Amber Archive Mar 2012: by date

Thursday, 1 March 2012
- [AMBER] problem with MMPBSA script kureeckal ramesh
- Re: [AMBER] problem with MMPBSA script Nadine.Homeyer.uni-duesseldorf.de
- [AMBER] MMPBSA and explicit ions: what should I do? tommaso.casalini.mail.polimi.it
- [AMBER] error in sander_com.1.out kureeckal ramesh
- Re: [AMBER] error in sander_com.1.out Nadine.Homeyer.uni-duesseldorf.de
- Re: [AMBER] MMPBSA and explicit ions: what should I do? David A Case
- Re: [AMBER] problem with MMPBSA script David A Case
- Re: [AMBER] mm_pbsa error: Flag "RADII" not found in PARM file g t
- Re: [AMBER] mm_pbsa error: Flag "RADII" not found in PARM file g t
- Re: [AMBER] mm_pbsa error: Flag "RADII" not found in PARM file Jason Swails
- [AMBER] MMPBSA issue: incosistency within internal potential error tommaso.casalini.mail.polimi.it
- Re: [AMBER] mm_pbsa error: Flag "RADII" not found in PARM file g t
- Re: [AMBER] Help with solvating organic molecule with input .prmtop file Andy Ballard
- [AMBER] slow : amber job akshar bhosale
- Re: [AMBER] slow : amber job Aron Broom
- [AMBER] ABMD in pmemd.cuda in AMBER 12 Aron Broom
- Re: [AMBER] ABMD in pmemd.cuda in AMBER 12 Jason Swails
- Re: [AMBER] slow : amber job Cannon, John F.
- Re: [AMBER] ABMD in pmemd.cuda in AMBER 12 M. L. Dodson
- Re: [AMBER] ABMD in pmemd.cuda in AMBER 12 Aron Broom
- Re: [AMBER] Help with solvating organic molecule with input .prmtop file Jason Swails
- Re: [AMBER] ABMD in pmemd.cuda in AMBER 12 Jason Swails
- Re: [AMBER] ABMD in pmemd.cuda in AMBER 12 Ross Walker
- [AMBER] Problem in creating topology of NAD Ashutosh Shandilya
- Re: [AMBER] Problem in creating topology of NAD Ashutosh Shandilya
- [AMBER] top and crd file error kanika sharma
- Re: [AMBER] Problem in creating topology of NAD FyD
- Re: [AMBER] top and crd file error Aron Broom
- Re: [AMBER] Problem in creating topology of NAD FyD
- Re: [AMBER] top and crd file error kanika sharma
- Re: [AMBER] top and crd file error Aron Broom
Friday, 2 March 2012
- [AMBER] Distance plot Beale, John
- [AMBER] AMBER force calculations David Condon
- Re: [AMBER] Distance plot Cannon, John F.
- Re: [AMBER] AMBER force calculations Brian Radak
- Re: [AMBER] Distance plot Beale, John
- [AMBER] Defining sulfonyl halide atom type Chris Bryant
- [AMBER] control_rmsd_in TMD neha sree
- Re: [AMBER] slow : amber job akshar bhosale
Saturday, 3 March 2012
- Re: [AMBER] slow : amber job Jason Swails
- Re: [AMBER] md sticking! amir abbasi
- [AMBER] MMPB(GB)SA: two questions George Tzotzos
- [AMBER] PDB trajectory format Dmitry Osolodkin
- Re: [AMBER] PDB trajectory format Aron Broom
- Re: [AMBER] slow : amber job akshar bhosale
- Re: [AMBER] slow : amber job Carlos Simmerling
- Re: [AMBER] Defining sulfonyl halide atom type FyD
- Re: [AMBER] PDB trajectory format Daniel Roe
- Re: [AMBER] slow : amber job akshar bhosale
- Re: [AMBER] slow : amber job Aron Broom
Sunday, 4 March 2012
- Re: [AMBER] implicit and explicit Carlos Simmerling
- [AMBER] using GAFF with TIP3P model for simulation of solvated organic molecule Andy Ballard
- [AMBER] different residues use different force to restrict xiaojiong
- Re: [AMBER] using GAFF with TIP3P model for simulation of solvated organic molecule Jason Swails
- [AMBER] Question about Simulated Annealing procedure filip fratev
Monday, 5 March 2012
- [AMBER] MM-PBSA: different dielectric constants for ligand and receptor? Antonija Tomić
- [AMBER] Free Energy Calculate mehdi bagherpoor
- Re: [AMBER] different residues use different force to restrict David A Case
- [AMBER] Error in amber output files souvik sur
- Re: [AMBER] Question about Simulated Annealing procedure Carlos Simmerling
- Re: [AMBER] MM-PBSA: different dielectric constants for ligand and receptor? David A Case
- Re: [AMBER] Free Energy Calculate David A Case
- Re: [AMBER] MMPB(GB)SA: two questions Cannon, John F.
- Re: [AMBER] Question about Simulated Annealing procedure filip fratev
- [AMBER] ./nab -c dna3.nab,nab2c failed! Yudong Sun
- Re: [AMBER] ./nab -c dna3.nab,nab2c failed! David A Case
- [AMBER] Alkali and Halide Monovalent Ion : paper CHAMI F.
- Re: [AMBER] MMPB(GB)SA: two questions George Tzotzos
- Re: [AMBER] Alkali and Halide Monovalent Ion : paper Brian Radak
- [AMBER] turning off solute-solvent interactions Andy Ballard
- Re: [AMBER] Error in amber output files Jason Swails
- Re: [AMBER] turning off solute-solvent interactions Brian Radak
- [AMBER] Modified phosphotyrosine parameters Ilya Belalov
- [AMBER] Parameters Maxier Acosta
- Re: [AMBER] Error in amber output files souvik sur
- Re: [AMBER] ATP minimization Sangita Kachhap
Tuesday, 6 March 2012
- Re: [AMBER] ATP minimization FyD
- Re: [AMBER] Parameters FyD
- Re: [AMBER] Modified phosphotyrosine parameters FyD
- [AMBER] performance dependency on OS amir abbasi
- Re: [AMBER] performance dependency on OS steinbrt.rci.rutgers.edu
- [AMBER] SASA Plot Beale, John
- Re: [AMBER] SASA Plot Rajeswari A.
- Re: [AMBER] SASA Plot Daniel Roe
- Re: [AMBER] Error in amber output files David A Case
- Re: [AMBER] SASA Plot Bruno Luís Pinto de Oliveira
- Re: [AMBER] Alkali and Halide Monovalent Ion : paper CHAMI F.
- Re: [AMBER] Error in amber output files Jason Swails
- [AMBER] correct inconsistencies in [DR]NA_CI.lib Thomas Gaillard
- Re: [AMBER-Developers] [AMBER] Alkali and Halide Monovalent Ion : paper David A Case
- [AMBER] Assignment of partial charge to a molecule gargi borgohai
- Re: [AMBER] Assignment of partial charge to a molecule Aron Broom
- [AMBER] RED resp step failed Albert
- [AMBER] Residual Dipolar Coupling Rahul Banerjee
- Re: [AMBER] RED resp step failed Ismail, Mohd F.
- [AMBER] Dedication from Ibrahim - Manchester/Minia Mahmoud Ibrahim
- [AMBER] cluster configuration help Sangeetha B
- Re: [AMBER] correct inconsistencies in [DR]NA_CI.lib Jason Swails
- [AMBER] MMGBSA residue-wise decomposition Rajeswari A.
- [AMBER] how to keep atom restrained in R.E.D? Albert
Wednesday, 7 March 2012
- Re: [AMBER] SASA Plot setyanto md
- [AMBER] Fwd: SASA Plot João Ribeiro
- [AMBER] covert CHARMM format PDB file to AMBER formart Tong Zhu
- Re: [AMBER] [q4md-fft] how to keep atom restrained in R.E.D? FyD
- Re: [AMBER] covert CHARMM format PDB file to AMBER formart c00jsw00.nchc.narl.org.tw
- [AMBER] AM1 Jacopo Sgrignani
- Re: [AMBER] Residual Dipolar Coupling case
- Re: [AMBER] covert CHARMM format PDB file to AMBER formart case
- [AMBER] GPU performance and GPU Direct steinbrt.rci.rutgers.edu
- Re: [AMBER] GPU performance and GPU Direct Gould, Ian R
- Re: [AMBER] Best way to implement PBC Ben Ahmady
- Re: [AMBER] AM1 Brian Radak
- [AMBER] cpptraj surf Segmentation fault Guillermo Mulliert Carlín
- Re: [AMBER] cpptraj surf Segmentation fault Daniel Roe
- [AMBER] non-linear PB solver within MMPBSA: questions regarding EEL, eneopt and cutnb Jan-Philip Gehrcke
- Re: [AMBER] SASA Plot Daniel Roe
- [AMBER] Dihedral analysis Ibrahim Moustafa
- [AMBER] Velocity kirtana S
- Re: [AMBER] Velocity Adrian Roitberg
- Re: [AMBER] Dedication from Ibrahim - Manchester/Minia David A Case
- [AMBER] SHAKE not available for parallel runs CHAMI F.
- Re: [AMBER] Best way to implement PBC steinbrt.rci.rutgers.edu
- [AMBER] Question about output files lnedialkova.gmail.com
- [AMBER] Comparison of the results manikanthan bhavaraju
- Re: [AMBER] SHAKE not available for parallel runs case
- Re: [AMBER] Question about output files case
- [AMBER] Harmonic Restraint in pmemd.cuda Aron Broom
- Re: [AMBER] Harmonic Restraint in pmemd.cuda Adrian Roitberg
- Re: [AMBER] Harmonic Restraint in pmemd.cuda Aron Broom
- Re: [AMBER] Harmonic Restraint in pmemd.cuda Adrian Roitberg
- [AMBER] How to get the information of hydrophobic contact? qiao xue
- Re: [AMBER] SASA Plot setyanto md
- [AMBER] MMGBSA residue-wise decomposition Rajeswari A.
- Re: [AMBER] Parameters setyanto md
- Re: [AMBER] RED resp step failed Albert
- [AMBER] Fwd: Comparison of the results manikanthan bhavaraju
- Re: [AMBER] AM1 Jacopo Sgrignani
- Re: [AMBER] [q4md-fft] Re: RED resp step failed FyD
- [AMBER] Viewing with VMD bonds set by the "bond" command Francesco Pietra
Thursday, 8 March 2012
- Re: [AMBER] Viewing with VMD bonds set by the "bond" command Lorenzo Gontrani
- Re: [AMBER] Viewing with VMD bonds set by the "bond" command Francesco Pietra
- Re: [AMBER] Viewing with VMD bonds set by the "bond" command Lorenzo Gontrani
- Re: [AMBER] Viewing with VMD bonds set by the "bond" command Francesco Pietra
- [AMBER] Base stacking amir abbasi
- Re: [AMBER] Viewing with VMD bonds set by the "bond" command FyD
- Re: [AMBER] Viewing with VMD bonds set by the "bond" command Francesco Pietra
- Re: [AMBER] Viewing with VMD bonds set by the "bond" command FyD
- Re: [AMBER] Dihedral analysis Niel Henriksen
- Re: [AMBER] Viewing with VMD bonds set by the "bond" command francesco oteri
- [AMBER] How to convert multiple mdcrd files to single files with minimium size? Catein Catherine
- Re: [AMBER] How to convert multiple mdcrd files to single files with minimium size? Marc van der Kamp
- [AMBER] NAB segmentation fault Michael F. Bruist
- Re: [AMBER] Dihedral analysis Ibrahim Moustafa
- Re: [AMBER] How to convert multiple mdcrd files to single files with minimium size? Aron Broom
- Re: [AMBER] Dihedral analysis CHAMI F.
- Re: [AMBER] Base stacking amirhossein taghavi
- Re: [AMBER] Base stacking amirhossein taghavi
- [AMBER] saltconc and string parameters in MM/PB(GB)SA mish
- Re: [AMBER] saltconc and string parameters in MM/PB(GB)SA Thomas Cheatham III
- Re: [AMBER] Base stacking amir abbasi
- Re: [AMBER] Viewing with VMD bonds set by the "bond" command Francesco Pietra
- Re: [AMBER] Base stacking Ilyas Yildirim
- [AMBER] Can I use Amber 10 PRMTOP with Amber 11? Kasprzak, Wojciech (NIH/NCI) [C]
- Re: [AMBER] Base stacking francesco oteri
- [AMBER] Mac OSX 10.7 George Tzotzos
- Re: [AMBER] saltconc and string parameters in MM/PB(GB)SA mish
- Re: [AMBER] Base stacking amir abbasi
- Re: [AMBER] saltconc and string parameters in MM/PB(GB)SA Aron Broom
- Re: [AMBER] Mac OSX 10.7 Jason Swails
- Re: [AMBER] Can I use Amber 10 PRMTOP with Amber 11? Jason Swails
- Re: [AMBER] Comparison of the results Jason Swails
- Re: [AMBER] Comparison of the results manikanthan bhavaraju
- [AMBER] Fwd: vmd-l: Re: Viewing with VMD bonds set by the "bond" command Francesco Pietra
- [AMBER] Hydrogen bond analysis tdo.chem.ucsb.edu
Friday, 9 March 2012
- Re: [AMBER] Hydrogen bond analysis Daniel Roe
- [AMBER] separated thermostat in AMBER mjyang
- Re: [AMBER] compiler-dependent error: "Invalid atom or grouping specified in restraint." Jan-Philip Gehrcke
- Re: [AMBER] separated thermostat in AMBER David A Case
- Re: [AMBER] Base stacking amirhossein taghavi
- [AMBER] cluster configuration help Sangeetha B
- Re: [AMBER] Viewing with VMD bonds set by the "bond" command FyD
- [AMBER] Job Opening at Simbios/Stanford University Ross Walker
- [AMBER] Energy and Coordinate Outputs David Minh
- [AMBER] Amber11 Intel compiler version 12 make parallel fail Andrew Petersen
- Re: [AMBER] Energy and Coordinate Outputs David Case
- Re: [AMBER] Amber11 Intel compiler version 12 make parallel fail David Case
- Re: [AMBER] Energy and Coordinate Outputs David Minh
- [AMBER] Amber10 paralel installation Shaandar Nyamtulga
Saturday, 10 March 2012
- Re: [AMBER] Energy and Coordinate Outputs David A. Case
- Re: [AMBER] cluster configuration help Thomas Cheatham
- Re: [AMBER] Amber10 paralel installation Jason Swails
- Re: [AMBER] non-linear PB solver within MMPBSA: questions regarding EEL, eneopt and cutnb Jason Swails
Sunday, 11 March 2012
- Re: [AMBER] cluster configuration help Sangeetha B
- Re: [AMBER] compiler-dependent error: "Invalid atom or grouping specified in restraint." David A. Case
- Re: [AMBER] NAB segmentation fault David A. Case
- Re: [AMBER] compiler-dependent error: "Invalid atom or grouping specified in restraint." Jason Swails
- [AMBER] asking about mden setyanto md
- Re: [AMBER] asking about mden Ben Roberts
Monday, 12 March 2012
- Re: [AMBER] asking about mden setyanto md
- Re: [AMBER] Energy and Coordinate Outputs David Minh
- [AMBER] April 3 deadline for application for ACS computational chemistry awards for the Fall 2012 national meeting Carlos Simmerling
- Re: [AMBER] NAB segmentation fault Michael F. Bruist
Tuesday, 13 March 2012
- Re: [AMBER] NAB segmentation fault David A. Case
- [AMBER] binding free energy kirtana S
- Re: [AMBER] binding free energy Sushil Mishra
- [AMBER] Use of SLEF1 force field in Amber Gonzalo Jimenez
- [AMBER] tleap and water molecules Enrico Caldarulo
- [AMBER] R: tleap and water molecules Giovanni Pavan
- [AMBER] MMGBSA residue-wise decomposition Rajeswari A.
- [AMBER] Replica Exchange Rajendra Sharma
- [AMBER] MMPBSA George Tzotzos
- [AMBER] MMPBSA George Tzotzos
- Re: [AMBER] MMPBSA Aron Broom
- Re: [AMBER] MMPBSA George Tzotzos
- Re: [AMBER] How to get the information of hydrophobic contact? g t
- Re: [AMBER] Dihedral analysis g t
- Re: [AMBER] MMPBSA Dmitry Mukha
- Re: [AMBER] MMPBSA George Tzotzos
- Re: [AMBER] MMPBSA Dmitry Mukha
- Re: [AMBER] Replica Exchange Dmitry Mukha
- Re: [AMBER] MMPBSA George Tzotzos
- [AMBER] PBSA sprob question Jesper Sørensen
- Re: [AMBER] Force Field Parameterization -- Torsion Potentials Ismail, Mohd F.
- Re: [AMBER] PBSA sprob question Qin Cai
- Re: [AMBER] Force Field Parameterization -- Torsion Potentials Ismail, Mohd F.
- Re: [AMBER] Energy and Coordinate Outputs Jason Swails
- [AMBER] Extra Bonds For Water Kyle Greenway
- Re: [AMBER] Extra Bonds For Water Adrian Roitberg
- Re: [AMBER] PBSA sprob question Jesper Sørensen
- Re: [AMBER] PBSA sprob question Qin Cai
- [AMBER] ptraj: Sort trajectory based on protein-ligand distance tdo.chem.ucsb.edu
- [AMBER] The value of Delta G is positive after MMPBSA calculation for metalloprotein JiYuan Liu
Wednesday, 14 March 2012
- [AMBER] Amber 10 parallel installation error Shaandar Nyamtulga
- [AMBER] antechamber error Syed Tarique Moin
- Re: [AMBER] Force Field Parameterization -- Torsion Potentials Karl N. Kirschner
- Re: [AMBER] MMGBSA residue-wise decomposition Carlos Simmerling
- Re: [AMBER] MMGBSA residue-wise decomposition Jason Swails
- [AMBER] both parallel and serial amir abbasi
- Re: [AMBER] both parallel and serial Jason Swails
- Re: [AMBER] Replica Exchange Rajendra Sharma
- Re: [AMBER] Replica Exchange Indrajit Deb
- Re: [AMBER] Replica Exchange Carlos Simmerling
- Re: [AMBER] Replica Exchange Alex Rodriguez
- Re: [AMBER] Replica Exchange Logan Ahlstrom
- Re: [AMBER] Replica Exchange Adrian Roitberg
- Re: [AMBER] PBSA sprob question Jesper Sørensen
- Re: [AMBER] ptraj: Sort trajectory based on protein-ligand distance g t
- Re: [AMBER] Use of SLEF1 force field in Amber CHAMI F.
- Re: [AMBER] Energy and Coordinate Outputs David A. Case
- Re: [AMBER] binding free energy David A. Case
- Re: [AMBER] binding free energy David A. Case
- Re: [AMBER] Energy and Coordinate Outputs David A. Case
- Re: [AMBER] Use of SLEF1 force field in Amber Gonzalo Jimenez
- [AMBER] Amber10 parallel installation test example run error Shaandar Nyamtulga
- [AMBER] Amber10 parallel installation test error Shaandar Nyamtulga
- Re: [AMBER] MMGBSA residue-wise decomposition Rajeswari A.
Thursday, 15 March 2012
- Re: [AMBER] Amber10 parallel installation test example run error Daniel Roe
- [AMBER] simulation with metal-containing ligands Fati
- [AMBER] Announcement: Large biomolecule benchmark report Hannes Loeffler
- Re: [AMBER] binding free energy David A Case
- [AMBER] puting restrains Urszula Uciechowska
- Re: [AMBER] puting restrains Brian Radak
- Re: [AMBER] MMGBSA residue-wise decomposition Jason Swails
- [AMBER] Is it possible to cluster several mdcrd files based on a dihedral angles of a particular residues? Catein Catherine
- [AMBER] rigid body simulation Qian Wang
- Re: [AMBER] PDB trajectory format Dmitry Osolodkin
- Re: [AMBER] PDB trajectory format Daniel Roe
- [AMBER] restrain water in a solvatecap Yi An
- Re: [AMBER] Amber10 parallel installation test error David A Case
- Re: [AMBER] rigid body simulation David A Case
- Re: [AMBER] rigid body simulation Ilyas Yildirim
- [AMBER] on the AMBER advanced tutorial 3 MM-PBSA Wholly Peach
- Re: [AMBER] Force Field Parameterization -- Torsion Potentials Ismail, Mohd F.
Friday, 16 March 2012
- [AMBER] the problem of RAMD xiaojiong
- Re: [AMBER] the problem of RAMD Vlad Cojocaru
- Re: [AMBER] puting restrains Urszula Uciechowska
- Re: [AMBER] antechamber error David A Case
- Re: [AMBER] Amber 10 parallel installation error David A Case
- [AMBER] MMPBSA, in parallel? Fernando Blanco
- [AMBER] mpi-allreduce in AMBER11 Carlos Sosa
- Re: [AMBER] mpi-allreduce in AMBER11 Jason Swails
- Re: [AMBER] MMPBSA, in parallel? Jason Swails
- [AMBER] Amber for Cuda on Mac OSX George Tzotzos
- Re: [AMBER] PDB trajectory format Dmitry Osolodkin
- Re: [AMBER] PDB trajectory format Daniel Roe
- Re: [AMBER] PDB trajectory format Dmitry Osolodkin
- Re: [AMBER] PDB trajectory format Daniel Roe
- Re: [AMBER] NAB segmentation fault Michael F. Bruist
- Re: [AMBER] mpi-allreduce in AMBER11 Carlos Sosa
- [AMBER] MMPBSA.py - Internal energy George Tzotzos
- Re: [AMBER] Amber for Cuda on Mac OSX Jason Swails
- Re: [AMBER] MMPBSA.py - Internal energy Jason Swails
- Re: [AMBER] MMPBSA.py - Internal energy George Tzotzos
- Re: [AMBER] AMBER force calculations David Condon
- Re: [AMBER] AMBER force calculations Brian Radak
- Re: [AMBER] AMBER force calculations David Condon
- Re: [AMBER] AMBER force calculations Jason Swails
- [AMBER] Implicit MD run Aditya Padhi
- [AMBER] No Na molecule type for genion Wholly Peach
- Re: [AMBER] Implicit MD run Aron Broom
- Re: [AMBER] No Na molecule type for genion raghav singh
- Re: [AMBER] Implicit MD run Aditya Padhi
- Re: [AMBER] Implicit MD run Aron Broom
- Re: [AMBER] Implicit MD run Aditya Padhi
Saturday, 17 March 2012
- Re: [AMBER] Implicit MD run Carlos Simmerling
- Re: [AMBER] Energy and Coordinate Outputs David Minh
- Re: [AMBER] No Na molecule type for genion M. L. Dodson
- [AMBER] PB with inp=2 doesn't recognize ff10 atom types? David Minh
- Re: [AMBER] on the AMBER advanced tutorial 3 MM-PBSA Bill Miller III
- Re: [AMBER] on the AMBER advanced tutorial 3 MM-PBSA Aron Broom
- [AMBER] Fwd: PB with inp=2 doesn't recognize ff10 atom types? Ray Luo, Ph.D.
Sunday, 18 March 2012
- [AMBER] Amber8 and RAMD xiaojiong
- Re: [AMBER] Amber8 and RAMD Vlad Cojocaru
- [AMBER] is GB/SA suitable for nonaqueous solvent? Junjian Miao
- Re: [AMBER] is GB/SA suitable for nonaqueous solvent? Carlos Simmerling
- Re: [AMBER] Implicit MD run Aditya Padhi
Monday, 19 March 2012
- Re: [AMBER] Which method is the best way to solve metalloprotein?MCPB or Only consider Electrostatic and VDW Ben Roberts
- [AMBER] Problems with tetrahedral Al in antechamber Gonzalo Jimenez
- [AMBER] Problems with tetrahedral Al in antechamber Gonzalo Jimenez
- Re: [AMBER] Implicit MD run Carlos Simmerling
- Re: [AMBER] Implicit MD run Aditya Padhi
- Re: [AMBER] Problems with tetrahedral Al in antechamber case
- Re: [AMBER] Implicit MD run Carlos Simmerling
- Re: [AMBER] Force Field Parameterization -- Torsion Potentials Karl N. Kirschner
- Re: [AMBER] Which method is the best way to solve metalloprotein?MCPB or Only consider Electrostatic and VDW JiYuan Liu
- [AMBER] To generate more than one structure using ptraj Souvik Sur
- Re: [AMBER] To generate more than one structure using ptraj Jason Swails
- Re: [AMBER] is GB/SA suitable for nonaqueous solvent? Dean Cuebas
- Re: [AMBER] is GB/SA suitable for nonaqueous solvent? Alex Rodriguez
- [AMBER] charges for ion and surrounding residues at the active site JORGE IULEK
- [AMBER] restrain water in a solvatecap Yi An
- [AMBER] How to calculate the energy contributed by hydrogen bonds? bin wang
- Re: [AMBER] PB with inp=2 doesn't recognize ff10 atom types? Qin Cai
- [AMBER] charges for ion and surrounding residues at the active site Jorge Iulek
- Re: [AMBER] How to calculate the energy contributed by hydrogen bonds? Jason Swails
- Re: [AMBER] restrain water in a solvatecap liu junjun
- Re: [AMBER] Implicit MD run Aditya Padhi
- Re: [AMBER] To generate more than one structure using ptraj Souvik Sur
- [AMBER] organics solvent radius setyanto md
Tuesday, 20 March 2012
- [AMBER] MD and RAMD xiaojiong
- [AMBER] Is there some constrains required for the REMD simulation on disaccharide in Amber11? 黄恋琦
- Re: [AMBER] MD and RAMD Vlad Cojocaru
- Re: [AMBER] Implicit MD run Carlos Simmerling
- Re: [AMBER] Implicit MD run Aditya Padhi
- Re: [AMBER] charges for ion and surrounding residues at the active site FyD
- Re: [AMBER] How to calculate the energy contributed by hydrogen bonds? bin wang
- [AMBER] Fast ibelly? David Minh
- Re: [AMBER] Which method is the best way to solve metalloprotein?MCPB or Only consider Electrostatic and VDW FyD
- Re: [AMBER] How to calculate the energy contributed by hydrogen bonds? Jason Swails
- Re: [AMBER] To generate more than one structure using ptraj Jason Swails
- Re: [AMBER] Fast ibelly? Ross Walker
- [AMBER] GBSA - surface tension question for calculation of ΔGnonpolar g t
- Re: [AMBER] GBSA - surface tension question for calculation of ΔGnonpolar Carlos Simmerling
- Re: [AMBER] Fast ibelly? David Minh
- [AMBER] disulfide bond warnings George Tzotzos
- Re: [AMBER] Fast ibelly? Ross Walker
- Re: [AMBER] Fast ibelly? David A Case
- Re: [AMBER] disulfide bond warnings Jason Swails
- Re: [AMBER] GBSA - surface tension question for calculation of ΔGnonpolar g t
- Re: [AMBER] disulfide bond warnings George Tzotzos
- Re: [AMBER] charges for ion and surrounding residues at the active site Jorge Iulek
- Re: [AMBER] NAB segmentation fault Brian Wolfe
- Re: [AMBER] NAB segmentation fault case
- Re: [AMBER] disulfide bond warnings Jason Swails
- [AMBER] Water coordinated with transition metal ashwini gupta
Wednesday, 21 March 2012
- Re: [AMBER] charges for ion and surrounding residues at the active site FyD
- Re: [AMBER] Water coordinated with transition metal Ben Roberts
- Re: [AMBER] Water coordinated with transition metal ashwini gupta
- Re: [AMBER] Water coordinated with transition metal Ben Roberts
- Re: [AMBER] Water coordinated with transition metal ashwini gupta
- Re: [AMBER] Water coordinated with transition metal Ben Roberts
- Re: [AMBER] GBSA - surface tension question for calculation of ΔGnonpolar Carlos Simmerling
- [AMBER] About ANAL problem: Amber 王伟
- Re: [AMBER] Water coordinated with transition metal ashwini gupta
- Re: [AMBER] About ANAL problem: Amber David A Case
- [AMBER] Amber 11 Compilation Error (again!) Adam Jion
- Re: [AMBER] Amber 11 Compilation Error (again!) Jason Swails
- Re: [AMBER] Fast ibelly? David Minh
- [AMBER] Converting Gromacs coordinate file to Amber input files for molecular dynamics Adam Jion
- Re: [AMBER] Converting Gromacs coordinate file to Amber input files formolecular dynamics Vlad Cojocaru
- Re: [AMBER] Converting Gromacs coordinate file to Amber input files for molecular dynamics Alex Rodriguez
- [AMBER] External Force Method in pmemd.cuda Ismail, Mohd F.
- Re: [AMBER] External Force Method in pmemd.cuda Jason Swails
- Re: [AMBER] External Force Method in pmemd.cuda Ismail, Mohd F.
- Re: [AMBER] charges for ion and surrounding residues at the active site Jorge Iulek
- Re: [AMBER] How to calculate the energy contributed by hydrogen bonds? bin wang
- Re: [AMBER] GBSA - surface tension question for calculation of ΔGnonpolar g t
- Re: [AMBER] About ANAL problem: Amber Soumya Lipsa Rath
Thursday, 22 March 2012
- Re: [AMBER] Test if MD converged or not. g t
- Re: [AMBER] problem in output file of the awk script in tutorial A6 g t
- [AMBER] Problem in Amber installation vishal Nemaysh
- [AMBER] Non - integral charge o unperturbed unit ashwini gupta
- [AMBER] Is it possible to just calculate translational and rotational entropy? Tan Yaw Sing
- Re: [AMBER] About ANAL problem: Amber David A Case
- Re: [AMBER] Problem in Amber installation David A Case
- Re: [AMBER] Is it possible to just calculate translational and rotational entropy? David A Case
- Re: [AMBER] Problem in Amber installation Jason Swails
- Re: [AMBER] About ANAL problem: Amber 王伟
- [AMBER] amber parameters for cytochrome c Gurunath Katagi
- [AMBER] atom type of Sulphur in CYS/CYM (MCPB) ashwini gupta
Friday, 23 March 2012
- [AMBER] Amber10 parallel installation test example Shaandar Nyamtulga
- [AMBER] esp and resp comparison jun kit
- Re: [AMBER] atom type of Sulphur in CYS/CYM (MCPB) Tong Zhu
- [AMBER] parameters for Lys-sugar Urszula Uciechowska
- Re: [AMBER] Amber10 parallel installation test example David A Case
- [AMBER] Problems compiling pmemd.cuda - undefined reference to ... Adam Jion
- [AMBER] About ANAL problem: Amber 王伟
- Re: [AMBER] Non - integral charge o unperturbed unit FyD
- Re: [AMBER] esp and resp comparison FyD
- Re: [AMBER] parameters for Lys-sugar FyD
- Re: [AMBER] parameters for Lys-sugar Lachele Foley (Lists)
- [AMBER] Conflict between AmberTools 1.5 and Cuda Adam Jion
- Re: [AMBER] parameters for Lys-sugar Urszula Uciechowska
- Re: [AMBER] parameters for Lys-sugar FyD
- Re: [AMBER] Conflict between AmberTools 1.5 and Cuda Daniel Roe
- Re: [AMBER] Problems compiling pmemd.cuda - undefined reference to ... Ross Walker
- Re: [AMBER] Conflict between AmberTools 1.5 and Cuda Ross Walker
- Re: [AMBER] Conflict between AmberTools 1.5 and Cuda Adam Jion
- Re: [AMBER] Problems compiling pmemd.cuda - undefined reference to ... Adam Jion
- Re: [AMBER] parameters for Lys-sugar Lachele Foley (Lists)
- Re: [AMBER] Problems compiling pmemd.cuda - undefined reference to ... Daniel Roe
- Re: [AMBER] Conflict between AmberTools 1.5 and Cuda David A Case
- [AMBER] GTX680 filip fratev
- Re: [AMBER] GTX680 Ross Walker
- Re: [AMBER] GTX680 Scott Le Grand
- Re: [AMBER] parameters for Lys-sugar Lachele Foley (Lists)
Saturday, 24 March 2012
- Re: [AMBER] About ANAL problem: Amber 王伟
- [AMBER] ANAL 王伟
- Re: [AMBER] parameters for Lys-sugar FyD
- Re: [AMBER] Conflict between AmberTools 1.5 and Cuda Adam Jion
- Re: [AMBER] Conflict between AmberTools 1.5 and Cuda Jan-Philip Gehrcke
- [AMBER] Error Compiling pmemd.cuda.MPI (i.e. Multiple GPUs) Adam Jion
- Re: [AMBER] parameters for Lys-sugar Lachele Foley (Lists)
- Re: [AMBER] Error Compiling pmemd.cuda.MPI (i.e. Multiple GPUs) Jason Swails
- Re: [AMBER] amber parameters for cytochrome c Jason Swails
- Re: [AMBER] Problems compiling pmemd.cuda - undefined reference to ... Jason Swails
- Re: [AMBER] Error Compiling pmemd.cuda.MPI (i.e. Multiple GPUs) Adam Jion
- Re: [AMBER] Error Compiling pmemd.cuda.MPI (i.e. Multiple GPUs) Scott Le Grand
- Re: [AMBER] Error Compiling pmemd.cuda.MPI (i.e. Multiple GPUs) Jason Swails
- Re: [AMBER] Error Compiling pmemd.cuda.MPI (i.e. Multiple GPUs) Adam Jion
- Re: [AMBER] parameters for Lys-sugar Urszula Uciechowska
- Re: [AMBER] parameters for Lys-sugar Urszula Uciechowska
- [AMBER] ptraj atomicfluct George Tzotzos
- Re: [AMBER] ptraj atomicfluct Thomas Cheatham
- Re: [AMBER] ptraj atomicfluct George Tzotzos
- Re: [AMBER] Error Compiling pmemd.cuda.MPI (i.e. Multiple GPUs) Adam Jion
- Re: [AMBER] Error Compiling pmemd.cuda.MPI (i.e. Multiple GPUs) Jason Swails
- Re: [AMBER] Error Compiling pmemd.cuda.MPI (i.e. Multiple GPUs) Adam Jion
- [AMBER] Problems testing pmemd.cuda.MPI Adam Jion
- Re: [AMBER] Error Compiling pmemd.cuda.MPI (i.e. Multiple GPUs) Jason Swails
- [AMBER] ANAL 王伟
- Re: [AMBER] Error Compiling pmemd.cuda.MPI (i.e. Multiple GPUs) Adam Jion
- [AMBER] ANAL wei wang
Sunday, 25 March 2012
- [AMBER] About ANAL wei wang
- [AMBER] Problems with pmemd.cuda.mpi (again!) Adam Jion
- Re: [AMBER] Problems with pmemd.cuda.mpi (again!) Ross Walker
- Re: [AMBER] Problems with pmemd.cuda.mpi (again!) Adam Jion
- Re: [AMBER] About ANAL David A. Case
- Re: [AMBER] Problems with pmemd.cuda.mpi (again!) Jason Swails
- Re: [AMBER] Problems with pmemd.cuda.mpi (again!) Adam Jion
- Re: [AMBER] atom type of Sulphur in CYS/CYM (MCPB) Ben Roberts
- Re: [AMBER] parameters for Lys-sugar Lachele Foley (Lists)
- Re: [AMBER] Problems testing pmemd.cuda.MPI Ben Roberts
- Re: [AMBER] Announcement: 2012 summer intern position at GSK 肖立
- Re: [AMBER] atom type of Sulphur in CYS/CYM (MCPB) ashwini gupta
- Re: [AMBER] parameters for Lys-sugar P2N file Urszula Uciechowska
Monday, 26 March 2012
- [AMBER] MP2 for RESP Tong Zhu
- [AMBER] amber12 Elisa Frezza
- Re: [AMBER] parameters for Lys-sugar P2N file FyD
- [AMBER] Fwd: V limit RAMON
- Re: [AMBER] Problems with pmemd.cuda.mpi (again!) Jason Swails
- [AMBER] cpptraj hbond George Tzotzos
- [AMBER] Amber and Short Bonds Aronica, Pietro
- [AMBER] TUTORIAL A1: Protein that Contains Non-Standard Residues Bala subramanian
- Re: [AMBER] amber12 Jason Swails
- Re: [AMBER] Problems with pmemd.cuda.mpi (again!) Adam Jion
- Re: [AMBER] amber12 Ross Walker
- Re: [AMBER] TUTORIAL A1: Protein that Contains Non-Standard Residues Ross Walker
- Re: [AMBER] Amber and Short Bonds Ross Walker
- Re: [AMBER] Problems with pmemd.cuda.mpi (again!) Jason Swails
- Re: [AMBER] Amber and Short Bonds Aronica, Pietro
- Re: [AMBER] Problems with pmemd.cuda.mpi (again!) Adam Jion
- Re: [AMBER] ABMD in pmemd.cuda in AMBER 12 Aron Broom
- Re: [AMBER] cpptraj hbond George Tzotzos
- [AMBER] compiling failure on ibm Yubo Fan
- Re: [AMBER] TUTORIAL A1: Protein that Contains Non-Standard Residues Bala subramanian
- Re: [AMBER] cpptraj hbond Daniel Roe
- Re: [AMBER] cpptraj hbond George Tzotzos
- Re: [AMBER] compiling failure on ibm Scott Brozell
- Re: [AMBER] compiling failure on ibm Jason Swails
- Re: [AMBER] Amber and Short Bonds Jason Swails
- Re: [AMBER] Amber and Short Bonds Thomas Cheatham
- Re: [AMBER] MP2 for RESP Ben Roberts
- Re: [AMBER] compiling failure on ibm Yubo Fan
- Re: [AMBER] Amber and Short Bonds Aronica, Pietro
- Re: [AMBER] Amber and Short Bonds Jason Swails
- Re: [AMBER] Amber and Short Bonds Aronica, Pietro
- Re: [AMBER] Amber and Short Bonds Adrian Roitberg
- [AMBER] Another question about Amber 12 Tong Zhu
- [AMBER] glycine sidechain contribution in MM-GBSA decompostion caobb0214
- Re: [AMBER] glycine sidechain contribution in MM-GBSA decompostion Carlos Simmerling
- Re: [AMBER] glycine sidechain contribution in MM-GBSA decompostion caobb0214
- [AMBER] ptraj removes my ligands DENILSON FERREIRA DE OLIVEIRA
- Re: [AMBER] ptraj removes my ligands Daniel Roe
- Re: [AMBER] glycine sidechain contribution in MM-GBSA decompostion Jason Swails
Tuesday, 27 March 2012
- [AMBER] assignment of partial charge to fullerene2160 gargi borgohai
- Re: [AMBER] assignment of partial charge to fullerene2160 steinbrt.rci.rutgers.edu
- [AMBER] angle restraint Elisa Frezza
- Re: [AMBER] glycine sidechain contribution in MM-GBSA decompostion Carlos Simmerling
- Re: [AMBER] Amber and Short Bonds Aronica, Pietro
- Re: [AMBER] amber12 Elisa Frezza
- Re: [AMBER] assignment of partial charge to fullerene2160 FyD
- Re: [AMBER] Amber and Short Bonds Jason Swails
- Re: [AMBER] amber12 Jason Swails
- Re: [AMBER] TUTORIAL A1: Protein that Contains Non-Standard Residues FyD
- [AMBER] AmberGS forcefield steinbrt.rci.rutgers.edu
- [AMBER] COM Olena Dobrovolska
- Re: [AMBER] AmberGS forcefield Carlos Simmerling
- Re: [AMBER] Another question about Amber 12 Ross Walker
Wednesday, 28 March 2012
- Re: [AMBER] COM David A. Case
- [AMBER] Segmentation fault Agostino Bruno
- Re: [AMBER] COM Olena Dobrovolska
- Re: [AMBER] GTX680 Scott Le Grand
- Re: [AMBER] GTX680 Aron Broom
- Re: [AMBER] GTX680 Scott Le Grand
- [AMBER] how to measure atom distance in md trajectories using ptraj program Bala Subramani
- Re: [AMBER] GTX680 Aron Broom
- Re: [AMBER] how to measure atom distance in md trajectories using ptraj program Daniel Roe
- Re: [AMBER] GTX680 Scott Le Grand
- Re: [AMBER] GTX680 Aron Broom
- Re: [AMBER] how to measure atom distance in md trajectories using ptraj program Bala Subramani
- [AMBER] error in nmode calculations manikanthan bhavaraju
- Re: [AMBER] error in nmode calculations Bill Miller III
- Re: [AMBER] how to measure atom distance in md trajectories using ptraj program Jason Swails
- Re: [AMBER] COM David A. Case
- Re: [AMBER] how to measure atom distance in md trajectories using ptraj program Daniel Roe
- Re: [AMBER] error in nmode calculations Cannon, John F.
- Re: [AMBER] Segmentation fault Ben Roberts
- Re: [AMBER] GTX680 Ross Walker
- Re: [AMBER] error in nmode calculations manikanthan bhavaraju
- Re: [AMBER] GTX680 Aron Broom
- Re: [AMBER] error in nmode calculations Jason Swails
- Re: [AMBER] Another question about Amber 12 Tong Zhu
- [AMBER] Problem with installation of MTKPP setyanto md
- Re: [AMBER] GTX680 Fenley, Andrew
- [AMBER] how to merge 10 trajectory files BALASUBRAMANI G L
- Re: [AMBER] how to merge 10 trajectory files Ben Roberts
- Re: [AMBER] Problem in Amber installation vishal Nemaysh
Thursday, 29 March 2012
- Re: [AMBER] Segmentation fault Agostino Bruno
- Re: [AMBER] Problem with installation of MTKPP Martin Peters
- Re: [AMBER] Segmentation fault Ben Roberts
- Re: [AMBER] Problem with installation of MTKPP setyanto md
- Re: [AMBER] Problem in Amber installation Jason Swails
- [AMBER] rfree: Error decoding variable 1 3 from: Elisa Frezza
- Re: [AMBER] error in nmode calculations David A. Case
- 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: David A Case
- Re: [AMBER] GTX680 Scott Le Grand
- Re: [AMBER] Fwd: V limit David A Case
- Re: [AMBER] rfree: Error decoding variable 1 3 from: Jason Swails
- Re: [AMBER] Fwd: V limit Ross Walker
- Re: [AMBER] Fwd: V limit Jason Swails
- Re: [AMBER] Fwd: V limit David A Case
- [AMBER] Particles moving outside of simulation box for pmemd.cuda.mpi Adam Jion
- Re: [AMBER] Particles moving outside of simulation box for pmemd.cuda.mpi Aron Broom
- Re: [AMBER] Particles moving outside of simulation box for pmemd.cuda.mpi Ben Roberts
- [AMBER] Amber10 parallel test example run error Shaandar Nyamtulga
Friday, 30 March 2012
- Re: [AMBER] Amber10 parallel test example run error Shaandar Nyamtulga
- Re: [AMBER] Problem in Amber installation setyanto md
- [AMBER] Asking About Differences between amber force field ff10 and ff03 setyanto md
- Re: [AMBER] Particles moving outside of simulation box for pmemd.cuda.mpi Adam Jion
- [AMBER] Fast moving system in targeted MD Thomas Exner
- [AMBER] Large Energy Jump in TMD simulation - Regarding Fredrick Devadoss
- [AMBER] Issue with running sander 板垣哲彦
- [AMBER] Query on error abinayar.imsc.res.in
- [AMBER] Query on error :Atom does not have a type abinayar.imsc.res.in
- 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
- Re: [AMBER] Problem in Amber installation Jason Swails
- Re: [AMBER] Issue with running sander Jason Swails
- Re: [AMBER] Query on error :Atom does not have a type Jason Swails
- Re: [AMBER] Asking About Differences between amber force field ff10 and ff03 Aron Broom
- [AMBER] Which methodology could estimate the binding affinity of zinc containing metalloprotei(wrong string) �Cligand complex accurately? JiYuan Liu
- Re: [AMBER] Large Energy Jump in TMD simulation - Regarding Carlos Simmerling
- Re: [AMBER] Asking About Differences between amber force field ff10 and ff03 David A Case
- Re: [AMBER] Issue with running sander David A Case
- [AMBER] ptraj: SegFault during SOM clustering Anselm Horn
- Re: [AMBER] Particles moving outside of simulation box for pmemd.cuda.mpi Ross Walker
- Re: [AMBER] Issue with running sander Jason Swails
- Re: [AMBER] Large Energy Jump in TMD simulation - Regarding Fredrick Devadoss
- Re: [AMBER] ptraj removes my ligands Daniel Roe
- Re: [AMBER] Large Energy Jump in TMD simulation - Regarding Jason Swails
- Re: [AMBER] Large Energy Jump in TMD simulation - Regarding Fredrick Devadoss
- Re: [AMBER] Large Energy Jump in TMD simulation - Regarding Jason Swails
Saturday, 31 March 2012
- [AMBER] test failure in the AMBERTOOL installation Acoot Brett

Last message date: Sat Mar 31 2012 - 23:30:03 PDT
Archived on: Fri Apr 26 2024 - 05:54:34 PDT

Amber Archive Mar 2012 by date