.f Mark Williamson
- Re: [AMBER] chamber At line 2692 of file _psfprm.f Ross Walker
- [AMBER] missing parameters (dihe) in parm10.dat? Alan
- Re: [AMBER] missing parameters (dihe) in parm10.dat? Jason Swails
- Re: [AMBER] missing parameters (dihe) in parm10.dat? Alan
- Re: [AMBER] ERROR: The unperturbed charge of the unit: 0.010000 is not integral Bongkeun Kim
- Re: [AMBER] missing parameters (dihe) in parm10.dat? case
- Re: [AMBER] ERROR: The unperturbed charge of the unit: 0.010000 is not integral James Maier
- Re: [AMBER] ERROR: The unperturbed charge of the unit: 0.010000 is not integral Bongkeun Kim
- Re: [AMBER] FW: MD on an array of small molecules Bozell, Joseph John
- Re: [AMBER] FW: MD on an array of small molecules Jason Swails
- Re: [AMBER] Xplor_to_Amber Raman Parkesh
- Re: [AMBER] mm_pbsa.pl frozen, hanging, stopped at end. Ray Luo
- [AMBER] Analysis of MD simulation Ashutosh Shandilya
- Re: [AMBER] Analysis of MD simulation steinbrt.rci.rutgers.edu
- Re: [AMBER] Analysis of MD simulation Ashutosh Shandilya
- [AMBER] Histamine Hydrogen hirdesh kumar
Saturday, 25 September 2010
- [AMBER] Query about restraint minimization hirdesh kumar
- Re: [AMBER] Problems with Amber 8 PMEMD Su Qiu
- Re: [AMBER] ERROR: The unperturbed charge of the unit: 0.010000 is not integral FyD
- Re: [AMBER] a pdb-trajout problems bingbing zhang
- Re: [AMBER] mm_pbsa.pl frozen, hanging, stopped at end. Oliver Grant
- Re: [AMBER] missing parameters (dihe) in parm10.dat? Alan
- Re: [AMBER] Query about restraint minimization case
- Re: [AMBER] Problems with Amber 8 PMEMD case
- Re: [AMBER] Histamine Hydrogen Jason Swails
- Re: [AMBER] ERROR: The unperturbed charge of the unit: 0.010000 is not integral Bongkeun Kim
- Re: [AMBER] missing parameters (dihe) in parm10.dat? Jason Swails
- [AMBER] integer divide by zero Pete Kekenes-Huskey
- Re: [AMBER] Histamine Hydrogen hirdesh kumar
- Re: [AMBER] Analysis of MD simulation Peter Charles Kahuna
- Re: [AMBER] Problems with Amber 8 PMEMD Bill Ross
- [AMBER] Cieplak work on RESP charges derivation Josmar R. da Rocha
- Re: [AMBER] Cieplak work on RESP charges derivation Kevin Hauser
- Re: [AMBER] Problems with Amber 8 PMEMD Su Qiu
- Re: [AMBER] Analysis of MD simulation steinbrt.rci.rutgers.edu
- [AMBER] can't save the PDB file to produce topology and coordinates file geyan
Sunday, 26 September 2010
- [AMBER] can't save the PDB file to produce topology and coordinates file geyan
- [AMBER] Phosphate group treatment shweta
- Re: [AMBER] MM_PBSA stopped at the last step rameshwar prajapati
- Re: [AMBER] Domainwise rmsd using ptraj rms moitrayee.mbu.iisc.ernet.in
- Re: [AMBER] can't save the PDB file to produce topology and coordinates file dhacademic
- Re: [AMBER] Phosphate group treatment case
- [AMBER] disulfide bonds in amoeba case
- Re: [AMBER] missing parameters (dihe) in parm10.dat? case
- [AMBER] loop relaxation with les Simon Becker
- [AMBER] problem with MMPBSA juzer stationwala
- Re: [AMBER] problem with MMPBSA Oliver Grant
- Re: [AMBER] can't save the PDB file to produce topology and coordinates file Bill Ross
- Re: [AMBER] Problems with Amber 8 PMEMD Su Qiu
- Re: [AMBER] AMBER 11: Line minimizer aborted: step at lower bound Amor San Juan
- Re: [AMBER] Phosphate group treatment shweta
- [AMBER] How to disable the function to look for N terminal in leap? Hugh Cheng
- [AMBER] cubic box subrata paul
Monday, 27 September 2010
- [AMBER] Addition of extra-interaction term to LJ-potential: modification of souce code kurisaki ikuo
- [AMBER] rmsd of a subunit I w.r.t subunit II moitrayee.mbu.iisc.ernet.in
- Re: [AMBER] can't save the PDB file to produce topology andcoordinates file geyan
- Re: [AMBER] can't save the PDB file to produce topology andcoordinates file geyan
- Re: [AMBER] problem with MMPBSA juzer stationwala
- Re: [AMBER] problem with MMPBSA Bill Miller III
- Re: [AMBER] problem with MMPBSA juzer stationwala
- Re: [AMBER] problem with MMPBSA Jason Swails
- Re: [AMBER] can't save the PDB file to produce topology andcoordinates file Jason Swails
- Re: [AMBER] How to disable the function to look for N terminal in leap? Jason Swails
- Re: [AMBER] problem with MMPBSA juzer stationwala
- Re: [AMBER] problem with MMPBSA Jason Swails
- Re: [AMBER] cubic box case
- Re: [AMBER] problem with MMPBSA juzer stationwala
- Re: [AMBER] problem with MMPBSA Bill Miller III
- Re: [AMBER] problem with MMPBSA Sushil Mishra
- Re: [AMBER] integer divide by zero case
- Re: [AMBER] integer divide by zero Pete Kekenes-Huskey
- Re: [AMBER] integer divide by zero case
- [AMBER] mmpbsa.py.mpi error Anuradha Mittal
- Re: [AMBER] A question regarding mm_pbsa_statistics.pl bin wang
- [AMBER] AMBER RESTART QUESTIONS Yu, Bingwu
- Re: [AMBER] mmpbsa.py.mpi error Bill Miller III
- Re: [AMBER] mmpbsa.py.mpi error Anuradha Mittal
- Re: [AMBER] AMBER RESTART QUESTIONS Paul S. Nerenberg
- Re: [AMBER] AMBER RESTART QUESTIONS case
- Re: [AMBER] mmpbsa.py.mpi error Jason Swails
- [AMBER] Missing atom types between leaprc.ff99SB and parm99.dat Christopher Roberts
- [AMBER] AMBER RESTART QUESTIONS Yu, Bingwu
- [AMBER] sander gb post-processing fail Trevor Gokey
- [AMBER] ibelly doesn't work qiaoyan
- [AMBER] parameters of SEP and TPO can't match SEP TPO fancy2012
- Re: [AMBER] ibelly doesn't work steinbrt.rci.rutgers.edu
- Re: [AMBER] Aromatic C and N atom type problems in Antechamber Gabriel Rocklin
- [AMBER] Disulphide bond breakage during minimization hirdesh kumar
- Re: [AMBER] Disulphide bond breakage during minimization steinbrt.rci.rutgers.edu
- Re: [AMBER] ibelly doesn't work David Watson
- Re: [AMBER] Disulphide bond breakage during minimization hirdesh kumar
- Re: [AMBER] Disulphide bond breakage during minimization steinbrt.rci.rutgers.edu
Tuesday, 28 September 2010
- [AMBER] calculation of inter atomic distances Ashutosh Shandilya
- Re: [AMBER] cubic box subrata paul
- Re: [AMBER] parameters of SEP and TPO can't match SEP TPO Anselm Horn
- Re: [AMBER] Disulphide bond breakage during minimization hirdesh kumar
- Re: [AMBER] Disulphide bond breakage during minimization Hannes Loeffler
- Re: [AMBER] parameters of SEP and TPO can't match SEP TPO fancy2012
- [AMBER] running pmemd fails Vijay Manickam Achari
- Re: [AMBER] Disulphide bond breakage during minimization hirdesh kumar
- Re: [AMBER] Disulphide bond breakage during minimization Hannes Loeffler
- [AMBER] Solvent accessible surface of certain residues hirdesh kumar
- Re: [AMBER] Disulphide bond breakage during minimization steinbrt.rci.rutgers.edu
- Re: [AMBER] Disulphide bond breakage during minimization Carlos Simmerling
- Re: [AMBER] Disulphide bond breakage during minimization hirdesh kumar
- Re: [AMBER] Disulphide bond breakage during minimization hirdesh kumar
- Re: [AMBER] Disulphide bond breakage during minimization case
- Re: [AMBER] cubic box case
- Re: [AMBER] running pmemd fails case
- Re: [AMBER] problem with MMPBSA juzer stationwala
- Re: [AMBER] problem with MMPBSA Sushil Mishra
- [AMBER] H-bonb calculation Sangita Kachhap
- Re: [AMBER] cubic box subrata paul
- Re: [AMBER] parameters of SEP and TPO can't match SEP TPO fancy2012
- Re: [AMBER] problem with MMPBSA Jason Swails
- Re: [AMBER] H-bonb calculation Jason Swails
- Re: [AMBER] calculation of inter atomic distances Daniel Roe
- Re: [AMBER] cubic box case
- Re: [AMBER] parameters of SEP and TPO can't match SEP TPO Daniel Roe
- Re: [AMBER] cubic box Daniel Roe
- Re: [AMBER] Solvent accessible surface of certain residues Daniel Roe
- Re: [AMBER] running pmemd fails Kevin Hauser
- Re: [AMBER] running pmemd fails Paul S. Nerenberg
- [AMBER] ptraj, unit cell wrapping and velocities Ben Roberts
- [AMBER] Question on simulation Jiang Yusheng
- Re: [AMBER] Question on simulation Jason Swails
- Re: [AMBER] running pmemd fails Vijay Manickam Achari
- Re: [AMBER] Question on simulation Bill Ross
- Re: [AMBER] running pmemd fails Vijay Manickam Achari
- Re: [AMBER] Solvent accessible surface of certain residues hirdesh kumar
- [AMBER] implicit solvent model and charged chain Jorgen Simonsen
- Re: [AMBER] implicit solvent model and charged chain manoj singh
- [AMBER] prep file Andrei Neamtu
Wednesday, 29 September 2010
- Re: [AMBER] parameters of SEP and TPO can't match SEP TPO Anselm Horn
- Re: [AMBER] problem with MMPBSA juzer stationwala
- Re: [AMBER] ptraj, unit cell wrapping and velocities case
- Re: [AMBER] running pmemd fails case
- Re: [AMBER] missing parameters (dihe) in parm10.dat? Alan
- [AMBER] FW: Atom type assignment for formyl group Carter M.K.
- Re: [AMBER] Xplor_to_Amber case
- Re: [AMBER] implicit solvent model and charged chain case
- Re: [AMBER] prep file case
- Re: [AMBER] missing parameters (dihe) in parm10.dat? Jason Swails
- [AMBER] NMR refinement in explicite water Baptiste Legrand
- Re: [AMBER] Xplor_to_Amber Raman Parkesh
- [AMBER] tLeap memory leak Martin Brieg
- Re: [AMBER] tLeap memory leak Jason Swails
- Re: [AMBER] tLeap memory leak Jason Swails
- Re: [AMBER] Question on simulation Jiang Yusheng
- Re: [AMBER] Question on simulation Guoxiong Su
- Re: [AMBER] Xplor_to_Amber case
- Re: [AMBER] Question on simulation case
- Re: [AMBER] NMR refinement in explicite water Daniel Roe
- [AMBER] MMPBSA.py.MPI with MVAPICH2 Senthil Natesan
- Re: [AMBER] MMPBSA.py.MPI with MVAPICH2 Jason Swails
- Re: [AMBER] prep file Bill Ross
- Re: [AMBER] tLeap memory leak Bill Ross
- Re: [AMBER] MMPBSA.py.MPI with MVAPICH2 Senthil Natesan
- Re: [AMBER] Question on simulation Bill Ross
- Re: [AMBER] MMPBSA.py.MPI with MVAPICH2 Jason Swails
- Re: [AMBER] Question on simulation Jiang Yusheng
- [AMBER] leap for peptide with new residue Francesco Pietra
- [AMBER] vlimit exceeds nicholus bhattacharjee
- Re: [AMBER] vlimit exceeds Jason Swails
- Re: [AMBER] ptraj, unit cell wrapping and velocities Ben Roberts
- Re: [AMBER] Xplor_to_Amber Raman Parkesh
- Re: [AMBER] vlimit exceeds case
- Re: [AMBER] Xplor_to_Amber case
- Re: [AMBER] Missing atom types between leaprc.ff99SB and parm99.dat case
- Re: [AMBER] loop relaxation with les Carlos Simmerling
- Re: [AMBER] Xplor_to_Amber Raman Parkesh
- Re: [AMBER] rmsd of a subunit I w.r.t subunit II Thomas Cheatham III
- Re: [AMBER] cubic box Andrew Jewett
- Re: [AMBER] cubic box Bill Ross
- [AMBER] Cluster analysis ros
- Re: [AMBER] Cluster analysis Niel Henriksen
- Re: [AMBER] running pmemd fails Vijay Manickam Achari
Thursday, 30 September 2010
- [AMBER] TI-Problems Kirsten Heitmann
- [AMBER] spc/e water subrata paul
- [AMBER] bonded model xuemeiwang1103
- [AMBER] Incorrect handling of phenylalanine amide by antechamber Francesco Pietra
- [AMBER] Cu2+ parameters babak minoofar
- Re: [AMBER] missing parameters (dihe) in parm10.dat? Alan
- Re: [AMBER] prep file Andrei Neamtu
- Re: [AMBER] Incorrect handling of phenylalanine amide by antechamber case
- Re: [AMBER] tLeap memory leak Martin Brieg
- Re: [AMBER] NMR refinement in explicite water Baptiste Legrand
- Re: [AMBER] missing parameters (dihe) in parm10.dat? Alan
- Re: [AMBER] Cu2+ parameters ros
- Re: [AMBER] tLeap memory leak Jason Swails
- Re: [AMBER] MMPBSA.py.MPI with MVAPICH2 Senthil Natesan
- Re: [AMBER] running pmemd fails Daniel Roe
- Re: [AMBER] TI-Problems case
- Re: [AMBER] Incorrect handling of phenylalanine amide by antechamber Francesco Pietra
- Re: [AMBER] Cluster analysis ros
- Re: [AMBER] Incorrect handling of phenylalanine amide by antechamber case
- Re: [AMBER] MMPBSA.py.MPI with MVAPICH2 Jason Swails
- Re: [AMBER] Incorrect handling of phenylalanine amide by antechamber Francesco Pietra
- [AMBER] GBOBC cutoff distances David Tanner
- Re: [AMBER] tLeap memory leak Bill Ross
- Re: [AMBER] TI-Problems Kirsten Heitmann
- Re: [AMBER] NMR refinement in explicite water Daniel Roe
- Re: [AMBER] GBOBC cutoff distances Carlos Simmerling
- Re: [AMBER] pmemd.cuda error with group restraint Ross Walker

Last message date: Thu Sep 30 2010 - 18:00:03 PDT
Archived on: Wed Apr 24 2024 - 05:54:08 PDT

Amber Archive Sep 2010 by date