Amber Archive Aug 2010: by date

Saturday, 31 July 2010
- [AMBER] obtain a .pdb file from a .prepin/.frcmod file Ehsan Habibi
Sunday, 1 August 2010
- Re: [AMBER] Parallel pmemd.cuda: any preliminary cross-node tests? Thomas Zeiser
- Re: [AMBER] how to generate porcupine plot Jia Xu
- [AMBER] how to extract temperatur and other data from mdout setyanto tri wahyudi
- Re: [AMBER] A clear procedure to do WHAM based on the REMD simulations outputs Daniel Sindhikara
- Re: [AMBER] how to extract temperatur and other data from mdout Bill Ross
- [AMBER] error in heating rameshwar prajapati
- [AMBER] errror in heating rameshwar prajapati
- Re: [AMBER] error in heating Bill Ross
- Re: [AMBER] error in heating Bill Ross
- [AMBER] NVE Philippe Pinard
- Re: [AMBER] errror in heating Bill Ross
- Re: [AMBER] how to extract temperatur and other data from mdout setyanto tri wahyudi
- Re: [AMBER] errror in heating rameshwar prajapati
Monday, 2 August 2010
- [AMBER] Problem with running PMEMD on a cluster ali naserian nik
- Re: [AMBER] NVE steinbrt.rci.rutgers.edu
- Re: [AMBER] minimization segmentation fault Jorgen Simonsen
- [AMBER] Gradually Compress Volume to Increase Density Shubhra Gupta
- Re: [AMBER] Gradually Compress Volume to Increase Density Jason Swails
- Re: [AMBER] NVE Jason Swails
- Re: [AMBER] errror in heating Jason Swails
- Re: [AMBER] Gradually Compress Volume to Increase Density Shubhra Gupta
- Re: [AMBER] how to extract temperatur and other data from mdout Jason Swails
- Re: [AMBER] Gradually Compress Volume to Increase Density Jason Swails
- Re: [AMBER] Gradually Compress Volume to Increase Density Bill Ross
- Re: [AMBER] errror in heating Bill Ross
- [AMBER] Writing trajectory for C-alpha atoms Ibrahim Moustafa
- Re: [AMBER] Writing trajectory for C-alpha atoms Daniel Roe
- [AMBER] conversion of the CYANA upl into amber format: QE, QD of Tyr and Phe Francesca Cantini
- Re: [AMBER] minimization segmentation fault Bill Ross
- Re: [AMBER] how to extract temperatur and other data from mdout Bill Ross
- Re: [AMBER] Parallel pmemd.cuda: any preliminary cross-node tests? Scott Le Grand
- Re: [AMBER] Writing trajectory for C-alpha atoms Ibrahim Moustafa
- Re: [AMBER] Writing trajectory for C-alpha atoms Jason Swails
- [AMBER] restraining only heavy atoms in PMEMD Senthil Natesan
- Re: [AMBER] Writing trajectory for C-alpha atoms Bill Ross
- Re: [AMBER] Writing trajectory for C-alpha atoms Ibrahim Moustafa
- [AMBER] antechamber Philippe Pinard
- Re: [AMBER] Writing trajectory for C-alpha atoms Ibrahim Moustafa
- [AMBER] RDPARM Philippe Pinard
- Re: [AMBER] RDPARM Thomas Cheatham III
- Re: [AMBER] conversion of the CYANA upl into amber format: QE, QD of Tyr and Phe case
- [AMBER] Mistake in using amber Rilei Yu
- Re: [AMBER] Mistake in using amber Gustavo Seabra
- Re: [AMBER] Mistake in using amber Bill Ross
- Re: [AMBER] Mistake in using amber Rilei Yu
- Re: [AMBER] antechamber case
- Re: [AMBER] how to extract temperatur and other data from mdout setyanto tri wahyudi
- [AMBER] questions about installing pmend.cuda 宋德寿
- Re: [AMBER] questions about installing pmend.cuda maluyao
- Re: [AMBER] questions about installing pmend.cuda 宋德寿
- Re: [AMBER] questions about installing pmend.cuda 宋德寿
Tuesday, 3 August 2010
- Re: [AMBER] Mistake in using amber steinbrt.rci.rutgers.edu
- [AMBER] how to run entropy calculation using pmemd fancy2012
- [AMBER] ptraj and image Thomas Exner
- Re: [AMBER] No solvent overlap Thomas Exner
- Re: [AMBER] ptraj and image steinbrt.rci.rutgers.edu
- Re: [AMBER] questions about installing pmend.cuda Jason Swails
- Re: [AMBER] how to run entropy calculation using pmemd Jason Swails
- Re: [AMBER] how to run entropy calculation using pmemd fancy2012
- [AMBER] How to parametrize ligand using AMOEBA polarizable potential sunita gupta
- Re: [AMBER] questions about installing pmend.cuda 宋德寿
- Re: [AMBER] questions about installing pmend.cuda case
- [AMBER] PTRAJ: problem with image command Xioling Chuang
- Re: [AMBER] PTRAJ: problem with image command InSuk Joung
- Re: [AMBER] RDPARM Philippe Pinard
- Re: [AMBER] PTRAJ: problem with image command Xioling Chuang
- Re: [AMBER] PTRAJ: problem with image command InSuk Joung
- Re: [AMBER] questions about installing pmend.cuda Ross Walker
- Re: [AMBER] PTRAJ: problem with image command InSuk Joung
- [AMBER] Solid surface simulation in Amber - the recommended approach ? Marek Maly
- Re: [AMBER] Solid surface simulation in Amber Bill Ross
- Re: [AMBER] RDPARM Thomas Cheatham III
- Re: [AMBER] RDPARM Philippe Pinard
- Re: [AMBER] RDPARM Philippe Pinard
- Re: [AMBER] RDPARM Thomas Cheatham III
- Re: [AMBER] RDPARM case
- [AMBER] ptraj question Jia Xu
- Re: [AMBER] Solid surface simulation in Amber Marek Maly
- Re: [AMBER] Solid surface simulation in Amber Bill Ross
- Re: [AMBER] Solid surface simulation in Amber Bill Ross
- Re: [AMBER] Solid surface simulation in Amber Marek Maly
- Re: [AMBER] ptraj question Jason Swails
- Re: [AMBER] questions about installing pmend.cuda 宋德寿
- Re: [AMBER] questions about installing pmend.cuda 宋德寿
- Re: [AMBER] PTRAJ: problem with image command Xioling Chuang
- Re: [AMBER] Solid surface simulation in Amber Tom Williams
- [AMBER] How to define putative reaction coordinates in AMBER? Catein Catherine
- [AMBER] analysis of mm_pbsa Asfa Ali
Wednesday, 4 August 2010
- [AMBER] Error message in runing Steered MD in AMBER 10 (tutorial A10) Catein Catherine
- [AMBER] entropy calculation using nmode Asfa Ali
- Re: [AMBER] Solid surface simulation in Amber case
- Re: [AMBER] No solvent overlap case
- Re: [AMBER] How to define putative reaction coordinates in AMBER? Jason Swails
- Re: [AMBER] analysis of mm_pbsa Jason Swails
- [AMBER] simulation with multiple docked ligand Ashutosh Shandilya
- Re: [AMBER] simulation with multiple docked ligand steinbrt.rci.rutgers.edu
- Re: [AMBER] Error message in runing Steered MD in AMBER 10 (tutorial A10) Jason Swails
- Re: [AMBER] analysis of mm_pbsa Asfa Ali
- Re: [AMBER] analysis of mm_pbsa Jason Swails
- Re: [AMBER] analysis of mm_pbsa Asfa Ali
- Re: [AMBER] Solid surface simulation in Amber Marek Maly
- Re: [AMBER] Solid surface simulation in Amber Tom Williams
- Re: [AMBER] RDPARM Philippe Pinard
- [AMBER] Energy abrupt rise in Energy minimization Jiang Yusheng
- Re: [AMBER] Permission to post Admin processes? Marc Moreau
- Re: [AMBER] Energy abrupt rise in Energy minimization Bill Ross
- Re: [AMBER] Energy abrupt rise in Energy minimization Jiang Yusheng
- Re: [AMBER] Energy abrupt rise in Energy minimization Bill Ross
- Re: [AMBER] Energy abrupt rise in Energy minimization Jiang Yusheng
- Re: [AMBER] Energy abrupt rise in Energy minimization Bill Ross
- Re: [AMBER] RDPARM case
- Re: [AMBER] RDPARM Philippe Pinard
- Re: [AMBER] RDPARM case
- [AMBER] How to make parameter files of GTP from PDB file. kurisaki ikuo
- Re: [AMBER] How to make parameter files of GTP from PDB file. kurisaki ikuo
- [AMBER] Parallel pmemd.cuda: local bandwidth question. Are dual host PCI-E cards make any sense? Sasha Buzko
Thursday, 5 August 2010
- [AMBER] Parametrization of Ligand using AMOEBA potential sunita gupta
- Re: [AMBER] Energy abrupt rise in Energy minimization Jiang Yusheng
- Re: [AMBER] Parallel pmemd.cuda: local bandwidth question. Are dual host PCI-E cards make any sense? Ross Walker
- Re: [AMBER] Parametrization of Ligand using AMOEBA potential Dian Jiao
- Re: [AMBER] Parallel pmemd.cuda: local bandwidth question. Are dual host PCI-E cards make any sense? Scott Le Grand
- [AMBER] Tutorial3 George Tzotzos
- Re: [AMBER] Parallel pmemd.cuda: local bandwidth question. Are dual host PCI-E cards make any sense? Sasha Buzko
- Re: [AMBER] Parallel pmemd.cuda: local bandwidth question. Are dual host PCI-E cards make any sense? Scott Le Grand
- [AMBER] Tutorial3 George Tzotzos
- Re: [AMBER] How to make parameter files of GTP from PDB file. Bill Ross
- [AMBER] error message about memory in antechamber Guoxiong Su
- Re: [AMBER] error message about memory in antechamber case
- [AMBER] Post-processing error arikcohen
- Re: [AMBER] Parallel pmemd.cuda: local bandwidth question. Are dual host PCI-E cards make any sense? Ross Walker
- [AMBER] H-bonding analysis Asfa Ali
Friday, 6 August 2010
- [AMBER] Can I use LCOD command for umbrella sampling PMF calculation? Catein Catherine
- [AMBER] Can I convert the umberlla sampling results to LCOD for 1D-PMF analysis? Catein Catherine
- [AMBER] Error message when doing A10 tutorial (SMD with LCOD) with AMBER 10. Catein Catherine
- Re: [AMBER] Can I use LCOD command for umbrella sampling PMF calculation? Jason Swails
- Re: [AMBER] Can I convert the umberlla sampling results to LCOD for 1D-PMF analysis? Jason Swails
- Re: [AMBER] H-bonding analysis Bill Ross
- Re: [AMBER] Post-processing error - NO NEED TO ANSWER, PROBLEM SOLVED arikcohen
- Re: [AMBER] Post-processing error - NO NEED TO ANSWER, PROBLEM SOLVED Bill Ross
- Re: [AMBER] Post-processing error - NO NEED TO ANSWER, PROBLEM SOLVED arikcohen
- Re: [AMBER] Solid surface simulation in Amber - the recommended approach ? Marek Maly
Sunday, 8 August 2010
- [AMBER] peptides not folding in remd with changing sequence of D and L isomer Jorgen Simonsen
- [AMBER] dear sir selva raj
- Re: [AMBER] peptides not folding in remd with changing sequence of D and L isomer Jason Swails
- Re: [AMBER] dear sir Sushil Mishra
- Re: [AMBER] dear sir Sushil Mishra
- [AMBER] How to run LCOD in AMBER 10? Catein Catherine
- [AMBER] Where to apply find computer resources to run AMBER? Catein Catherine
- [AMBER] How can I run Random Acceleration Molecular Dynamics with AMBER10? Catein Catherine
- [AMBER] The Result of PARMCHK setyanto tri wahyudi
- Re: [AMBER] peptides not folding in remd with changing sequence of D and L isomer Daniel Sindhikara
Monday, 9 August 2010
- Re: [AMBER] peptides not folding in remd with changing sequence of D and L isomer Jorgen Simonsen
- [AMBER] Soft-core Coulomb potential Samuel Genheden
- [AMBER] error when compiling pmemd Jorgen Simonsen
- Re: [AMBER] peptides not folding in remd with changing sequence of D and L isomer Carlos Simmerling
- Re: [AMBER] peptides not folding in remd with changing sequence of D and L isomer Jorgen Simonsen
- Re: [AMBER] peptides not folding in remd with changing sequence of D and L isomer Carlos Simmerling
- Re: [AMBER] The Result of PARMCHK case
- Re: [AMBER] Soft-core Coulomb potential case
- Re: [AMBER] peptides not folding in remd with changing sequence of D and L isomer Jorgen Simonsen
- Re: [AMBER] error when compiling pmemd case
- Re: [AMBER] error when compiling pmemd Jorgen Simonsen
- Re: [AMBER] How can I run Random Acceleration Molecular Dynamics with AMBER10? Jason Swails
- Re: [AMBER] error when compiling pmemd Ross Walker
- Re: [AMBER] How to run LCOD in AMBER 10? Jason Swails
- Re: [AMBER] Where to apply find computer resources to run AMBER? Ross Walker
- Re: [AMBER] How can I run Random Acceleration Molecular Dynamics with AMBER10? Vlad Cojocaru
- [AMBER] question about empirical valence bond theory Ganesh Kamath
- Re: [AMBER] peptides not folding in remd with changing sequence of D and L isomer Carlos Simmerling
- Re: [AMBER] Where to apply find computer resources to run AMBER? Catein Catherine
- Re: [AMBER] How to run LCOD in AMBER 10? Catein Catherine
- [AMBER] using nab to create peptides and minimise Alan
- Re: [AMBER] using nab to create peptides and minimise case
- [AMBER] SASA over trajectory Beale, John
- Re: [AMBER] SASA over trajectory Carlos Simmerling
- Re: [AMBER] peptides not folding in remd with changing sequence of D and L isomer Jorgen Simonsen
- Re: [AMBER] peptides not folding in remd with changing sequence of D and L isomer Carlos Simmerling
- Re: [AMBER] How to run LCOD in AMBER 10? M. L. Dodson
- Re: [AMBER] error message about memory in antechamber Guoxiong Su
- Re: [AMBER] error when compiling pmemd Jorgen Simonsen
- Re: [AMBER] error message about memory in antechamber case
- [AMBER] Amber: saveamberparm error Karan Mehra
- Re: [AMBER] Amber: saveamberparm error Bill Ross
- Re: [AMBER] error when compiling pmemd Jason Swails
- Re: [AMBER] The Result of PARMCHK setyanto tri wahyudi
- [AMBER] Name for Glucosamine Shubhra Gupta
- Re: [AMBER] error when compiling pmemd Jorgen Simonsen
Tuesday, 10 August 2010
- [AMBER] AMBER ff02 r1 Neha Gandhi
- Re: [AMBER] The Result of PARMCHK case
- Re: [AMBER] Amber: saveamberparm error case
- Re: [AMBER] Name for Glucosamine Shubhra Gupta
- Re: [AMBER] error when compiling pmemd Jason Swails
- Re: [AMBER] Name for Glucosamine Lachele Foley (Lists)
- [AMBER] Resource for trying out various GPU setups with AMBER Ross Walker
- [AMBER] restrain group specification for GPU Qizhi Cui
- [AMBER] determining closest water molecules Beale, John
- Re: [AMBER] determining closest water molecules Thomas Cheatham III
- Re: [AMBER] restrain group specification for GPU Scott Le Grand
- Re: [AMBER] error when compiling pmemd Jorgen Simonsen
- Re: [AMBER] restrain group specification for GPU Bill Ross
- Re: [AMBER] restrain group specification for GPU Ross Walker
- Re: [AMBER] error when compiling pmemd Ross Walker
- Re: [AMBER] error when compiling pmemd Jorgen Simonsen
- Re: [AMBER] error when compiling pmemd Daniel Roe
- Re: [AMBER] error when compiling pmemd Ross Walker
- Re: [AMBER] error when compiling pmemd Jorgen Simonsen
- Re: [AMBER] error message about memory in antechamber Guoxiong Su
- Re: [AMBER] restrain group specification for GPU Qizhi Cui
- Re: [AMBER] restrain group specification for GPU Qizhi Cui
- [AMBER] simulation output for explicit and implicit model Yan Gao
- [AMBER] simulation output for explicit and implicit model--please disregard the previous message Yan Gao
- Re: [AMBER] simulation output for explicit and implicit model Jason Swails
- [AMBER] nonbond interactions Philippe Pinard
- Re: [AMBER] simulation output for explicit and implicit model--please disregard the previous message Bill Ross
- Re: [AMBER] restrain group specification for GPU Scott Le Grand
- Re: [AMBER] nonbond interactions Jason Swails
- [AMBER] BUG and FIX: pmemd crashes when vlimit exceeded Don.Bashford.stjude.org
- Re: [AMBER] BUG and FIX: pmemd crashes when vlimit exceeded Robert Duke
- [AMBER] How to change temperature in mm_pbsa.pl script pxq
Wednesday, 11 August 2010
- [AMBER] constant volume Jorgen Simonsen
- [AMBER] test $AMBERHOME/AmberTools/test/sqm/nma/Run: check_slko_files.x should be executable Alan
- [AMBER] How to define "generalized distance coordinate restraint" in AMBER10? Catein Catherine
- Re: [AMBER] test $AMBERHOME/AmberTools/test/sqm/nma/Run: check_slko_files.x should be executable Andreas Goetz
- Re: [AMBER] constant volume case
- Re: [AMBER] constant volume Andrew Purkiss-Trew
- Re: [AMBER] constant volume Jorgen Simonsen
- Re: [AMBER] constant volume Jorgen Simonsen
- Re: [AMBER] How to define "generalized distance coordinate restraint" in AMBER10? Jason Swails
- Re: [AMBER] How to change temperature in mm_pbsa.pl script Jason Swails
- Re: [AMBER] restrain group specification for GPU Scott Le Grand
- [AMBER] query on invoking ff99SB and ff99 Bala subramanian
- Re: [AMBER] query on invoking ff99SB and ff99 Jason Swails
- [AMBER] NMR refinement = increase in RMSD Andrew Olson
- Re: [AMBER] error message about memory in antechamber case
- Re: [AMBER] query on invoking ff99SB and ff99 case
- Re: [AMBER] query on invoking ff99SB and ff99 Bill Ross
- [AMBER] Horrific pmemd.cuda performance on an 8-GPU system Sasha Buzko
- Re: [AMBER] Amber: saveamberparm error Karan Mehra
- Re: [AMBER] Amber: saveamberparm error case
- Re: [AMBER] Horrific pmemd.cuda performance on an 8-GPU system Ross Walker
- [AMBER] drawing sphere in each frame and update Sun, Yufang
- Re: [AMBER] BUG and FIX: pmemd crashes when vlimit exceeded. . Don.Bashford.stjude.org
- Re: [AMBER] BUG and FIX: pmemd crashes when vlimit exceeded. . Jason Swails
- Re: [AMBER] Horrific pmemd.cuda performance on an 8-GPU system michael
- [AMBER] snapshots Philippe Pinard
- Re: [AMBER] snapshots arikcohen
- [AMBER] Ionic Strength Limits for MMPBSA Hopkins, Robert
- Re: [AMBER] snapshots Jason Swails
- [AMBER] Bug in MMPBSA.py.MPI Matthias Negri
- Re: [AMBER] Bug in MMPBSA.py.MPI Jason Swails
- Re: [AMBER] The Result of PARMCHK setyanto tri wahyudi
Thursday, 12 August 2010
- Re: [AMBER] drawing sphere in each frame and update steinbrt.rci.rutgers.edu
- Re: [AMBER] How to define "generalized distance coordinate restraint" in AMBER10? Catein Catherine
- Re: [AMBER] query on invoking ff99SB and ff99 Alan
- Re: [AMBER] How to define "generalized distance coordinate restraint" in AMBER10? Jason Swails
- Re: [AMBER] query on invoking ff99SB and ff99 case
- Re: [AMBER] query on invoking ff99SB and ff99 Alan
- Re: [AMBER] query on invoking ff99SB and ff99 case
- Re: [AMBER] BUG and FIX: pmemd crashes when vlimit exceeded. . Robert Duke
- Re: [AMBER] How to change temperature in mm_pbsa.pl script pxq
- [AMBER] How to change fillratio in mm_pbsa.pl pxq
- Re: [AMBER] How to change fillratio in mm_pbsa.pl Jason Swails
- Re: [AMBER] How to change temperature in mm_pbsa.pl script Bill Miller III
- Re: [AMBER] Horrific pmemd.cuda performance on an 8-GPU system Sasha Buzko
- Re: [AMBER] Installation_problem_Ambertools1.4_in Mac OSX Raman Parkesh
- Re: [AMBER] Installation_problem_Ambertools1.4_in Mac OSX Jason Swails
- Re: [AMBER] Installation_problem_Ambertools1.4_in Mac OSX Raman Parkesh
- Re: [AMBER] BUG and FIX: pmemd crashes when vlimit exceeded. .. . Don.Bashford.stjude.org
- Re: [AMBER] BUG and FIX: pmemd crashes when vlimit exceeded. .. . Jason Swails
- [AMBER] gbsa in pmemd Yi Xue
- Re: [AMBER] gbsa in pmemd Ross Walker
- [AMBER] How to define center of mass for two separate residues in the restraint file? Catein Catherine
- Re: [AMBER] How to define center of mass for two separate residues in the restraint file? Jason Swails
Friday, 13 August 2010
- [AMBER] mm_pbsa analysis failure Sangita Kachhap
- Re: [AMBER] NMR refinement = increase in RMSD case
- Re: [AMBER] mm_pbsa analysis failure Anselm Horn
- [AMBER] Query regarding radius of H atoms of TIP3 water model sunita gupta
- [AMBER] problem of NM calculations fancy2012
- [AMBER] makeCHIR_RST and proline Jorgen Simonsen
- Re: [AMBER] Query regarding radius of H atoms of TIP3 water model case
- [AMBER] Deleting bonds in sleap Ben Roberts
- Re: [AMBER] problem of NM calculations Jason Swails
- Re: [AMBER] Deleting bonds in sleap case
- Re: [AMBER] Deleting bonds in sleap Ben Roberts
- Re: [AMBER] Deleting bonds in sleap Andreas Goetz
- Re: [AMBER] Deleting bonds in sleap Bill Ross
- Re: [AMBER] Deleting bonds in sleap Ben Roberts
- Re: [AMBER] random number seed - range Hopkins, Robert
- Re: [AMBER] random number seed - range Robert Duke
- Re: [AMBER] random number seed - range Ross Walker
- Re: [AMBER] random number seed - range Paul S. Nerenberg
- Re: [AMBER] random number seed - range Robert Duke
- Re: [AMBER] random number seed - range Robert Duke
- Re: [AMBER] random number seed - range Ross Walker
- Re: [AMBER] random number seed - range Dean Cuebas
- Re: [AMBER] random number seed - range Ross Walker
- Re: [AMBER] random number seed - range Ross Walker
- Re: [AMBER] Deleting bonds in sleap Ben Roberts
Saturday, 14 August 2010
- Re: [AMBER] problem of NM calculations fancy2012
- Re: [AMBER] Deleting bonds in sleap case
- [AMBER] regarding random number generator Sangita Kachhap
- Re: [AMBER] regarding random number generator Ross Walker
- Re: [AMBER] regarding random number generator Sangita Kachhap
- [AMBER] How to include parmbsc0 force field in preparing prmtop/inpcrd files? Catein Catherine
- [AMBER] AmberTools and OS X John McGuigan
- Re: [AMBER] How to include parmbsc0 force field in preparing prmtop/inpcrd files? Paul S. Nerenberg
- Re: [AMBER] AmberTools and OS X Paul S. Nerenberg
Sunday, 15 August 2010
- Re: [AMBER] problem of NM calculations fancy2012
- Re: [AMBER] AmberTools and OS X John McGuigan
- [AMBER] How to identify water molecules at the interface ? Amor San Juan
- Re: [AMBER] How to include parmbsc0 force field in preparing prmtop/inpcrd files? Catein Catherine
- Re: [AMBER] How to identify water molecules at the interface ? follow up .... Amor San Juan
Monday, 16 August 2010
- [AMBER] protonate kamlesh sahu
- [AMBER] segmentation fault - ptrajin image familiar Jorgen Simonsen
- Re: [AMBER] segmentation fault - ptrajin image familiar manikanthan bhavaraju
- [AMBER] how to overcome the memory issues in mm-gbsa calculation for DS analysis? Catein Catherine
- Re: [AMBER] protonate case
- Re: [AMBER] segmentation fault - ptrajin image familiar case
- Re: [AMBER] segmentation fault - ptrajin image familiar Daniel Roe
- Re: [AMBER] How to identify water molecules at the interface ? Jason Swails
- Re: [AMBER] segmentation fault - ptrajin image familiar Jorgen Simonsen
- Re: [AMBER] How to identify water molecules at the interface ? follow up .... Jason Swails
- Re: [AMBER] segmentation fault - ptrajin image familiar Jason Swails
- [AMBER] Configure gnu P Bhattacharya
- Re: [AMBER] Configure gnu Daniel Roe
- Re: [AMBER] Configure gnu P Bhattacharya
- Re: [AMBER] protonate kamlesh sahu
- [AMBER] Unit for Van der Waals and Electrostatic Eq. Hector Chang
- Re: [AMBER] Unit for Van der Waals and Electrostatic Eq. Paul S. Nerenberg
- Re: [AMBER] Unit for Van der Waals and Electrostatic Eq. case
- Re: [AMBER] Unit for Van der Waals and Electrostatic Eq. Jason Swails
- [AMBER] Adding lambda points less than 0.1 and greater than 0.9 in TI calculations g t
- Re: [AMBER] Adding lambda points less than 0.1 and greater than 0.9 in TI calculations steinbrt.rci.rutgers.edu
- Re: [AMBER] Deleting bonds in sleap Ben Roberts
- [AMBER] single-point energy calculation on selected atoms Yi Xue
Tuesday, 17 August 2010
- [AMBER] Creating new topology file from close.mdcrd file Amor San Juan
- Re: [AMBER] Creating new topology file from close.mdcrd file : SOLUTION found Amor San Juan
- [AMBER] How to find the most important drug dissociation pathway theoretically? PMF? Catein Catherine
- [AMBER] Created a new atom named: H within residue: .R<NASP 1> Jorgen Simonsen
- Re: [AMBER] Creating new topology file from close.mdcrd file Jason Swails
- Re: [AMBER] How to find the most important drug dissociation pathway theoretically? PMF? Jason Swails
- Re: [AMBER] Created a new atom named: H within residue: .R<NASP 1> case
- [AMBER] Question about mdinfo file. Mayank Daga
- [AMBER] amber ：FAD parameters and RESP charge xqkong
- Re: [AMBER] Question about mdinfo file. Jason Swails
- Re: [AMBER] How to find the most important drug dissociation pathway theoretically? PMF? Catein Catherine
- Re: [AMBER] Question about mdinfo file. Robert Duke
- Re: [AMBER] Question about mdinfo file. Mayank Daga
- Re: [AMBER] Question about mdinfo file. Robert Duke
- Re: [AMBER] Question about mdinfo file. Jason Swails
- Re: [AMBER] How to find the most important drug dissociation pathway theoretically? PMF? Jason Swails
- Re: [AMBER] How to find the most important drug dissociation pathway theoretically? PMF? Daniel Sindhikara
- Re: [AMBER] Question about mdinfo file. Mayank Daga
- Re: [AMBER] Question about mdinfo file. Ross Walker
- Re: [AMBER] Question about mdinfo file. Ross Walker
- Re: [AMBER] Question about mdinfo file. Mayank Daga
- Re: [AMBER] Question about mdinfo file. Robert Duke
- Re: [AMBER] Question about mdinfo file. Robert Duke
- [AMBER] Double bonds ? Marek Maly
- Re: [AMBER] Question about mdinfo file. Ross Walker
- Re: [AMBER] How to find the most important drug dissociation pathway theoretically? PMF? Jason Swails
- Re: [AMBER] Question about mdinfo file. Mayank Daga
- Re: [AMBER] Question about mdinfo file. Ross Walker
- [AMBER] parmbsc0 Jason Swails
- Re: [AMBER] How to find the most important drug dissociation pathway theoretically? PMF? Balazs Jojart
- Re: [AMBER] Question about mdinfo file. Mayank Daga
- Re: [AMBER] Question about mdinfo file. Jason Swails
- [AMBER] Diffusion coefficient in PTRAJ. Hoshin Kim
- Re: [AMBER] Double bonds ? case
- Re: [AMBER] parmbsc0 case
- Re: [AMBER] entropy calculations MMPBSA.py.MPI Matthias Negri
- [AMBER] combination of CPU + GPU for Amber 11 CHAMI F.
- Re: [AMBER] combination of CPU + GPU for Amber 11 Ross Walker
- [AMBER] (no subject) xqkong
- [AMBER] Error in snader execution arikcohen
- Re: [AMBER] Error in snader execution Jason Swails
- [AMBER] Cut-off distance "in Closest" command of ptraj Amor San Juan
Wednesday, 18 August 2010
- Re: [AMBER] How to find the most important drug dissociation pathway theoretically? PMF? danglena1411.gmail.com
- [AMBER] MMPBSA Warnings George Tzotzos
- [AMBER] Defining restraint by distance Olotu Odunayo
- [AMBER] antechamber issue with gasteiger Alan
- Re: [AMBER] combination of CPU + GPU for Amber 11 CHAMI F.
- Re: [AMBER] combination of CPU + GPU for Amber 11 CHAMI F.
- Re: [AMBER] MMPBSA Warnings Bill Miller III
- Re: [AMBER] Double bonds ? Marek Maly
- Re: [AMBER] Cut-off distance "in Closest" command of ptraj Jason Swails
- Re: [AMBER] antechamber issue with gasteiger Jason Swails
- Re: [AMBER] MMPBSA Warnings Jason Swails
- Re: [AMBER] antechamber issue with gasteiger Alan
- Re: [AMBER] Error in snader execution arikcohen
Tuesday, 17 August 2010
- [AMBER] Calculating diffusion coefficient in PTRAJ Hoshin Kim
Wednesday, 18 August 2010
- [AMBER] Trivial syntax problem ? Marek Maly
- [AMBER] FAD parameters and RESP charge xqkong
- Re: [AMBER] FAD parameters and RESP charge Jason Swails
- Re: [AMBER] Trivial syntax problem ? case
- Re: [AMBER] FAD parameters and RESP charge xqkong
- [AMBER] How to define twist angle with DOC? Catein Catherine
- [AMBER] Extremely high activation energy was found for a PMF. Any potential source of errors? Catein Catherine
- [AMBER] MMPBSA.py error message. Wookyung Yu
- Re: [AMBER] MMPBSA.py error message. Jason Swails
- Re: [AMBER] Extremely high activation energy was found for a PMF. Any potential source of errors? Jason Swails
- [AMBER] restart reimage manikanthan bhavaraju
Thursday, 19 August 2010
- Re: [AMBER] Cut-off distance "in Closest" command of ptraj Amor San Juan
- [AMBER] O2'methyl RNA waleed zalloum
- Re: [AMBER] Cut-off distance "in Closest" command of ptraj Jason Swails
- Re: [AMBER] restart reimage Jason Swails
- Re: [AMBER] O2'methyl RNA Jason Swails
- Re: [AMBER] O2'methyl RNA waleed zalloum
- Re: [AMBER] O2'methyl RNA Jason Swails
- Re: [AMBER] Adding lambda points less than 0.1 and greater than 0.9 in TI calculations g t
- [AMBER] Unit for Van der Waals and Electrostatic Eq. Hector Chang
- Re: [AMBER] Unit for Van der Waals and Electrostatic Eq. Bill Ross
- [AMBER] Basic question: is protonation of receptor amino acid recidues needed for MD calculations? George Tzotzos
- Re: [AMBER] Basic question: is protonation of receptor amino acid recidues needed for MD calculations? Jason Swails
- Re: [AMBER] Basic question: is protonation of receptor amino acid recidues needed for MD calculations? Hegazy,Lamees
- Re: [AMBER] Trivial syntax problem ? Marek Maly
- [AMBER] MM-PBSA fails with a division by zero error Sasha Buzko
- [AMBER] Syntax for using RRES and LRES to turn on per residue decomposition (idecomp = 2) in a TI calculation g t
- Re: [AMBER] MM-PBSA fails with a division by zero error Jason Swails
- Re: [AMBER] Syntax for using RRES and LRES to turn on per residue decomposition (idecomp = 2) in a TI calculation Jason Swails
- Re: [AMBER] Syntax for using RRES and LRES to turn on per residue decomposition (idecomp = 2) in a TI calculation g t
- [AMBER] PBC arikcohen
Friday, 20 August 2010
- [AMBER] bond energy spikes in conjugent gradient minimization Vickie Roberts
- [AMBER] PTRAJ: closest & strip in one script or separate Amor San Juan
- [AMBER] How to run NED in amber10? PIMD or MPI or LES.MPI? Catein Catherine
- [AMBER] mm_pbsa failure Sangita Kachhap
- Re: [AMBER] PBC Jason Swails
- Re: [AMBER] bond energy spikes in conjugent gradient minimization case
- Re: [AMBER] bond energy spikes in conjugent gradient minimization Jason Swails
- Re: [AMBER] PTRAJ: closest & strip in one script or separate Jason Swails
- Re: [AMBER] How to run NED in amber10? PIMD or MPI or LES.MPI? Jason Swails
- [AMBER] sander.MPI error George Tzotzos
- Re: [AMBER] sander.MPI error case
- Re: [AMBER] O2'methyl RNA waleed zalloum
- Re: [AMBER] sander.MPI error George Tzotzos
- Re: [AMBER] sander.MPI error Jason Swails
- Re: [AMBER] How to run NED in amber10? PIMD or MPI or LES.MPI? Carlos Simmerling
- [AMBER] exchange probability in remd Lekpa Duukori
- Re: [AMBER] exchange probability in remd Carlos Simmerling
- Re: [AMBER] exchange probability in remd Lekpa Duukori
- [AMBER] too many titratable groups piotrek.vega.umcs.lublin.pl
- Re: [AMBER] too many titratable groups Jason Swails
- Re: [AMBER] PBC arikcohen
- Re: [AMBER] PBC Jason Swails
- [AMBER] Implicit Solvent Equation Hector Chang
- Re: [AMBER] PBC case
- [AMBER] About dipoles hong-bin Xie
- Re: [AMBER] PBC arikcohen
- Re: [AMBER] PBC arikcohen
- [AMBER] FEP help William Flak
- [AMBER] protein protein interaction manikanthan bhavaraju
Saturday, 21 August 2010
- Re: [AMBER] FEP help case
- Re: [AMBER] protein protein interaction case
- [AMBER] hydration status monica.imtech.res.in
- [AMBER] volume in a cavity Ganesh Kamath
Sunday, 22 August 2010
- [AMBER] questions for the different atom style and resp charge xqkong
- Re: [AMBER] questions for the different atom style and resp charge xqkong
- [AMBER] mm_pbsa ERROR Sangita Kachhap
- Re: [AMBER] Implicit Solvent Equation case
- Re: [AMBER] AMBER question Ross Walker
- [AMBER] Dipole moment in QM/MM hong-bin Xie
- Re: [AMBER] protein protein interaction manikanthan bhavaraju
- Re: [AMBER] protein protein interaction Carlos Simmerling
- Re: [AMBER] protein protein interaction manikanthan bhavaraju
- Re: [AMBER] protein protein interaction Carlos Simmerling
- [AMBER] entropies from nmode in MMPBSA Cristina Sisu
Monday, 23 August 2010
- Re: [AMBER] questions for the different atom style and resp charge FyD
- [AMBER] Equilibration M. Reza Ganjalikhany
- [AMBER] how we increase the number of sugar molecule in a system subrata paul
- Re: [AMBER] how we increase the number of sugar molecule in a system Sushil Mishra
- [AMBER] Dipole moment calculation from ptraj Siddharth Rastogi
- Re: [AMBER] how we increase the number of sugar molecule in a system subrata paul
- [AMBER] Interaction energy_mm_pbsa moitrayee.mbu.iisc.ernet.in
- Re: [AMBER] entropies from nmode in MMPBSA Bill Miller III
- [AMBER] amber11: Applying restraint weights George Tzotzos
- Re: [AMBER] Interaction energy_mm_pbsa Bill Miller III
- [AMBER] ptraj "closest" Amor San Juan
- Re: [AMBER] entropies from nmode in MMPBSA Cristina Sisu
- Re: [AMBER] Interaction energy_mm_pbsa moitrayee.mbu.iisc.ernet.in
- Re: [AMBER] Interaction energy_mm_pbsa Bill Miller III
- Re: [AMBER] amber11: Applying restraint weights Carlos Simmerling
- Re: [AMBER] Interaction energy_mm_pbsa moitrayee.mbu.iisc.ernet.in
- [AMBER] [Fwd: Re: Interaction energy_mm_pbsa] moitrayee.mbu.iisc.ernet.in
- Re: [AMBER] [Fwd: Re: Interaction energy_mm_pbsa] Bill Miller III
- Re: [AMBER] [Fwd: Re: Interaction energy_mm_pbsa] moitrayee.mbu.iisc.ernet.in
- Re: [AMBER] Dipole moment calculation from ptraj case
- Re: [AMBER] amber11: Applying restraint weights case
- Re: [AMBER] [Fwd: Re: Interaction energy_mm_pbsa] Jason Swails
- Re: [AMBER] ptraj "closest" Daniel Roe
- Re: [AMBER] Equilibration Gustavo Seabra
- Re: [AMBER] questions for the different atom style and resp charge xqkong
- [AMBER] slowly releasing restraint_wt force Sangita Kachhap
- Re: [AMBER] About dipoles Ross Walker
- Re: [AMBER] About dipoles hong-bin Xie
- Re: [AMBER] About dipoles Ross Walker
- Re: [AMBER] About dipoles hong-bin Xie
- [AMBER] calculation of volume of active site Ganesh Kamath
- [AMBER] ACS Division of Computers in Chemistry: award applications due October 15 Carlos Simmerling
- Re: [AMBER] calculation of volume of active site Jia Xu
- Re: [AMBER] ACS Division of Computers in Chemistry: award applications due October 15 Carlos Simmerling
- Re: [AMBER] calculation of volume of active site Peter Schmidtke
- Re: [AMBER] calculation of volume of active site Ganesh Kamath
- Re: [AMBER] ACS Division of Computers in Chemistry: award applications due October 15 Carlos Simmerling
- Re: [AMBER] ACS Division of Computers in Chemistry: award applications due October 15 Dima A Sabbah
- Re: [AMBER] About dipoles Ross Walker
- Re: [AMBER] About dipoles Adrian Roitberg
- [AMBER] Installing Amber9 on Ubuntu platform Arun Gupta
- Re: [AMBER] About dipoles Ross Walker
- Re: [AMBER] questions for the different atom style and resp charge FyD
- Re: [AMBER] Installing Amber9 on Ubuntu platform Jason Swails
- Re: [AMBER] Installing Amber9 on Ubuntu platform Bill Ross
- Re: [AMBER] Installing Amber9 on Ubuntu platform case
- Re: [AMBER] Equilibration M. Reza Ganjalikhany
- Re: [AMBER] Equilibration manikanthan bhavaraju
- [AMBER] Problem: ambertool1.2 mopac is ok for my molecules, but ambertool1.4 sqm fails Shulin Zhuang
- Re: [AMBER] Problem: ambertool1.2 mopac is ok for my molecules, but ambertool1.4 sqm fails Gustavo Seabra
- Re: [AMBER] Problem: ambertool1.2 mopac is ok for my molecules, but ambertool1.4 sqm fails Shulin Zhuang
- [AMBER] solvateBox - what is the suitable value for distance? colvin
- Re: [AMBER] Equilibration Gustavo Seabra
- Re: [AMBER] questions for the different atom style and resp charge xqkong
- [AMBER] Running AMBER on a GPU Cluster. Mayank Daga
- Re: [AMBER] questions for the different atom style and resp charge xqkong
- [AMBER] flying out William Flak
- Re: [AMBER] flying out manikanthan bhavaraju
- [AMBER] acceptance ration in rem.log Toshifumi Yui
- [AMBER] Quantifying Hydrophobic interaction aneesh cna
- Re: [AMBER] questions for the different atom style and resp charge FyD
- Re: [AMBER] questions for the different atom style and resp charge xqkong
Tuesday, 24 August 2010
- Re: [AMBER] Equilibration M. Reza Ganjalikhany
- [AMBER] loading MG.off (./MG.off is not a valid database) Ehsan Habibi
- Re: [AMBER] [Fwd: Re: Interaction energy_mm_pbsa] moitrayee.mbu.iisc.ernet.in
- Re: [AMBER] calculation of volume of active site Peter Schmidtke
- [AMBER] Packmol file cannot minimized setyanto tri wahyudi
- Re: [AMBER] Problem: ambertool1.2 mopac is ok for my molecules, but ambertool1.4 sqm fails case
- Re: [AMBER] flying out case
- Re: [AMBER] Quantifying Hydrophobic interaction case
- Re: [AMBER] ptraj "closest" Amor San Juan
- Re: [AMBER] loading MG.off (./MG.off is not a valid database) case
- Re: [AMBER] Packmol file cannot minimized Jason Swails
- Re: [AMBER] Packmol file cannot minimized case
- [AMBER] MMPBSA.py indexError Amor San Juan
- Re: [AMBER] MMPBSA.py indexError Bill Miller III
- Re: [AMBER] MMPBSA.py indexError Jason Swails
- Re: [AMBER] Problem: ambertool1.2 mopac is ok for my molecules, but ambertool1.4 sqm fails Shulin Zhuang
- Re: [AMBER] acceptance ration in rem.log Carlos Simmerling
- [AMBER] Dipole moment calculation from ptraj v.satish.iitg.ernet.in
- Re: [AMBER] Quantifying Hydrophobic interaction aneesh cna
- Re: [AMBER] Equilibration Gustavo Seabra
- Re: [AMBER] antechamber issue with gasteiger Alan
- Re: [AMBER] antechamber issue with gasteiger Jason Swails
- Re: [AMBER] Quantifying Hydrophobic interaction case
- Re: [AMBER] solvateBox - what is the suitable value for distance? case
- Re: [AMBER] solvateBox - what is the suitable value for distance? Brent Krueger
- Re: [AMBER] Running AMBER on a GPU Cluster. Sasha Buzko
- Re: [AMBER] Running AMBER on a GPU Cluster. Ross Walker
- Re: [AMBER] Running AMBER on a GPU Cluster. Mayank Daga
- Re: [AMBER] questions for the different atom style and resp charge FyD
- [AMBER] question on improper dihedrals Jason Swails
- Re: [AMBER] question on improper dihedrals case
- Re: [AMBER] question on improper dihedrals Jason Swails
- [AMBER] simulation of a restrained protein fragment + pmemd.cuda issues Sasha Buzko
- [AMBER] average structre William Flak
- [AMBER] Tutorial 3: MM-PBSA George Tzotzos
- [AMBER] To obtain academic license of AMBER 11 program package sonali dhindwal
Wednesday, 25 August 2010
- [AMBER] how we increase the number of sugar molecule in a system subrata paul
- Re: [AMBER] MMPBSA.py indexError Amor San Juan
- [AMBER] MMPBSA.py nmode Amor San Juan
- Re: [AMBER] questions for the different atom style and resp charge xqkong
- [AMBER] Water deeply buried for MMPBSA calculations Amor San Juan
- Re: [AMBER] MMPBSA.py nmode Bill Miller III
- Re: [AMBER] Water deeply buried for MMPBSA calculations Jason Swails
- Re: [AMBER] Tutorial 3: MM-PBSA Jason Swails
- Re: [AMBER] how we increase the number of sugar molecule in a system Lachele Foley (Lists)
- Re: [AMBER] Dipole moment calculation from ptraj Thomas Cheatham III
- Re: [AMBER] simulation of a restrained protein fragment + pmemd.cuda issues Ross Walker
- [AMBER] Enthalpy estimate Lekpa Duukori
- Re: [AMBER] Workaround for gfortran-4.1.2? Richard Owczarzy
- [AMBER] Parameter extraction arikcohen
- Re: [AMBER] Parameter extraction Jason Swails
- Re: [AMBER] Workaround for gfortran-4.1.2? Jason Swails
- Re: [AMBER] Enthalpy estimate Jason Swails
- Re: [AMBER] Enthalpy estimate Lekpa Duukori
- Re: [AMBER] Parameter extraction arikcohen
- Re: [AMBER] Workaround for gfortran-4.1.2? Lachele Foley (Lists)
- Re: [AMBER] Workaround for gfortran-4.1.2? Marc Moreau
Thursday, 26 August 2010
- Re: [AMBER] Packmol file cannot minimized setyanto tri wahyudi
- Re: [AMBER] how we increase the number of sugar molecule in a system subrata paul
- Re: [AMBER] simulation of a restrained protein fragment +pmemd.cuda issues Paul Mortenson
- Re: [AMBER] MMPBSA.py nmode Amor San Juan
- [AMBER] To obtain academic license of AMBER 11 program package sonali dhindwal
- Re: [AMBER] MMPBSA.py nmode Bill Miller III
- Re: [AMBER] Water deeply buried for MMPBSA calculations Amor San Juan
- Re: [AMBER] MMPBSA.py nmode Amor San Juan
- Re: [AMBER] MMPBSA.py nmode Bill Miller III
- Re: [AMBER] Packmol file cannot minimized case
- Re: [AMBER] how we increase the number of sugar molecule in a system case
- Re: [AMBER] simulation of a restrained protein fragment +pmemd.cuda issues Ross Walker
- Re: [AMBER] To obtain academic license of AMBER 11 program package case
- Re: [AMBER] Enthalpy estimate case
- Re: [AMBER] Packmol file cannot minimized Jason Swails
- Re: [AMBER] To obtain academic license of AMBER 11 program package sonali dhindwal
- Re: [AMBER] how we increase the number of sugar molecule in a system ros
- [AMBER] Antechamber issue P Bhattacharya
- Re: [AMBER] how we increase the number of sugar molecule in a system Lachele Foley (Lists)
- Re: [AMBER] Antechamber issue case
- [AMBER] dipole moment of molecule of trans and cis azobenzene ? Chih-Ying Lin
- Re: [AMBER] how we increase the number of sugar molecule in a system FyD
- [AMBER] vlimit and shake manikanthan bhavaraju
- Re: [AMBER] vlimit and shake manikanthan bhavaraju
- Re: [AMBER] Antechamber issue P Bhattacharya
- Re: [AMBER] Antechamber issue Jason Swails
- [AMBER] ptraj help William Flak
- [AMBER] cuda lauch time out error in Amber 11 Sergio R Aragon
- Re: [AMBER] cuda lauch time out error in Amber 11 Sasha Buzko
- Re: [AMBER] ptraj help Jason Swails
- Re: [AMBER] cuda lauch time out error in Amber 11 Sergio R Aragon
- Re: [AMBER] cuda lauch time out error in Amber 11 Sasha Buzko
- Re: [AMBER] cuda lauch time out error in Amber 11 Scott Le Grand
- Re: [AMBER] cuda lauch time out error in Amber 11 Scott Le Grand
- Re: [AMBER] vlimit and shake Jason Swails
- Re: [AMBER] vlimit and shake manikanthan bhavaraju
- Re: [AMBER] ptraj help William Flak
- Re: [AMBER] vlimit and shake Daniel Roe
- Re: [AMBER] cuda launch time out error in Amber 11 Sergio R Aragon
Friday, 27 August 2010
- [AMBER] error in mmpbsa Asfa Ali
- Re: [AMBER] error in mmpbsa Amor San Juan
- Re: [AMBER] error in mmpbsa Asfa Ali
- Re: [AMBER] cuda lauch time out error in Amber 11 Ross Walker
- Re: [AMBER] cuda lauch time out error in Amber 11 Ross Walker
- Re: [AMBER] cuda launch time out error in Amber 11 Ross Walker
- [AMBER] very slow work of ptraj on cluster Andrew Voronkov
- Re: [AMBER] error in mmpbsa Ray Luo
- Re: [AMBER] cuda launch time out error in Amber 11 Sasha Buzko
- Re: [AMBER] cuda launch time out error in Amber 11 Sergio R Aragon
- [AMBER] Latest Na+ and Cl- ion parameters Ilyas Yildirim
- Re: [AMBER] very slow work of ptraj on cluster Daniel Roe
- Re: [AMBER] Latest Na+ and Cl- ion parameters Dean Cuebas
- Re: [AMBER] Antechamber issue P Bhattacharya
- Re: [AMBER] Antechamber issue case
- Re: [AMBER] cuda launch time out error in Amber 11 Scott Le Grand
- Re: [AMBER] cuda launch time out error in Amber 11 Sergio R Aragon
Saturday, 28 August 2010
- [AMBER] Binary trajectory format in Amber8 Anselm Horn
- Re: [AMBER] very slow work of ptraj on cluster Andrew Voronkov
- Re: [AMBER] very slow work of ptraj on cluster Daniel Roe
- [AMBER] force field parameters for ionic liquids Ganesh Kamath
- Re: [AMBER] Binary trajectory format in Amber8 case
- Re: [AMBER] Binary trajectory format in Amber8 Anselm Horn
- Re: [AMBER] very slow work of ptraj on cluster Andrew Voronkov
- Re: [AMBER] very slow work of ptraj on cluster Daniel Roe
- [AMBER] FEP with EP William Flak
Sunday, 29 August 2010
- [AMBER] ERROR: Bond: Maximum coordination exceededon .R<Ca2 193>.A<Ca1> Majid Taghdir
- Re: [AMBER] ERROR: Bond: Maximum coordination exceededon .R<Ca2 193>.A<Ca1> Jason Swails
- [AMBER] How to define an unbiased reaction coordinate for potential of mean force calculations? Catein Catherine
Monday, 30 August 2010
- [AMBER] Is there any training program in Europe in the future? albert
- [AMBER] Regarding protein diffusion aneesh cna
- Re: [AMBER] very slow work of ptraj on cluster Andrew Voronkov
- Re: [AMBER] ERROR: Bond: Maximum coordination exceededon .R<Ca2 193>.A<Ca1> Jason Swails
- Re: [AMBER] ERROR: Bond: Maximum coordination exceededon .R<Ca2 193>.A<Ca1> Majid Taghdir
- [AMBER] RE : Regarding protein diffusion ABEL Stephane 175950
- Re: [AMBER] ERROR: Bond: Maximum coordination exceededon .R<Ca2 193>.A<Ca1> Jason Swails
- [AMBER] Free energy using MMPBSA shenna shearin
- [AMBER] parameters for ionic liquids Ganesh Kamath
- [AMBER] How to calculate the equilbrium constant for a protein-drug binding reaction Catein Catherine
- Re: [AMBER] ERROR: Bond: Maximum coordination exceededon .R<Ca2 193>.A<Ca1> Majid Taghdir
- Re: [AMBER] Free energy using MMPBSA Bill Miller III
- Re: [AMBER] Free energy using MMPBSA Jason Swails
- [AMBER] amber11: segmentation fault error George Tzotzos
- Re: [AMBER] Antechamber issue P Bhattacharya
- Re: [AMBER] How to calculate the equilbrium constant for a protein-drug binding reaction Jason Swails
- Re: [AMBER] amber11: segmentation fault error Jason Swails
- Re: [AMBER] Antechamber issue Jason Swails
- Re: [AMBER] Antechamber issue P Bhattacharya
- [AMBER] the modified Bondi radii zhihong ke
- Re: [AMBER] the modified Bondi radii Jason Swails
- Re: [AMBER] the modified Bondi radii zhihong ke
- [AMBER] How to solvate a molecule in a water spherocylinder in leap? Guoxiong Su
- Re: [AMBER] Antechamber issue P Bhattacharya
- Re: [AMBER] Antechamber issue David A. Case
- Re: [AMBER] How to solvate a molecule in a water spherocylinder in leap? David A. Case
- Re: [AMBER] the modified Bondi radii Jason Swails
- [AMBER] pmemd installation problem Carra, Claudio (JSC-SK)[Universities Space Research Association]
- [AMBER] addions2 function missing from sleap Ben Roberts
- [AMBER] Another missing sleap command: check Ben Roberts
- [AMBER] addions causes "assertion failed" in sleap Ben Roberts
- Re: [AMBER] pmemd installation problem Jason Swails
Tuesday, 31 August 2010
- [AMBER] Amber9 compilation/Westmere platform eric henon
- Re: [AMBER] pmemd installation problem Ross Walker
- [AMBER] MMPBSA.py: minimization issue with nmode Nicolas SAPAY
- Re: [AMBER] MMPBSA.py: minimization issue with nmode Bill Miller III
- Re: [AMBER] the modified Bondi radii Asfa Ali
- Re: [AMBER] MMPBSA.py: minimization issue with nmode Jason Swails
- Re: [AMBER] MMPBSA.py: minimization issue with nmode Jason Swails
- Re: [AMBER] Amber9 compilation/Westmere platform Jason Swails
- Re: [AMBER] MMPBSA.py: minimization issue with nmode Nicolas SAPAY
- Re: [AMBER] MMPBSA.py: minimization issue with nmode Nicolas SAPAY
- [AMBER] regarding trap simulation Jorgen Simonsen
- Re: [AMBER] regarding trap simulation Jason Swails
- Re: [AMBER] addions causes "assertion failed" in sleap Jason Swails
- [AMBER] Amber9 compilation/Westmere platform eric henon
- Re: [AMBER] regarding trap simulation Jorgen Simonsen
- Re: [AMBER] regarding trap simulation Jason Swails
- Re: [AMBER] How to solvate a molecule in a water spherocylinder in leap? Guoxiong Su
- Re: [AMBER] Another missing sleap command: check Ben Roberts
- [AMBER] phenylalanine amide Francesco Pietra
- Re: [AMBER] phenylalanine amide Paul S. Nerenberg
- Re: [AMBER] phenylalanine amide Francesco Pietra
- Re: [AMBER] phenylalanine amide Paul S. Nerenberg
- Re: [AMBER] phenylalanine amide Francesco Pietra
- Re: [AMBER] pmemd installation problem Carra, Claudio (JSC-SK)[Universities Space Research Association]
- [AMBER] Residue name problem in PTRAJ Hoshin Kim
- [AMBER] MD and LES Computational Chemist

Last message date: Tue Aug 31 2010 - 23:30:03 PDT
Archived on: Mon Apr 22 2024 - 05:54:01 PDT

Amber Archive Aug 2010 by date