Amber Archive Apr 2012: by date

Saturday, 31 March 2012
- [AMBER] How to set VMD_PLUGIN_PATH ? (in order to analysis mdcrd by GROMACS directly) Catein Catherine
Sunday, 1 April 2012
- [AMBER] Can anyone point out whether my ambertools and amber test failures are significant Acoot Brett
- Re: [AMBER] How to set VMD_PLUGIN_PATH ? (in order to analysis mdcrd by GROMACS directly) Jason Swails
- Re: [AMBER] Can anyone point out whether my ambertools and amber test failures are significant Jason Swails
- Re: [AMBER] rfree: Error decoding variable 1 3 from: Elisa Frezza
- Re: [AMBER] rfree: Error decoding variable 1 3 from: Jason Swails
- Re: [AMBER] rfree: Error decoding variable 1 3 from: Elisa Frezza
- Re: [AMBER] rfree: Error decoding variable 1 3 from: Jason Swails
- Re: [AMBER] rfree: Error decoding variable 1 3 from: Elisa Frezza
- Re: [AMBER] rfree: Error decoding variable 1 3 from: Elisa Frezza
- Re: [AMBER] test failure in the AMBERTOOL installation Ben Roberts
- Re: [AMBER] rfree: Error decoding variable 1 3 from: Niel Henriksen
- Re: [AMBER] rfree: Error decoding variable 1 3 from: Jason Swails
- Re: [AMBER] rfree: Error decoding variable 1 3 from: Niel Henriksen
- [AMBER] debug energy into individual atoms Jorgen Simonsen
- [AMBER] a question related to force field Acoot Brett
- Re: [AMBER] a question related to force field Carlos Simmerling
- Re: [AMBER] a question related to force field Ben Roberts
- Re: [AMBER] a question related to force field M. L. Dodson
- Re: [AMBER] a question related to force field Acoot Brett
- [AMBER] generating non-standard residue ashwini gupta
- Re: [AMBER] a question related to force field FyD
- Re: [AMBER] generating non-standard residue FyD
- [AMBER] error in making prmtop & inpcrd for ligand-protein complex Aditya Setiajid
Monday, 2 April 2012
- Re: [AMBER] Problem in Amber installation setyanto md
- Re: [AMBER] Asking About Differences between amber force field ff10 and ff03 setyanto md
- [AMBER] MM-PBSA Question Hoshin Kim
- [AMBER] Error: unspecified launch failure launching kernel kReduceForces Giovanni Pavan
- [AMBER] AmberTools-1.5 installation problems Genzo Tanaka
- [AMBER] Exporting and Boxing Amber Trajectories by Frame Adam Jion
- Re: [AMBER] error in making prmtop & inpcrd for ligand-protein complex David A Case
- Re: [AMBER] Asking About Differences between amber force field ff10 and ff03 David A Case
- Re: [AMBER] AmberTools-1.5 installation problems David A Case
- Re: [AMBER] Exporting and Boxing Amber Trajectories by Frame Jason Swails
- Re: [AMBER] error in making prmtop & inpcrd for ligand-protein complex Aditya Setiajid
- Re: [AMBER] Error: unspecified launch failure launching kernel kReduceForces Aron Broom
- Re: [AMBER] error in making prmtop & inpcrd for ligand-protein complex steinbrt.rci.rutgers.edu
- Re: [AMBER] ptraj removes my ligands denilson.dqi.ufla.br
- [AMBER] R: Error: unspecified launch failure launching kernel kReduceForces Giovanni Pavan
- Re: [AMBER] Error: unspecified launch failure launching kernel kReduceForces Ross Walker
- Re: [AMBER] Error: unspecified launch failure launching kernel kReduceForces Aron Broom
- Re: [AMBER] Error: unspecified launch failure launching kernel kReduceForces Ross Walker
- Re: [AMBER] Error: unspecified launch failure launching kernel kReduceForces Aron Broom
- [AMBER] Use of PCASuite in analyzing DNA-MD trajectories Muhammad Khaled Tumbi
- [AMBER] metal site Per Jr. Greisen
- Re: [AMBER] AmberTools-1.5 installation problems Genzo Tanaka
- Re: [AMBER] AmberTools-1.5 installation problems case
- [AMBER] Setting the cut-off and size of box Pengzhi
- [AMBER] Amber GPU test fails Mohammad Ashraf Bhuiyan
- Re: [AMBER] Setting the cut-off and size of box case
- Re: [AMBER] error in making prmtop & inpcrd for ligand-protein complex Aditya Setiajid
- Re: [AMBER] Setting the cut-off and size of box Pengzhi
- Re: [AMBER] error in making prmtop & inpcrd for ligand-protein complex Jason Swails
- Re: [AMBER] metal site Jason Swails
- Re: [AMBER] Amber GPU test fails Jason Swails
- [AMBER] on my AMBER AND AMBERTOOLS installation test failures Acoot Brett
- Re: [AMBER] Amber GPU test fails Ross Walker
- [AMBER] how where to read the amber and amber test failure diff files Acoot Brett
- [AMBER] on "-v" in mdrun Acoot Brett
- Re: [AMBER] Use of PCASuite in analyzing DNA-MD trajectories francesco oteri
Tuesday, 3 April 2012
- Re: [AMBER] metal site FyD
- [AMBER] "Possible Failures" in Amber 11 and Amber tools tests Dureid El-Moghraby
- [AMBER] Inconsistent Internal energy from monomer to dimer Josep Maria Campanera Alsina
- Re: [AMBER] Inconsistent Internal energy from monomer to dimer Carlos Simmerling
- Re: [AMBER] Large Energy Jump in TMD simulation - Regarding Carlos Simmerling
- [AMBER] RE GPU test fails Mohammad Ashraf Bhuiyan
- Re: [AMBER] RE GPU test fails Ross Walker
- Re: [AMBER] GPU test fails Mohammad Ashraf Bhuiyan
- Re: [AMBER] GPU test fails Ross Walker
- [AMBER] error with chamber Albert
- Re: [AMBER] error with chamber Crowley, Michael
- Re: [AMBER] error with chamber Albert
- Re: [AMBER] error with chamber Crowley, Michael
- Re: [AMBER] error with chamber Albert
- Re: [AMBER] error with chamber Crowley, Michael
- Re: [AMBER] error with chamber Albert
- Re: [AMBER] error with chamber Crowley, Michael
- Re: [AMBER] error with chamber Joshua Adelman
- Re: [AMBER] Particles moving outside of simulation box for pmemd.cuda.mpi Ross Walker
- Re: [AMBER] Setting the cut-off and size of box case
Wednesday, 4 April 2012
- Re: [AMBER] Particles moving outside of simulation box for pmemd.cuda.mpi Adam Jion
- Re: [AMBER] Inconsistent Internal energy from monomer to dimer Josep Maria Campanera Alsina
- Re: [AMBER] Inconsistent Internal energy from monomer to dimer Carlos Simmerling
- Re: [AMBER] Large Energy Jump in TMD simulation - Regarding Fredrick Devadoss
- Re: [AMBER] Large Energy Jump in TMD simulation - Regarding Carlos Simmerling
- Re: [AMBER] Large Energy Jump in TMD simulation - Regarding Fredrick Devadoss
- Re: [AMBER] Large Energy Jump in TMD simulation - Regarding Carlos Simmerling
- Re: [AMBER] Large Energy Jump in TMD simulation - Regarding Fredrick Devadoss
- [AMBER] distance dependent dielectric constant kanika sharma
- Re: [AMBER] distance dependent dielectric constant David A Case
- Re: [AMBER] Particles moving outside of simulation box for pmemd.cuda.mpi David A Case
- [AMBER] Announcement: release of Amber12 and AmberTools12 David A Case
- Re: [AMBER] Inconsistent Internal energy from monomer to dimer Jason Swails
- Re: [AMBER] Large Energy Jump in TMD simulation - Regarding Carlos Simmerling
- [AMBER] close PME in AMBER 10 Qian Wang
- Re: [AMBER] close PME in AMBER 10 Jason Swails
- [AMBER] AMBERHOME is not recognized by ./configure Genzo Tanaka
- Re: [AMBER] AMBERHOME is not recognized by ./configure Ben Roberts
- [AMBER] Fwd: error in making prmtop & inpcrd for ligand-protein complex Muhammad Aditya Setiajid
- Re: [AMBER] AMBERHOME is not recognized by ./configure Jason Swails
- Re: [AMBER] Fwd: error in making prmtop & inpcrd for ligand-protein complex Jason Swails
- [AMBER] distance dependent dielectric constant kanika sharma
Thursday, 5 April 2012
- Re: [AMBER] rfree: Error decoding variable 1 3 from: Elisa Frezza
- [AMBER] on the protonation of the HIS, etc Acoot Brett
- Re: [AMBER] Inconsistent Internal energy from monomer to dimer Josep Maria Campanera Alsina
- Re: [AMBER] on the protonation of the HIS, etc Marc van der Kamp
- [AMBER] ion parameters in simulations with nucleic acids Vlad Cojocaru
- Re: [AMBER] distance dependent dielectric constant David A Case
- [AMBER] using both the ILDN and NMR-based modifications of ff99SB Vlad Cojocaru
- [AMBER] Odd coordinate writing problem in pmemd.MPI steinbrt.rci.rutgers.edu
- [AMBER] how to add a electric field? Xianwei Wang
- [AMBER] cygwin xleap cannot open display Acoot Brett
- Re: [AMBER] using both the ILDN and NMR-based modifications of ff99SB David A Case
- Re: [AMBER] Odd coordinate writing problem in pmemd.MPI David A Case
- Re: [AMBER] using both the ILDN and NMR-based modifications of ff99SB Vlad Cojocaru
- Re: [AMBER] cygwin xleap cannot open display David A Case
- Re: [AMBER] Odd coordinate writing problem in pmemd.MPI David A Case
- Re: [AMBER] Odd coordinate writing problem in pmemd.MPI Aron Broom
- Re: [AMBER] Inconsistent Internal energy from monomer to dimer Carlos Simmerling
- Re: [AMBER] rfree: Error decoding variable 1 3 from: Niel Henriksen
- Re: [AMBER] Odd coordinate writing problem in pmemd.MPI steinbrt.rci.rutgers.edu
- Re: [AMBER] Odd coordinate writing problem in pmemd.MPI Aron Broom
- Re: [AMBER] using both the ILDN and NMR-based modifications of ff99SB Carlos Simmerling
- Re: [AMBER] Odd coordinate writing problem in pmemd.MPI Ross Walker
- Re: [AMBER] Odd coordinate writing problem in pmemd.MPI steinbrt.rci.rutgers.edu
- Re: [AMBER] AMBERHOME is not recognized by ./configure Genzo Tanaka
- Re: [AMBER] using both the ILDN and NMR-based modifications of ff99SB Jason Swails
Friday, 6 April 2012
- [AMBER] Fwd: Problem? krati sharma
- [AMBER] Further question on protonation state of histidine Acoot Brett
- Re: [AMBER] Further question on protonation state of histidine Brian Radak
- Re: [AMBER] Further question on protonation state of histidine Rajendra Sharma
- Re: [AMBER] Further question on protonation state of histidine David A Case
- [AMBER] What is major difference between Amber11 and Amber12 K. Uebayashi
- Re: [AMBER] What is major difference between Amber11 and Amber12 David A Case
- Re: [AMBER] What is major difference between Amber11 and Amber12 Ross Walker
- [AMBER] binding energy calculations kirtana S
- [AMBER] question on protonation state of histidine Acoot Brett
- Re: [AMBER] binding energy calculations case
- Re: [AMBER] question on protonation state of histidine Dean Cuebas
- Re: [AMBER] question on protonation state of histidine Acoot Brett
- Re: [AMBER] binding energy calculations kirtana S
- Re: [AMBER] binding energy calculations Aron Broom
- Re: [AMBER] question on protonation state of histidine Jason Swails
Saturday, 7 April 2012
- [AMBER] PDB file conversion server to meet the atom type requirement Acoot Brett
- Re: [AMBER] Inconsistent Internal energy from monomer to dimer Josep Maria Campanera Alsina
- Re: [AMBER] Inconsistent Internal energy from monomer to dimer Carlos Simmerling
- Re: [AMBER] PDB file conversion server to meet the atom type requirement M. L. Dodson
- Re: [AMBER] binding energy calculations kirtana S
- Re: [AMBER] binding energy calculations Jason Swails
- Re: [AMBER] question on protonation state of histidine case
- Re: [AMBER] PDB file conversion server to meet the atom type requirement case
- [AMBER] an error message in installation of AMBERTOOLS12 Acoot Brett
Sunday, 8 April 2012
- [AMBER] How can I fix two ends of DNA? mehdi bagherpoor
- Re: [AMBER] an error message in installation of AMBERTOOLS12 Jason Swails
- [AMBER] the command to make the sander running visible Acoot Brett
- Re: [AMBER] the command to make the sander running visible Acoot Brett
- Re: [AMBER] the command to make the sander running visible Fredrick Devadoss
- Re: [AMBER] the command to make the sander running visible Aron Broom
- Re: [AMBER] the command to make the sander running visible Adrian Roitberg
- [AMBER] Ligand and receptor separated when setting iwrap=1 Liu Denis
- Re: [AMBER] How can I fix two ends of DNA? case
- Re: [AMBER] Ligand and receptor separated when setting iwrap=1 Brian Radak
- Re: [AMBER] the command to make the sander running visible Acoot Brett
- Re: [AMBER] the command to make the sander running visible Adrian Roitberg
- [AMBER] sander minimization *.i file for protein complex Acoot Brett
- [AMBER] sander minimization mini.in file for protein complex Acoot Brett
- Re: [AMBER] How can I fix two ends of DNA? Jason Swails
- Re: [AMBER] Ligand and receptor separated when setting iwrap=1 Liu Denis
Monday, 9 April 2012
- [AMBER] GB and Dielectric constant kanika sharma
- Re: [AMBER] GB and Dielectric constant Carlos Simmerling
- Re: [AMBER] sander minimization mini.in file for protein complex David A Case
- Re: [AMBER] GB and Dielectric constant David A Case
- Re: [AMBER] sander minimization mini.in file for protein complex Anselm Horn
- Re: [AMBER] GB and Dielectric constant kanika sharma
- [AMBER] query regarding gaussian and antechamber jun kit
- [AMBER] GB/SA Aron Broom
- Re: [AMBER] query regarding gaussian and antechamber Jason Swails
- Re: [AMBER] GB/SA Jason Swails
- Re: [AMBER] GB/SA Aron Broom
- Re: [AMBER] GB/SA Carlos Simmerling
- Re: [AMBER] binding energy calculations kirtana S
- Re: [AMBER] binding energy calculations David A Case
- Re: [AMBER] How can I fix two ends of DNA? mehdi bagherpoor
- Re: [AMBER] GB/SA Aron Broom
- Re: [AMBER] binding energy calculations kirtana S
- Re: [AMBER] GB/SA Jason Swails
- Re: [AMBER] binding energy calculations Jason Swails
- Re: [AMBER] How can I fix two ends of DNA? Jason Swails
- [AMBER] crystallographic artifacts ashwini gupta
Tuesday, 10 April 2012
- [AMBER] How to overcome the limitation of file size when using ptraj? Catein Catherine
- [AMBER] PBC Fernando Martín García
- [AMBER] installation of Amber 12 under Cygwin Acoot Brett
- Re: [AMBER] How to overcome the limitation of file size when using ptraj? David A Case
- Re: [AMBER] installation of Amber 12 under Cygwin David A Case
- Re: [AMBER] PBC David A Case
- Re: [AMBER] PBC Fernando Martín García
- [AMBER] is there any tutorial for membrane protein simulations for Amber 12? Albert
- [AMBER] Units of the output file. Arthur Roberts
- Re: [AMBER] Units of the output file. steinbrt.rci.rutgers.edu
- [AMBER] Could not read velocities from restart file David Condon
- [AMBER] AMBER 99SB force field used by GROMACS Acoot Brett
- Re: [AMBER] AMBER 99SB force field used by GROMACS Adrian Roitberg
- Re: [AMBER] Could not read velocities from restart file steinbrt.rci.rutgers.edu
- Re: [AMBER] AMBER 99SB force field used by GROMACS steinbrt.rci.rutgers.edu
- Re: [AMBER] AMBER 99SB force field used by GROMACS Lorenzo Gontrani
- Re: [AMBER] is there any tutorial for membrane protein simulations for Amber 12? Benjamin D Madej
- Re: [AMBER] is there any tutorial for membrane protein simulations for Amber 12? Albert
- Re: [AMBER] is there any tutorial for membrane protein simulations for Amber 12? Ross Walker
- Re: [AMBER] is there any tutorial for membrane protein simulations for Amber 12? Aron Broom
- Re: [AMBER] is there any tutorial for membrane protein simulations for Amber 12? Albert
- Re: [AMBER] is there any tutorial for membrane protein simulations for Amber 12? Ross Walker
- Re: [AMBER] is there any tutorial for membrane protein simulations for Amber 12? Aron Broom
- [AMBER] 2FE-2S cluster proteins topology and parameters files Angelo Gallo CERM
- Re: [AMBER] binding energy calculations kirtana S
- Re: [AMBER] Units of the output file. David A Case
- [AMBER] Calculating B-factor in ptraj mish
- Re: [AMBER] Calculating B-factor in ptraj Gonzalo Jimenez
- Re: [AMBER] Could not read velocities from restart file David Condon
- Re: [AMBER] Could not read velocities from restart file Aron Broom
- Re: [AMBER] Calculating B-factor in ptraj mish
- Re: [AMBER] Could not read velocities from restart file Ross Walker
- Re: [AMBER] ion parameters in simulations with nucleic acids Thomas Cheatham III
- Re: [AMBER] Could not read velocities from restart file David Condon
- Re: [AMBER] Could not read velocities from restart file David A Case
- Re: [AMBER] Could not read velocities from restart file Ross Walker
- Re: [AMBER] Could not read velocities from restart file Aron Broom
- Re: [AMBER] Could not read velocities from restart file Ross Walker
Wednesday, 4 April 2012
- Re: [AMBER] Large Energy Jump in TMD simulation - Regarding Fredrick Devadoss
Tuesday, 10 April 2012
- Re: [AMBER] binding energy calculations Jason Swails
- [AMBER] Residue mismatch - Amber11 sławek bojarowski
- Re: [AMBER] ion parameters in simulations with nucleic acids Vlad Cojocaru
- Re: [AMBER] Could not read velocities from restart file Bill Ross
- Re: [AMBER] Could not read velocities from restart file Ross Walker
- Re: [AMBER] Could not read velocities from restart file Ross Walker
- Re: [AMBER] Could not read velocities from restart file Bill Ross
- Re: [AMBER] Could not read velocities from restart file Ross Walker
- Re: [AMBER] Residue mismatch - Amber11 Jason Swails
- Re: [AMBER] AMBER 99SB force field used by GROMACS Acoot Brett
- Re: [AMBER] 2FE-2S cluster proteins topology and parameters files Markus Kaukonen
Wednesday, 11 April 2012
- [AMBER] SOM clustering Anselm Horn
- Re: [AMBER] rfree: Error decoding variable 1 3 from: Elisa Frezza
- Re: [AMBER] rfree: Error decoding variable 1 3 from: David A Case
- [AMBER] how does frcmod work specifially. rdparm Knips, Alexander
- Re: [AMBER] rfree: Error decoding variable 1 3 from: Elisa Frezza
- Re: [AMBER] Could not read velocities from restart file David Condon
- Re: [AMBER] Odd coordinate writing problem in pmemd.MPI SOLVED steinbrt.rci.rutgers.edu
- Re: [AMBER] Could not read velocities from restart file Aron Broom
- [AMBER] nmode list index out of range manikanthan bhavaraju
- Re: [AMBER] rfree: Error decoding variable 1 3 from: Niel Henriksen
- [AMBER] Fwd: no info contained in Residues to print section - MMPBSA.py Alfredo Quevedo
- Re: [AMBER] how does frcmod work specifially. rdparm David A Case
- Re: [AMBER] rfree: Error decoding variable 1 3 from: David A Case
- [AMBER] Error: Could not parse GB output files! Check for missing values (*********). zhangaidi
- Re: [AMBER] rfree: Error decoding variable 1 3 from: Elisa Frezza
- Re: [AMBER] rfree: Error decoding variable 1 3 from: Elisa Frezza
- [AMBER] Error: Could not parse GB output files! Check for missing values (*********). zhangaidi
- Re: [AMBER] rfree: Error decoding variable 1 3 from: Niel Henriksen
- Re: [AMBER] rfree: Error decoding variable 1 3 from: Elisa Frezza
- Re: [AMBER] rfree: Error decoding variable 1 3 from: Niel Henriksen
- [AMBER] R: Error: unspecified launch failure launching kernel kReduceForces Giovanni Pavan
- Re: [AMBER] Error: unspecified launch failure launching kernel kReduceForces Scott Le Grand
- Re: [AMBER] R: Error: unspecified launch failure launching kernel kReduceForces Ross Walker
- Re: [AMBER] parameters for Lys-sugar P2N file Urszula Uciechowska
- [AMBER] about sander and pmemd bmartini
- Re: [AMBER] about sander and pmemd David A Case
- [AMBER] Ambertools12 cygwin install keeps asking for csh????? Dean Cuebas
- Re: [AMBER] Fwd: no info contained in Residues to print section - MMPBSA.py Jason Swails
- Re: [AMBER] Could not read velocities from restart file David Condon
- Re: [AMBER] Error: Could not parse GB output files! Check for missing values (*********). Jason Swails
- Re: [AMBER] Ambertools12 cygwin install keeps asking for csh????? Dean Cuebas
- Re: [AMBER] nmode list index out of range Jason Swails
- Re: [AMBER] nmode list index out of range manikanthan bhavaraju
- Re: [AMBER] AMBER Digest, Vol 121, Issue 2 Alfredo Quevedo
- Re: [AMBER] Could not read velocities from restart file Ross Walker
- [AMBER] MMPBSA error Kumar, Sonu
- Re: [AMBER] Could not read velocities from restart file David Condon
- [AMBER] which methods calculate the binding energy most accurate Acoot Brett
- Re: [AMBER] which methods calculate the binding energy most accurate Aron Broom
Thursday, 12 April 2012
- [AMBER] parameters for Lys-sugar P2N file Urszula Uciechowska
- Re: [AMBER] parameters for Lys-sugar P2N file FyD
- Re: [AMBER] Large Energy Jump in TMD simulation - Regarding Carlos Simmerling
- [AMBER] Query regarding Amber 11 Somnath Nandy
- Re: [AMBER] rfree: Error decoding variable 1 3 from: David A Case
- Re: [AMBER] rfree: Error decoding variable 1 3 from: Jason Swails
- Re: [AMBER] MMPBSA error Jason Swails
- [AMBER] Query regarding Amber Installation Somnath Nandy
- [AMBER] MMPBSA.py.MPI calls sander instead of sander.MPI Alfredo Quevedo
- Re: [AMBER] MMPBSA.py.MPI calls sander instead of sander.MPI Jason Swails
- Re: [AMBER] rfree: Error decoding variable 1 3 from: David A Case
- Re: [AMBER] Query regarding Amber Installation David A Case
- Re: [AMBER] rfree: Error decoding variable 1 3 from: Elisa Frezza
- Re: [AMBER] rfree: Error decoding variable 1 3 from: David A Case
- Re: [AMBER] rfree: Error decoding variable 1 3 from: Elisa Frezza
- Re: [AMBER] rfree: Error decoding variable 1 3 from: Niel Henriksen
- Re: [AMBER] rfree: Error decoding variable 1 3 from: Elisa Frezza
- [AMBER] Fwd: [q4md-fft] Re: parameters for Lys-sugar P2N file FyD
- [AMBER] how to use Amber99SB-ILDN in Amber11? Albert
- Re: [AMBER] how to use Amber99SB-ILDN in Amber11? David A Case
- [AMBER] closest command Qiong Zhang
- Re: [AMBER] closest command Daniel Roe
- Re: [AMBER] closest command Qiong Zhang
Friday, 13 April 2012
- [AMBER] MMPBSA error in segmentation fault Aditya Setiajid
- Re: [AMBER] Query regarding Amber Installation Somnath Nandy
- [AMBER] pcacovar in ptraj Bala Subramani
- Re: [AMBER] closest command Daniel Roe
- Re: [AMBER] MMPBSA error in segmentation fault Bill Miller III
- Re: [AMBER] closest command Qiong Zhang
- Re: [AMBER] closest command Daniel Roe
- [AMBER] Electrostatic potential calculation Sudarshan Debnath
- [AMBER] installing Amber12 in parallel Marc van der Kamp
- [AMBER] Can MMPBSA calculate the binding energy in organic solvent? Liu Denis
- Re: [AMBER] closest command Qiong Zhang
- [AMBER] Error compiling pmemd.cuda.MPI Alfredo Quevedo
- [AMBER] reduce and trim function Mahendra B Thapa
- Re: [AMBER] Error compiling pmemd.cuda.MPI Ross Walker
- [AMBER] Electrostatic potential calculation Sudarshan Debnath
- [AMBER] how to restrain the ligand in minimization and NVT equilibration step? Albert
- Re: [AMBER] how to restrain the ligand in minimization and NVT equilibration step? Carlos Simmerling
- [AMBER] Error loading Glycam_06 parameters in xLEaP / tleap Kepa K. Burusco
- Re: [AMBER] Error loading Glycam_06 parameters in xLEaP / tleap Lachele Foley (Lists)
- [AMBER] is it possible strip off restrain linearly? Albert
- [AMBER] NVT error Albert
- Re: [AMBER] Error compiling pmemd.cuda.MPI Alfredo Quevedo
- Re: [AMBER] Error compiling pmemd.cuda.MPI Ross Walker
- [AMBER] Problem with mdnab: ERROR in RATTLE Andrey
- Re: [AMBER] reduce and trim function Jason Swails
- Re: [AMBER] is it possible strip off restrain linearly? Jason Swails
- [AMBER] Problem with MCPB moitrayee.mbu.iisc.ernet.in
- [AMBER] saveamberparm in xleap does not recognize atom type F Genzo Tanaka
- [AMBER] : wrong charge calculation by xleap Sharma, Purshotam
- Re: [AMBER] : wrong charge calculation by xleap raghav singh
- Re: [AMBER] installing Amber12 in parallel case
- Re: [AMBER] Electrostatic potential calculation case
- Re: [AMBER] NVT error case
- Re: [AMBER] saveamberparm in xleap does not recognize atom type F case
- Re: [AMBER] : wrong charge calculation by xleap case
- Re: [AMBER] : wrong charge calculation by xleap Sharma, Purshotam
- Re: [AMBER] : wrong charge calculation by xleap Sharma, Purshotam
- [AMBER] restrain syntax Albert
- [AMBER] Electrostatic potential calculation Sudarshan Debnath
- Re: [AMBER] : wrong charge calculation by xleap Bill Ross
- Re: [AMBER] : wrong charge calculation by xleap Sharma, Purshotam
- Re: [AMBER] Electrostatic potential calculation Ray Luo, Ph.D.
- Re: [AMBER] MMPBSA error in segmentation fault Aditya Setiajid
- [AMBER] strange output information Albert
Saturday, 14 April 2012
- [AMBER] Ambertools 12 installation: Help needed Acoot Brett
- Re: [AMBER] strange output information Carlos Simmerling
- Re: [AMBER] strange output information Albert
- [AMBER] what's the amber efficiency? Albert
- Re: [AMBER] [amber] error: could not parse gb output files! check for missing values (*********). zhangaidi
- Re: [AMBER] MMPBSA error in segmentation fault Bill Miller III
- [AMBER] Electrostatic potential calculation Sudarshan Debnath
- Re: [AMBER] Ambertools 12 installation: Help needed case
- Re: [AMBER] what's the amber efficiency? case
- Re: [AMBER] Electrostatic potential calculation case
- [AMBER] Amber12 compile with "intel" err. javacfish
- [AMBER] my ambertools 12 test Acoot Brett
- Re: [AMBER] Amber12 compile with "intel" err. Jason Swails
- Re: [AMBER] my ambertools 12 test M. L. Dodson
- Re: [AMBER] [amber] error: could not parse gb output files! check for missing values (*********). Jason Swails
- Re: [AMBER] restrain syntax Jason Swails
- Re: [AMBER] what's the amber efficiency? Scott Le Grand
- Re: [AMBER] Query regarding Amber Installation Jason Swails
- Re: [AMBER] Amber12 compile with "intel" err. case
- Re: [AMBER] Problem with mdnab: ERROR in RATTLE case
- Re: [AMBER] Amber12 compile with "intel" err. Jason Swails
- [AMBER] 回复： Amber12 compile with "intel" err. javacfish
- [AMBER] reply： Amber12 compile with "intel" err. javacfish
- [AMBER] Problem with gaussian input file generation moitrayee.mbu.iisc.ernet.in
- Re: [AMBER] Electrostatic potential calculation Ray Luo, Ph.D.
Sunday, 15 April 2012
- [AMBER] abertools12 installation failure Francesco Pietra
- [AMBER] Fwd: abertools12 installation failure Francesco Pietra
- Re: [AMBER] Problem with MCPB Ben Roberts
- Re: [AMBER] Problem with MCPB Ben Roberts
- [AMBER] Fw: MMPBSA error in segmentation fault Aditya Setiajid
- Re: [AMBER] Fw: MMPBSA error in segmentation fault Jason Swails
- Re: [AMBER] abertools12 installation failure Jason Swails
- Re: [AMBER] Problem with MCPB moitrayee.mbu.iisc.ernet.in
- Re: [AMBER] abertools12 installation failure Francesco Pietra
- Re: [AMBER] abertools12 installation failure case
- Re: [AMBER] FW: reduce and trim function Mahendra B Thapa
- Re: [AMBER] abertools12 installation failure Jason Swails
- [AMBER] Partitioning issue of sander 板垣哲彦
- Re: [AMBER] FW: reduce and trim function case
- Re: [AMBER] Partitioning issue of sander Jason Swails
Monday, 16 April 2012
- [AMBER] 回复： abertools12 installation failure javacfish
- Re: [AMBER] abertools12 installation failure Francesco Pietra
- [AMBER] parallelization of paramfit in ambertools12 Francesco Pietra
- [AMBER] error installing Amber12-gpu version Vijay Manickam Achari
- Re: [AMBER] installing Amber12 in parallel Marc van der Kamp
- Re: [AMBER] error installing Amber12-gpu version javacfish
- [AMBER] AMBER USER José Guilherme Vilhena Albuquerque d'Orey
- [AMBER] MICA SURFACE José Guilherme Vilhena Albuquerque d'Orey
- Re: [AMBER] Error loading Glycam_06 parameters in xLEaP / tleap Kepa K. Burusco
- Re: [AMBER] error installing Amber12-gpu version Vijay Manickam Achari
- [AMBER] when will the membrane protein simulation tutorial be available? Albert
- Re: [AMBER] Partitioning issue of sander David A Case
- [AMBER] Good cluster configuration for running PMEMD.MPI? Juan Carlos Muñoz García
- Re: [AMBER] error installing Amber12-gpu version David A Case
- [AMBER] Electrostatic potential calculation Sudarshan Debnath
- Re: [AMBER] Electrostatic potential calculation Ray Luo, Ph.D.
- [AMBER] problem with "make test.parallel" for AMBER12 Marc van der Kamp
- [AMBER] Error while running mm_pbsa.pl Prashant Kumar
- [AMBER] AMBER12 QM/MM: is d-orbital code going to be parallelized? Marc van der Kamp
- [AMBER] Need help with MMPBSA.MPI Victor Ma
- Re: [AMBER] saveamberparm in xleap does not recognize atom type F Genzo Tanaka
- Re: [AMBER] Need help with MMPBSA.MPI Bill Miller III
- [AMBER] forcefield modifications Knips, Alexander
- Re: [AMBER] AMBER12 QM/MM: is d-orbital code going to be parallelized? filip fratev
- Re: [AMBER] Need help with MMPBSA.MPI Victor Ma
- Re: [AMBER] Error while running mm_pbsa.pl Ray Luo, Ph.D.
- Re: [AMBER] forcefield modifications David A Case
- Re: [AMBER] AMBER12 QM/MM: is d-orbital code going to be parallelized? David A Case
- Re: [AMBER] AMBER12 QM/MM: is d-orbital code going to be parallelized? Brian Radak
- Re: [AMBER] error installing Amber12-gpu version Jason Swails
- [AMBER] problem converting AmbertoDesmond Albert
- Re: [AMBER] problem with "make test.parallel" for AMBER12 Jason Swails
- Re: [AMBER] problem converting AmbertoDesmond David A Case
- [AMBER] "closest" command in cpptraj Alfredo Quevedo
- [AMBER] AmberTools12 Installation Error Senthil Natesan
- Re: [AMBER] Need help with MMPBSA.MPI Bill Miller III
- Re: [AMBER] problem converting AmbertoDesmond Albert
- Re: [AMBER] "closest" command in cpptraj Daniel Roe
- Re: [AMBER] Good cluster configuration for running PMEMD.MPI? Jason Swails
- Re: [AMBER] AmberTools12 Installation Error Jason Swails
- Re: [AMBER] parallelization of paramfit in ambertools12 Robin Betz
- Re: [AMBER] AmberTools12 Installation Error - [SOLVED] Senthil Natesan
- [AMBER] sander error during GB calculations Qiong Zhang
- Re: [AMBER] sander error during GB calculations Qiong Zhang
- Re: [AMBER] when will the membrane protein simulation tutorial be available? Benjamin D Madej
- Re: [AMBER] parallelization of paramfit in ambertools12 Francesco Pietra
- Re: [AMBER] parallelization of paramfit in ambertools12 Robin Betz
- Re: [AMBER] problem converting AmbertoDesmond Albert
Tuesday, 17 April 2012
- Re: [AMBER] parallelization of paramfit in ambertools12 Sidney Elmer
- [AMBER] Creating input file for Protein-protein simulation Tommy Yap
- Re: [AMBER] error installing Amber12-gpu version Vijay Manickam Achari
- Re: [AMBER] problem with "make test.parallel" for AMBER12 Marc van der Kamp
- Re: [AMBER] AMBER12 QM/MM: is d-orbital code going to be parallelized? Marc van der Kamp
- Re: [AMBER] Large Energy Jump in TMD simulation - Regarding Fredrick Devadoss
- Re: [AMBER] MMPBSA error Kumar, Sonu
- Re: [AMBER] problem converting AmbertoDesmond David A Case
- Re: [AMBER] saveamberparm in xleap does not recognize atom type F David A Case
- Re: [AMBER] MMPBSA error Jan-Philip Gehrcke
- Re: [AMBER] Partitioning issue of sander 板垣哲彦
- Re: [AMBER] MMPBSA error Jan-Philip Gehrcke
- Re: [AMBER] :Re: "closest" command in cpptraj Alfredo Quevedo
- [AMBER] P2N file error from RED Urszula Uciechowska
- Re: [AMBER] Good cluster configuration for running PMEMD.MPI? Matthew Zwier
- Re: [AMBER] :Re: "closest" command in cpptraj Daniel Roe
- Re: [AMBER] Partitioning issue of sander David A Case
- Re: [AMBER] P2N file error from RED FyD
- Re: [AMBER] MMPBSA error Jason Swails
- Re: [AMBER] MMPBSA error Kumar, Sonu
- Re: [AMBER] Problem with mdnab: ERROR in RATTLE Andrey
- Re: [AMBER] :Re: "closest" command in cpptraj Alfredo Quevedo
- Re: [AMBER] :Re: "closest" command in cpptraj Thomas Evangelidis
- Re: [AMBER] :Re: "closest" command in cpptraj Daniel Roe
- Re: [AMBER] :Re: "closest" command in cpptraj Alfredo Quevedo
- Re: [AMBER] :Re: "closest" command in cpptraj Daniel Roe
- Re: [AMBER] :Re: "closest" command in cpptraj Alfredo Quevedo
- Re: [AMBER] Partitioning issue of sander Jason Swails
- Re: [AMBER] error installing Amber12-gpu version Vijay Manickam Achari
- Re: [AMBER] Creating input file for Protein-protein simulation filip fratev
- Re: [AMBER] parallelization of paramfit in ambertools12 Robin Betz
- Re: [AMBER] error installing Amber12-gpu version Jason Swails
- [AMBER] Using Antechamber to generate RESP prepi file Lianhu Wei
- Re: [AMBER] Problem with mdnab: ERROR in RATTLE case
- Re: [AMBER] problem converting AmbertoDesmond Bill Ross
- [AMBER] Why RMSD goes fast to 5 angstrom? Shulin Zhuang
- [AMBER] About restraint Jun Wang
- Re: [AMBER] error installing Amber12-gpu version Vijay Manickam Achari
- Re: [AMBER] Why RMSD goes fast to 5 angstrom? Aron Broom
- Re: [AMBER] About restraint Aron Broom
- Re: [AMBER] error installing Amber12-gpu version Aron Broom
- Re: [AMBER] error installing Amber12-gpu version Thomas Cheatham
- Re: [AMBER] Creating input file for Protein-protein simulation Tommy Yap
- [AMBER] Fwd: Why RMSD goes fast to 5 angstrom? Shulin Zhuang
- Re: [AMBER] Why RMSD goes fast to 5 angstrom? Jason Swails
- Re: [AMBER] About restraint Thomas Cheatham
- [AMBER] how to improve GPU running? Albert
Wednesday, 18 April 2012
- Re: [AMBER] error installing Amber12-gpu version Vijay Manickam Achari
- Re: [AMBER] Why RMSD goes fast to 5 angstrom? steinbrt.rci.rutgers.edu
- Re: [AMBER] how to improve GPU running? steinbrt.rci.rutgers.edu
- Re: [AMBER] Using Antechamber to generate RESP prepi file FyD
- [AMBER] problem installing AmberTools 12 on Mac OS X Lion Sidney Elmer
- Re: [AMBER] error installing Amber12-gpu version Jan-Philip Gehrcke
- [AMBER] on The Nudged Elastic Band Approach (Tutorial 5) Acoot Brett
- [AMBER] Use effective core potential in amber QM/MM calculation with Gaussian Tong Zhu
- [AMBER] Dielectric constant and scaled charges Lorenzo Gontrani
- Re: [AMBER] how to improve GPU running? Albert
- Re: [AMBER] how to improve GPU running? steinbrt.rci.rutgers.edu
- Re: [AMBER] how to improve GPU running? Ross Walker
- Re: [AMBER] how to improve GPU running? Ross Walker
- Re: [AMBER] Problem with mdnab: ERROR in RATTLE David A Case
- Re: [AMBER] error installing Amber12-gpu version David A Case
- Re: [AMBER] how to improve GPU running? Scott Le Grand
- Re: [AMBER] Creating input file for Protein-protein simulation David A Case
- Re: [AMBER] Dielectric constant and scaled charges David A Case
- Re: [AMBER] Why RMSD goes fast to 5 angstrom? Jason Swails
- Re: [AMBER] Why RMSD goes fast to 5 angstrom? Shulin Zhuang
- Re: [AMBER] Using Antechamber to generate RESP prepi file Lianhu Wei
- Re: [AMBER] About Restraint Jun Wang
- Re: [AMBER] error installing Amber12-gpu version Vijay Manickam Achari
- Re: [AMBER] Using Antechamber to generate RESP prepi file FyD
- Re: [AMBER] abertools12 installation failure Jason Swails
- [AMBER] SCEE and SCNB GLYCAM_06 values with amber11 top crd files Kepa K. Burusco
- Re: [AMBER] problem installing AmberTools 12 on Mac OS X Lion Sidney Elmer
- [AMBER] Amber11: running ptraj bmartini
- Re: [AMBER] Amber11: running ptraj Thomas Cheatham III
- Re: [AMBER] Amber11: running ptraj bmartini
- Re: [AMBER] SCEE and SCNB GLYCAM_06 values with amber11 top crd files David A Case
- [AMBER] why no periodic information? Albert
- Re: [AMBER] why no periodic information? Aron Broom
- Re: [AMBER] SCEE and SCNB GLYCAM_06 values with amber11 top crd files Lachele Foley (Lists)
- Re: [AMBER] Using Antechamber to generate RESP prepi file Lianhu Wei
- Re: [AMBER] why no periodic information? Albert
- Re: [AMBER] why no periodic information? Albert
- Re: [AMBER] why no periodic information? Aron Broom
- Re: [AMBER] why no periodic information? Albert
- Re: [AMBER] why no periodic information? Brian Radak
- Re: [AMBER] why no periodic information? Aron Broom
- Re: [AMBER] why no periodic information? Albert
- Re: [AMBER] why no periodic information? Albert
- [AMBER] problem in tleap with head and tail atom assignment Cramariuc Oana
- Re: [AMBER] problem in tleap with head and tail atom assignment Jason Swails
Thursday, 19 April 2012
- [AMBER] NUCGEN and FORCE Field disfunction VladanStefanovic.kg.ac.rs
- Re: [AMBER] Using Antechamber to generate RESP prepi file FyD
- Re: [AMBER] problem in tleap with head and tail atom assignment FyD
- Re: [AMBER] problem in tleap with head and tail atom assignment Cramariuc Oana
- Re: [AMBER] NUCGEN and FORCE Field disfunction David A Case
- Re: [AMBER] NUCGEN and FORCE Field disfunction Jason Swails
- [AMBER] How can I exert external force in the end of DNA? mehdi bagherpoor
- Re: [AMBER] How can I exert external force in the end of DNA? Bahareh honarparvar
- Re: [AMBER] Using Antechamber to generate RESP prepi file Lianhu Wei
- Re: [AMBER] How can I exert external force in the end of DNA? ros
- [AMBER] xleap pdb file loading problem. DoYong Kim
- [AMBER] cpptraj, ptraj and time interval Fabrício Bracht
- [AMBER] About force constant in umbrella sampling Mo Chen
- Re: [AMBER] About force constant in umbrella sampling Brian Radak
- Re: [AMBER] xleap pdb file loading problem. David A Case
- [AMBER] Amber 12 - Check for updates failed Shaw, Sharon
- [AMBER] ★what's new?◆amber◆ ZhaoLei
- Re: [AMBER] Amber 12 - Check for updates failed Jason Swails
- Re: [AMBER] Amber 12 - Check for updates failed Shaw, Sharon
- Re: [AMBER] AMBER12 QM/MM: is d-orbital code going to be parallelized? Andreas Goetz
- [AMBER] Bug? Antechamber, Ambertools-1.4 Lianhu Wei
- Re: [AMBER] Old version Thales Kronenberger
- Re: [AMBER] Amber 12 - Check for updates failed Shaw, Sharon
- [AMBER] How to determine the protonation state of phosphorylated residue in a protein? Rajendra Sharma
- Re: [AMBER] cpptraj, ptraj and time interval Liu Denis
- Re: [AMBER] cpptraj, ptraj and time interval Daniel Roe
- Re: [AMBER] Old version case
Friday, 20 April 2012
- [AMBER] The error of installing mpi4py in ambertools12 for MMPBSA parallel JiYuan Liu
Thursday, 19 April 2012
- Re: [AMBER] AMBER12 QM/MM: is d-orbital code going to be parallelized? filip fratev
- [AMBER] Some problem with building Non-standard residue Nicholus Bhattacharjee
Friday, 20 April 2012
- Re: [AMBER] Old version Alan
- Re: [AMBER] P2N file error from RED Urszula Uciechowska
- Re: [AMBER] P2N file error from RED Per Jr. Greisen
- [AMBER] QM/MM and water box type Fernando Martín García
- Re: [AMBER] P2N file error from RED Urszula Uciechowska
- Re: [AMBER] P2N file error from RED FyD
- [AMBER] Confusion in adding TER cards Asmita Gupta
- [AMBER] running the on-line tutorial B1 (DNA) by Amber 12 Acoot Brett
- Re: [AMBER] on The Nudged Elastic Band Approach (Tutorial 5) Carlos Simmerling
- [AMBER] MM/PBSA calculations mish
- [AMBER] Fw: running the on-line tutorial B1 (DNA) by Amber 12 Acoot Brett
- Re: [AMBER] error installing Amber12-gpu version Vijay Manickam Achari
- Re: [AMBER] running the on-line tutorial B1 (DNA) by Amber 12 David A Case
- Re: [AMBER] on The Nudged Elastic Band Approach (Tutorial 5) Aron Broom
- Re: [AMBER] cpptraj, ptraj and time interval Fabrício Bracht
- [AMBER] imin = 5, expected numerical error when re-calculating energy Brian Radak
- Re: [AMBER] cpptraj, ptraj and time interval Jan-Philip Gehrcke
- [AMBER] (GPU) preformance of amber 12 István Lőrincz
- Re: [AMBER] imin = 5, expected numerical error when re-calculating energy Jason Swails
- Re: [AMBER] The error of installing mpi4py in ambertools12 for MMPBSA parallel Jason Swails
- Re: [AMBER] imin = 5, expected numerical error when re-calculating energy Brian Radak
- Re: [AMBER] (GPU) preformance of amber 12 Scott Le Grand
- [AMBER] error Building proper torsion parameters. zhangaidi
- Re: [AMBER] QM/MM and water box type Qiantao Wang
- Re: [AMBER] cpptraj, ptraj and time interval Fabrício Bracht
- Re: [AMBER] xleap pdb file loading problem. DoYong Kim
- Re: [AMBER] error Building proper torsion parameters. David A Case
- Re: [AMBER] cpptraj, ptraj and time interval David A Case
- Re: [AMBER] Confusion in adding TER cards David A Case
- [AMBER] external force in the end of DNA strands mehdi bagherpoor
- Re: [AMBER] MM/PBSA calculations Ray Luo, Ph.D.
- [AMBER] using two GPUs Vijay Manickam Achari
- Re: [AMBER] using two GPUs Robert Crovella
- Re: [AMBER] using two GPUs David Jones
- Re: [AMBER] using two GPUs Vijay Manickam Achari
- Re: [AMBER] AMBER12 QM/MM: is d-orbital code going to be parallelized? filip fratev
- [AMBER] addions command in the xleap Acoot Brett
- [AMBER] constant pH titration Acoot Brett
Saturday, 21 April 2012
- [AMBER] using AMBER forcefield by GROMACS Acoot Brett
- Re: [AMBER] using AMBER forcefield by GROMACS Francesco Oteri
- Re: [AMBER] using AMBER forcefield by GROMACS Acoot Brett
- Re: [AMBER] addions command in the xleap Aron Broom
- Re: [AMBER] using two GPUs Robert Crovella
- Re: [AMBER] constant pH titration Jason Swails
- Re: [AMBER] using two GPUs Jason Swails
- Re: [AMBER] using AMBER forcefield by GROMACS Jason Swails
- Re: [AMBER] cpptraj, ptraj and time interval Jason Swails
- Re: [AMBER] xleap pdb file loading problem. Jason Swails
- [AMBER] implicit MD and explicit MD Acoot Brett
- [AMBER] is membrane protein simulation tutorial ready? Albert
- Re: [AMBER] implicit MD and explicit MD Carlos Simmerling
- Re: [AMBER] is membrane protein simulation tutorial ready? Jason Swails
Sunday, 22 April 2012
- [AMBER] Installation problem for Ambertools 12 on Mac OS X Lion Richard Lonsdale
- [AMBER] Where can I find silhouette.pl? Irene Newhouse
- Re: [AMBER] Installation problem for Ambertools 12 on Mac OS X Lion Jason Swails
- Re: [AMBER] Installation problem for Ambertools 12 on Mac OS X Lion Richard Lonsdale
- Re: [AMBER] Installation problem for Ambertools 12 on Mac OS X Lion David Case
- Re: [AMBER] Installation problem for Ambertools 12 on Mac OS X Lion Richard Lonsdale
- Re: [AMBER] How to determine the protonation state of phosphorylated residue in a protein? Jason Swails
- [AMBER] QM/MM ATP-Mg2+ system filip fratev
- Re: [AMBER] Installation problem for Ambertools 12 on Mac OS X Lion Jason Swails
Monday, 23 April 2012
- Re: [AMBER] Problem with mdnab: ERROR in RATTLE Andrey
- [AMBER] amber 10 nmode error. xmzpzengs
- [AMBER] error in AMBER while generatting prmtop and ipcrd kureeckal ramesh
- [AMBER] H-Bonding and Amber's Shake algorithm Adam Jion
- Re: [AMBER] (GPU) preformance of amber 12 István Lőrincz
- Re: [AMBER] parameters for Lys-sugar Urszula Uciechowska
- [AMBER] RMSD analysis for cyclo-tetra-peptide mcj452500
- Re: [AMBER] RMSD analysis for cyclo-tetra-peptide Carlos Simmerling
- Re: [AMBER] Installation problem for Ambertools 12 on Mac OS X Lion David A Case
- Re: [AMBER] H-Bonding and Amber's Shake algorithm David A Case
- Re: [AMBER] Installation problem for Ambertools 12 on Mac OS X Lion Jason Swails
- Re: [AMBER] [amber] error building proper torsion parameters. 本人
- [AMBER] Problems with atom type in sidechain.bcl Fabrício Bracht
- Re: [AMBER] QM/MM ATP-Mg2+ system Brian Radak
- Re: [AMBER] parameters for Lys-sugar FyD
- Re: [AMBER] [amber] error building proper torsion parameters. David A Case
- Re: [AMBER] error in AMBER while generatting prmtop and ipcrd David A Case
- [AMBER] Huge discrepancy in el part of "solvation energy" using Thermodynamic Integration Marek Maly
- [AMBER] AMBER12 build on Linux x86_64 Shaw, Sharon
- Re: [AMBER] AMBER12 build on Linux x86_64 Matthew Zwier
- Re: [AMBER] AMBER12 build on Linux x86_64 Jason Swails
- Re: [AMBER] parameters for Lys-sugar Lachele Foley (Lists)
- Re: [AMBER] AMBER12 build on Linux x86_64 Shaw, Sharon
- Re: [AMBER] AMBER12 build on Linux x86_64 Jason Swails
- Re: [AMBER] QM/MM ATP-Mg2+ system Yang, Yue
- Re: [AMBER] Problems with atom type in sidechain.bcl Yang, Yue
- [AMBER] AMBER 11 sander segmentation fault Shuyi Cao
- Re: [AMBER] AMBER12 build on Linux x86_64 case
- Re: [AMBER] AMBER 11 sander segmentation fault case
- Re: [AMBER] (GPU) preformance of amber 12 Ross Walker
- Re: [AMBER] using two GPUs Vijay Manickam Achari
- Re: [AMBER] Amber using Gaussian input ashley chen
Tuesday, 24 April 2012
- Re: [AMBER] Amber using Gaussian input Scott Brozell
- [AMBER] Amber 12 Installation errors relevant to fftw3 Shulin Zhuang
- [AMBER] Entropy: nmode and quasi-harmonic approximation George Tzotzos
- [AMBER] error in parallel amber 11 installation Asmita Gupta
- [AMBER] Protein nanoparticle interaction Navin Jain
- Re: [AMBER] Entropy: nmode and quasi-harmonic approximation Hannes Loeffler
- Re: [AMBER] Entropy: nmode and quasi-harmonic approximation George Tzotzos
- Re: [AMBER] Amber 12 Installation errors relevant to fftw3 David A Case
- Re: [AMBER] error in parallel amber 11 installation David A Case
- Re: [AMBER] error in parallel amber 11 installation Jason Swails
- Re: [AMBER] using two GPUs Robert Crovella
- Re: [AMBER] AMBER12 build on Linux x86_64 Shaw, Sharon
- [AMBER] AM1 scalability Jacopo Sgrignani
- Re: [AMBER] AM1 scalability Marc van der Kamp
- Re: [AMBER] AMBER12 build on Linux x86_64 Jason Swails
- Re: [AMBER] AMBER12 build on Linux x86_64 Jason Swails
- [AMBER] For atom: .R<Na+ 127>.A<Na+ 1> Could not find type: Na+ George Tzotzos
- [AMBER] Trouble installing AmberTools 1.5 on mac Andrew Ritchie
- Re: [AMBER] For atom: .R<Na+ 127>.A<Na+ 1> Could not find type: Na+ InSuk Joung
- Re: [AMBER] For atom: .R<Na+ 127>.A<Na+ 1> Could not find type: Na+ George Tzotzos
- Re: [AMBER] AMBER12 build on Linux x86_64 Shaw, Sharon
- Re: [AMBER] QM/MM ATP-Mg2+ system filip fratev
- Re: [AMBER] Trouble installing AmberTools 1.5 on mac Jason Swails
- Re: [AMBER] Amber 12 Installation errors relevant to fftw3 Shulin Zhuang
- Re: [AMBER] Protein nanoparticle interaction Ben Roberts
- Re: [AMBER] using two GPUs Vijay Manickam Achari
Wednesday, 25 April 2012
- Re: [AMBER] [amber] error building proper torsion parameters. 本人
- [AMBER] AMBER12 installation error Peter Fojan
- Re: [AMBER] error in parallel amber 11 installation Asmita Gupta
- [AMBER] add_pdb colvin
- [AMBER] ff12SB with Na+ ion Tong Zhu
- Re: [AMBER] ff12SB with Na+ ion Marc van der Kamp
- Re: [AMBER] parameters for Lys-sugar Jan-Philip Gehrcke
- Re: [AMBER] Amber 12 Installation errors relevant to fftw3 David A Case
- Re: [AMBER] AMBER12 installation error David A Case
- [AMBER] QM/MM simulation ashwini gupta
- Re: [AMBER] error in parallel amber 11 installation David A Case
- Re: [AMBER] add_pdb David A Case
- Re: [AMBER] [amber] error building proper torsion parameters. David A Case
- Re: [AMBER] AMBER12 installation error Peter Fojan
- Re: [AMBER] QM/MM simulation Brian Radak
- [AMBER] is it possible to convert gromacs MD system into Amber? Albert
- [AMBER] Angle restrained minimization Ashutosh Shandilya
- [AMBER] computational scanning Hector A. Baldoni
- Re: [AMBER] computational scanning Carlos Simmerling
- Re: [AMBER] computational scanning Gould, Ian R
- Re: [AMBER] using two GPUs Jason Swails
- Re: [AMBER] AMBER12 installation error Jason Swails
- Re: [AMBER] is it possible to convert gromacs MD system into Amber? Jason Swails
- Re: [AMBER] Angle restrained minimization David A Case
- Re: [AMBER] AMBER12 installation error Peter Fojan
- [AMBER] Lmode_in_Amber11 JAIME RUBIO MARTINEZ
- [AMBER] 1-4 EEL meaning Camille Sultana
- Re: [AMBER] 1-4 EEL meaning Thomas Cheatham
- Re: [AMBER] using two GPUs Vijay Manickam Achari
- Re: [AMBER] using two GPUs Jason Swails
- Re: [AMBER] Lmode_in_Amber11 case
- Re: [AMBER] 1-4 EEL meaning Camille Sultana
- Re: [AMBER] 1-4 EEL meaning Jason Swails
- Re: [AMBER] add_pdb colvin
- Re: [AMBER] add_pdb Jason Swails
- Re: [AMBER] Amber 12 Installation errors relevant to fftw3 Shulin Zhuang
- Re: [AMBER] Amber 12 Installation errors relevant to fftw3 Jason Swails
- Re: [AMBER] add_pdb colvin
- Re: [AMBER] Amber 12 Installation errors relevant to fftw3 Shulin Zhuang
- Re: [AMBER] using two GPUs Vijay Manickam Achari
- Re: [AMBER] add_pdb Jason Swails
- Re: [AMBER] add_pdb case
- Re: [AMBER] Amber 12 Installation errors relevant to fftw3 case
- [AMBER] the real binding free energy bmartini
Thursday, 26 April 2012
- [AMBER] problems installing pmedm.cuda Peter Fojan
- Re: [AMBER] Lmode_in_Amber11 JAIME RUBIO MARTINEZ
- Re: [AMBER] Lmode_in_Amber11 JAIME RUBIO MARTINEZ
- Re: [AMBER] add_pdb colvin
- Re: [AMBER] parameters for Lys-sugar leap errors Urszula Uciechowska
- [AMBER] creating a box of fixed size Bala subramanian
- [AMBER] sander and pmemd xiaojiong
- Re: [AMBER] Lmode_in_Amber11 David A Case
- Re: [AMBER] error in parallel amber 11 installation Asmita Gupta
- Re: [AMBER] the real binding free energy David A Case
- Re: [AMBER] add_pdb Jason Swails
- Re: [AMBER] problems installing pmedm.cuda Jason Swails
- Re: [AMBER] creating a box of fixed size francesco oteri
- [AMBER] "Spiderweb" jun kit
- Re: [AMBER] problems installing pmedm.cuda Jason Swails
- Re: [AMBER] sander and pmemd Ross Walker
- Re: [AMBER] creating a box of fixed size Lorenzo Gontrani
- Re: [AMBER] "Spiderweb" Ross Walker
- Re: [AMBER] parameters for Lys-sugar leap errors Lachele Foley (Lists)
- Re: [AMBER] parameters for Lys-sugar leap errors Lachele Foley (Lists)
- Re: [AMBER] problems installing pmedm.cuda Peter Fojan
- Re: [AMBER] Amber 12 Installation errors relevant to fftw3 Jason Swails
- Re: [AMBER] Amber 12 Installation errors relevant to fftw3 M. L. Dodson
- Re: [AMBER] parameters for Lys-sugar leap errors FyD
- Re: [AMBER] "Spiderweb" FyD
- [AMBER] is lipid 11 FF compatible with GAFF? Albert
- [AMBER] Radii in prmtop Jesper Sørensen
- Re: [AMBER] Radii in prmtop Carlos Simmerling
- Re: [AMBER] Radii in prmtop Jesper Sørensen
- Re: [AMBER] is lipid 11 FF compatible with GAFF? Benjamin D Madej
- [AMBER] GTP parameter set for RNA luca codutti
- Re: [AMBER] is lipid 11 FF compatible with GAFF? Albert
- [AMBER] GLYCAM 06h and 06EPb Lachele Foley (Lists)
- Re: [AMBER] Radii in prmtop Jason Swails
- Re: [AMBER] Amber 12 Installation errors relevant to fftw3 David A Case
- Re: [AMBER] GTP parameter set for RNA Jacopo Sgrignani
- Re: [AMBER] Radii in prmtop Jesper Sørensen
- Re: [AMBER] Radii in prmtop Jason Swails
- [AMBER] Creating a concatenated coordinate file for LES Sajeewa Pemasinghe
- Re: [AMBER] Radii in prmtop case
- [AMBER] Creating a concatenated coordinate file for LES Sajeewa Pemasinghe
Friday, 27 April 2012
- Re: [AMBER] GTP parameter set for RNA luca codutti
- [AMBER] Angle restraints Komal Soni
- Re: [AMBER] Angle restraints David A Case
- Re: [AMBER] GTP parameter set for RNA luca codutti
- Re: [AMBER] GTP parameter set for RNA Jason Swails
- Re: [AMBER] GTP parameter set for RNA luca codutti
- [AMBER] Problem with molegro file Chris Chris
- [AMBER] IBM compiler for Amber12? Albert
- [AMBER] amber 12 with intel compiler failed Albert
- Re: [AMBER] amber 12 with intel compiler failed Jason Swails
- Re: [AMBER] amber 12 with intel compiler failed Albert
- Re: [AMBER] amber 12 with intel compiler failed Albert
- Re: [AMBER] amber 12 with intel compiler failed Jason Swails
- [AMBER] water cap simulation Yi An
- Re: [AMBER] Amber 12 Installation errors relevant to fftw3 Shulin Zhuang
Saturday, 28 April 2012
- [AMBER] calculation mean B factor of a PDB file Acoot Brett
- [AMBER] Electrostatic potential calculation Sudarshan Debnath
- [AMBER] preparation of silver metal parameter file Navin Jain
- Re: [AMBER] Amber 12 Installation errors relevant to fftw3 M. L. Dodson
- Re: [AMBER] calculation mean B factor of a PDB file Daniel Roe
- Re: [AMBER] Problem with molegro file case
- Re: [AMBER] water cap simulation case
- [AMBER] Problems with atom type in sidechain.bcl Fabrício Bracht
- Re: [AMBER] preparation of silver metal parameter file Jason Swails
- Re: [AMBER] mbondi3 Mike NG
- [AMBER] multiple GPU compile failed for Amber12 Albert
- Re: [AMBER] multiple GPU compile failed for Amber12 Jason Swails
- Re: [AMBER] mbondi3 Jason Swails
- Re: [AMBER] Radii in prmtop Jesper Sørensen
- [AMBER] calculation parallel xiaojiong
- [AMBER] the problem of charge xiaojiong
- Re: [AMBER] Radii in prmtop case
- Re: [AMBER] Electrostatic potential calculation Ray Luo, Ph.D.
- Re: [AMBER] multiple GPU compile failed for Amber12 Albert
- Re: [AMBER] Problems with atom type in sidechain.bcl ashwini gupta
- Re: [AMBER] the problem of charge Ben Roberts
- Re: [AMBER] calculation parallel Ben Roberts
Sunday, 29 April 2012
- Re: [AMBER] Problem with molegro file FyD
- Re: [AMBER] preparation of silver metal parameter file FyD
- Re: [AMBER] the problem of charge FyD
- [AMBER] testing amber12 fails Vijay Manickam Achari
- [AMBER] how can apply external force to DNA residues? mehdi bagherpoor
- Re: [AMBER] the problem of charge FyD
- Re: [AMBER] testing amber12 fails case
- [AMBER] Fwd: Creating a concatenated coordinate file for LES Sajeewa Pemasinghe
- Re: [AMBER] Radii in prmtop Jesper Sørensen
- Re: [AMBER] Radii in prmtop case
- Re: [AMBER] Radii in prmtop Ray Luo
- [AMBER] is there a second methods to use CHARMM FF in amber? Albert
- Re: [AMBER] Radii in prmtop Jesper Sørensen
Monday, 30 April 2012
- Re: [AMBER] mbondi3 Jesper Sørensen
- Re: [AMBER] is there a second methods to use CHARMM FF in amber? Marc van der Kamp
- [AMBER] MPI with options "-ip" and "-axSTPW" kurisaki
- Re: [AMBER] MPI with options "-ip" and "-axSTPW" Ben Roberts
- Re: [AMBER] MPI with options "-ip" and "-axSTPW" kurisaki
- [AMBER] RAMD simulations Agostino Bruno
- Re: [AMBER] RAMD simulations Vlad Cojocaru
- Re: [AMBER] RAMD simulations Jacopo Sgrignani
- Re: [AMBER] Radii in prmtop Daniel Roe
- Re: [AMBER] mbondi3 Ray Luo, Ph.D.
- [AMBER] input format for qms Genzo Tanaka
- Re: [AMBER] mbondi3 Niel Henriksen
- Re: [AMBER] Creating a concatenated coordinate file for LES Carlos Simmerling
- [AMBER] Fwd: mbondi3 Ray Luo, Ph.D.
- Re: [AMBER] is there a second methods to use CHARMM FF in amber? Albert
- Re: [AMBER] mbondi3 Qin Cai
- Re: [AMBER] water cap simulation anyiphysics.gmail.com
- [AMBER] error in decomposition analysis using ambertools 1.5 manikanthan bhavaraju
- Re: [AMBER] error in decomposition analysis using ambertools 1.5 Jason Swails
- Re: [AMBER] FW: FW: reduce and trim function Mahendra B Thapa
- Re: [AMBER] error in decomposition analysis using ambertools 1.5 manikanthan bhavaraju
- [AMBER] getting metal ions coordinates of nmr structures of a protein Mahendra B Thapa
- Re: [AMBER] error in decomposition analysis using ambertools 1.5 Jason Swails
- Re: [AMBER] error in decomposition analysis using ambertools 1.5 manikanthan bhavaraju
- Re: [AMBER] input format for qms Genzo Tanaka

Last message date: Mon Apr 30 2012 - 21:00:02 PDT
Archived on: Fri Nov 22 2024 - 05:54:29 PST

Amber Archive Apr 2012 by date