Amber Archive Aug 2011: by date

Sunday, 31 July 2011
- Re: [AMBER] Undefined symbols when compiling AMBER11 on Mac OSX 10.6 Daniel Sindhikara
Monday, 1 August 2011
- Re: [AMBER] Question about ptraj hbond schematic Kamali Sripathi
- [AMBER] Proble related to with dipole-dipole correlation function Sindrila Dutta banik
- [AMBER] Protein-sugar interactions Thomas Exner
- Re: [AMBER] Protein-sugar interactions David A Case
- [AMBER] Announcement: Release of DOCK 6.5 Scott Brozell
- Re: [AMBER] Protein-sugar interactions Lachele Foley (Lists)
- [AMBER] loadPdb segmentation fault Massimiliano Porrini
- Re: [AMBER] loadPdb segmentation fault David A Case
- Re: [AMBER] CHARMM format to Amber format David Cantu
- Re: [AMBER] loadPdb segmentation fault Massimiliano Porrini
- Re: [AMBER] CHARMM format to Amber format Ross Walker
- [AMBER] About running sander parallel Aimin
- Re: [AMBER] About running sander parallel Ross Walker
- Re: [AMBER] About running sander parallel Aimin
- Re: [AMBER] CHARMM format to Amber format David Cantu
- Re: [AMBER] loadPdb segmentation fault David A Case
- Re: [AMBER] loadPdb segmentation fault Jason Swails
- [AMBER] MMGBSA error Irene Newhouse
- [AMBER] Using NMR restraints during minimization Kamali Sripathi
- Re: [AMBER] About running sander parallel Aimin
- Re: [AMBER] About running sander parallel Ross Walker
- Re: [AMBER] MMGBSA error Jason Swails
- Re: [AMBER] About running sander parallel Aimin
- Re: [AMBER] About running sander parallel Ross Walker
- Re: [AMBER] Failure kReduceSoluteCOM with GPU Scott Le Grand
- Re: [AMBER] About running sander parallel Jason Swails
- Re: [AMBER] Using NMR restraints during minimization Jason Swails
- [AMBER] ambpdb not installed Chirag Vora
- [AMBER] QUASI-HARMONIC APPROXIMATION belal najjar
Tuesday, 2 August 2011
- [AMBER] 2011年7月20日 19:53:32 自动保存草稿 zhouhaibin2008.ok
- Re: [AMBER] ambpdb not installed Bruno Rodrigues
- Re: [AMBER] ambpdb not installed Bruno Rodrigues
- Re: [AMBER] ambpdb not installed Chirag Vora
- Re: [AMBER] QUASI-HARMONIC APPROXIMATION Bill Miller III
- Re: [AMBER] Using NMR restraints during minimization Kamali Sripathi
- Re: [AMBER] 2011年7月20日 19:53:32 自动保存草稿 Jason Swails
- Re: [AMBER] Using NMR restraints during minimization Jason Swails
- Re: [AMBER] ambpdb not installed Jason Swails
- [AMBER] Movement of molecules to satisfy distance constraints David Condon
- Re: [AMBER] Using NMR restraints during minimization case
- [AMBER] Fwd: Problem with MMPBSA.py Ray Luo, Ph.D.
- Re: [AMBER] Movement of molecules to satisfy distance constraints David A Case
- Re: [AMBER] [Amber] Amber vs ab initio Steven M. Graham
- Re: [AMBER] Movement of molecules to satisfy distance constraints David Condon
- [AMBER] NAB for a mismatch RNA sequence Charles Johnson
- [AMBER] can non-bonded interactions be switched off? Jose Borreguero
- Re: [AMBER] can non-bonded interactions be switched off? Ross Walker
- Re: [AMBER] can non-bonded interactions be switched off? Jose Borreguero
- Re: [AMBER] Using NMR restraints during minimization Kamali Sripathi
- Re: [AMBER] Using NMR restraints during minimization Kamali Sripathi
- Re: [AMBER] loadPdb segmentation fault Massimiliano Porrini
- [AMBER] Distorted waters in restrained mini Maura Catherine Mooney
- Re: [AMBER] Distorted waters in restrained mini David Case
- Re: [AMBER] Distorted waters in restrained mini Maura Catherine Mooney
- Re: [AMBER] About running sander parallel Aimin
- Re: [AMBER] About running sander parallel Jason Swails
- Re: [AMBER] [Amber] Amber vs ab initio David Cantu
- Re: [AMBER] Distorted waters in restrained mini David Case
- Re: [AMBER] loadPdb segmentation fault Jason Swails
- [AMBER] Electrostatci and van der Waals energy in Amber11 Okabe_Atsutoshi.takeda.co.jp
- Re: [AMBER] loadPdb segmentation fault Jason Swails
Wednesday, 3 August 2011
- [AMBER] MD stop but this job in cluster still run tien dung
- Re: [AMBER] Energy or Temperature Fluctuation Bruno Rodrigues
- Re: [AMBER] Problem related to the RMSD Bruno Rodrigues
- Re: [AMBER] loadPdb segmentation fault Massimiliano Porrini
- [AMBER] Dipole-dipole correlation Function Sindrila Dutta banik
- Re: [AMBER] NAB for a mismatch RNA sequence David A Case
- [AMBER] more info on using the Amber force field in NAMD David A Case
- Re: [AMBER] NAB for a mismatch RNA sequence Charles Johnson
- Re: [AMBER] loadPdb segmentation fault Jason Swails
- Re: [AMBER] NAB for a mismatch RNA sequence David A Case
- [AMBER] van der Waals atom parent list r smith
- [AMBER] "softcore potential" problem in TI calculation Victor Ma
- Re: [AMBER] more info on using the Amber force field in NAMD George Madalin Giambasu
- Re: [AMBER] "softcore potential" problem in TI calculation steinbrt.rci.rutgers.edu
- Re: [AMBER] loadPdb segmentation fault Massimiliano Porrini
- Re: [AMBER] more info on using the Amber force field in NAMD David A Case
- Re: [AMBER] "softcore potential" problem in TI calculation Victor Ma
- [AMBER] convert netcdf to crd moitrayee.mbu.iisc.ernet.in
- Re: [AMBER] loadPdb segmentation fault Jason Swails
- Re: [AMBER] convert netcdf to crd Daniel Roe
- Re: [AMBER] MD stop but this job in cluster still run Daniel Roe
- Re: [AMBER] MD stop but this job in cluster still run Jason Swails
- Re: [AMBER] MD stop but this job in cluster still run Ross Walker
- Re: [AMBER] Distorted waters in restrained mini Maura Catherine Mooney
- Re: [AMBER] loadPdb segmentation fault Bill Ross
- [AMBER] AmberTools 1.5 top and cord files Molybdos Kirkimpolakis
- Re: [AMBER] QUASI-HARMONIC APPROXIMATION belal najjar
- [AMBER] Problems when I wanted to restart the MD production zhouhaibin2008.ok
- Re: [AMBER] AmberTools 1.5 top and cord files Jason Swails
- Re: [AMBER] Problems when I wanted to restart the MD production Jason Swails
- Re: [AMBER] Problems when I wanted to restart the MD production zhouhaibin2008.ok
- Re: [AMBER] AmberTools 1.5 top and cord files Molybdos Kirkimpolakis
- Re: [AMBER] Problems when I wanted to restart the MD production Bill Ross
Thursday, 4 August 2011
- [AMBER] simulating a protein-peptide complex Xiao Chen
- Re: [AMBER] simulating a protein-peptide complex steinbrt.rci.rutgers.edu
- [AMBER] Job Termination problem souvik sur
- Re: [AMBER] simulating a protein-peptide complex Carlos Simmerling
- Re: [AMBER] Distorted waters in restrained mini David A Case
- Re: [AMBER] Distorted waters in restrained mini Carlos Simmerling
- Re: [AMBER] Problems when I wanted to restart the MD production Jason Swails
- [AMBER] 6 error: No torsion terms for ca-ca-ce-c2 Shulin Zhuang
- [AMBER] AmberTools 1.5 nmode error manikanthan bhavaraju
- Re: [AMBER] AmberTools 1.5 nmode error Jason Swails
- Re: [AMBER] 6 error: No torsion terms for ca-ca-ce-c2 Jason Swails
- [AMBER] Dipole-dipole correlation Function Sindrila Dutta banik
- [AMBER] Problem related to the correlation function Sindrila Dutta banik
- Re: [AMBER] AmberTools 1.5 top and cord files Molybdos Kirkimpolakis
- Re: [AMBER] QUASI-HARMONIC APPROXIMATION Bill Miller III
- Re: [AMBER] Problem related to the correlation function David A Case
- [AMBER] About Charge Assigning Method using Gaff Bin Wu
- [AMBER] Nvidia M2070 Tesla ?? E. Nihal Korkmaz
- Re: [AMBER] Nvidia M2070 Tesla ?? Ross Walker
- Re: [AMBER] Nvidia M2070 Tesla ?? arikcohen
- [AMBER] Water residue and atom Numbering on Xleap David Cantu
- [AMBER] 1st shell WITH solvent in ptraj Bruno Rodrigues
- Re: [AMBER] 1st shell WITH solvent in ptraj Niel Henriksen
- [AMBER] How to know whether the sander is running parallel Aimin
- [AMBER] EPTOT shows big difference between the different force fields zhouhaibin2008.ok
- Re: [AMBER] QUASI-HARMONIC APPROXIMATION belal najjar
- Re: [AMBER] Water residue and atom Numbering on Xleap David Case
- Re: [AMBER] How to know whether the sander is running parallel David Case
- [AMBER] EPTOT shows big difference between the different force fields zhouhaibin2008.ok
- [AMBER] dodecahedron box ? E. Nihal Korkmaz
Friday, 5 August 2011
- [AMBER] how to scale energy barriers to get the harmonic constants in GAFF gloriarg
- [AMBER] Error in output file Aditya Padhi
- Re: [AMBER] simulating a protein-peptide complex Xiao Chen
- Re: [AMBER] simulating a protein-peptide complex Carlos Simmerling
- Re: [AMBER] EPTOT shows big difference between the different force fields Carlos Simmerling
- Re: [AMBER] AmberTools 1.5 top and cord files Jason Swails
- Re: [AMBER] 1st shell WITH solvent in ptraj Bruno Rodrigues
- Re: [AMBER] About Charge Assigning Method using Gaff David A Case
- Re: [AMBER] Error in output file Ross Walker
- [AMBER] Problem related to the correlation function Sindrila Dutta banik
- Re: [AMBER] 1st shell WITH solvent in ptraj Niel Henriksen
- Re: [AMBER] How to know whether the sander is running parallel Aimin
- Re: [AMBER] How to know whether the sander is running parallel tdo.chem.ucsb.edu
- Re: [AMBER] How to know whether the sander is running parallel David A Case
- Re: [AMBER] How to know whether the sander is running parallel Aimin
- Re: [AMBER] How to know whether the sander is running parallel Jason Swails
- [AMBER] Amoeba seems not work with free energy calculation li he
- Re: [AMBER] How to know whether the sander is running parallel Aimin
- [AMBER] About installation problems Mo Chen
- Re: [AMBER] About installation problems Carlos Sosa
- Re: [AMBER] About installation problems Mo Chen
- Re: [AMBER] How to know whether the sander is running parallel Jason Swails
- [AMBER] Amber 11 parallel installation problem 于丽影 Liying E\. Yu
- Re: [AMBER] Amber 11 parallel installation problem Jason Swails
- Re: [AMBER] EPTOT shows big difference between the different force fields Jason Swails
- Re: [AMBER] EPTOT shows big difference between the different force fields zhouhaibin2008.ok
Saturday, 6 August 2011
- [AMBER] Chemical shift restraints Siavoush Dastmalchi
- Re: [AMBER] QUASI-HARMONIC APPROXIMATION Bill Miller III
- Re: [AMBER] Amber 11 parallel installation problem case
- Re: [AMBER] Chemical shift restraints case
- [AMBER] Problem related to the correlation function Sindrila Dutta banik
- Re: [AMBER] Amoeba seems not work with free energy calculation case
- Re: [AMBER] MD stop but this job in cluster still run tien dung
- Re: [AMBER] How to know whether the sander is running parallel Aimin
- Re: [AMBER] Chemical shift restraints Siavoush Dastmalchi
Sunday, 7 August 2011
- Re: [AMBER] MD stop but this job in cluster still run Marc van der Kamp
- Re: [AMBER] Chemical shift restraints case
- Re: [AMBER] How to know whether the sander is running parallel case
- Re: [AMBER] Chemical shift restraints Siavoush Dastmalchi
- Re: [AMBER] Chemical shift restraints Siavoush Dastmalchi
- Re: [AMBER] Chemical shift restraints Siavoush Dastmalchi
- [AMBER] EQMMM modification Anglea A.
- Re: [AMBER] Chemical shift restraints case
- Re: [AMBER] Distorted waters in restrained mini Maura Catherine Mooney
- Re: [AMBER] Distorted waters in restrained mini Maura Catherine Mooney
- Re: [AMBER] EQMMM modification Jason Swails
- [AMBER] error in pmemd parallel installation hari krishna
Monday, 8 August 2011
- [AMBER] free energy decomposition Sangita Kachhap
- [AMBER] mmpbsa calculation using amber11 Siavoush Dastmalchi
- Re: [AMBER] Error in output file Aditya Padhi
- Re: [AMBER] error in pmemd parallel installation David A Case
- Re: [AMBER] free energy decomposition David A Case
- Re: [AMBER] Distorted waters in restrained mini David A Case
- Re: [AMBER] error in pmemd parallel installation hari krishna
- Re: [AMBER] error in pmemd parallel installation Daniel Roe
- Re: [AMBER] error in pmemd parallel installation hari krishna
- Re: [AMBER] free energy decomposition Jason Swails
- Re: [AMBER] error in pmemd parallel installation Jason Swails
- Re: [AMBER] error in pmemd parallel installation hari krishna
- Re: [AMBER] Distorted waters in restrained mini Maura Catherine Mooney
- Re: [AMBER] Distorted waters in restrained mini David A Case
- Re: [AMBER] Distorted waters in restrained mini Maura Catherine Mooney
- Re: [AMBER] error in pmemd parallel installation Jason Swails
- Re: [AMBER] free energy decomposition Sangita Kachhap
- [AMBER] Problem related to the correlation function Sindrila Dutta banik
- [AMBER] DNA-22mer manikanthan bhavaraju
- Re: [AMBER] DNA-22mer ros
- Re: [AMBER] DNA-22mer Jason Swails
- [AMBER] GAFF, Charges, and Cutoff Ismail, Mohd F.
- Re: [AMBER] GAFF, Charges, and Cutoff Jason Swails
- [AMBER] need suggestion about cutoff setyanto md
- Re: [AMBER] need suggestion about cutoff Jason Swails
- [AMBER] residuewise energy decomposition in Amber moitrayee.mbu.iisc.ernet.in
- [AMBER] problem running with restraints Sangeetha B
- [AMBER] problem running with restraints Sangeetha B
Tuesday, 9 August 2011
- Re: [AMBER] need suggestion about cutoff setyanto md
- Re: [AMBER] need suggestion about cutoff Catein Catherine
- [AMBER] GBSA calculations for protein-protein complexes Catein Catherine
- Re: [AMBER] GBSA calculations for protein-protein complexes Carlos Simmerling
- Re: [AMBER] residuewise energy decomposition in Amber Bill Miller III
- Re: [AMBER] need suggestion about cutoff case
- Re: [AMBER] problem running with restraints case
- Re: [AMBER] problem running with restraints Sangeetha B
- Re: [AMBER] GBSA calculations for protein-protein complexes Catein Catherine
- Re: [AMBER] using sleap to load mol2 files Guenegou, Guillaume [ORDFR]
- Re: [AMBER] Failure kReduceSoluteCOM with GPU Ismail, Mohd F.
- Re: [AMBER] GAFF, Charges, and Cutoff Ismail, Mohd F.
- [AMBER] MMPBSA.py - Entropy: Error message George Tzotzos
- Re: [AMBER] MMPBSA.py - Entropy: Error message Bill Miller III
- [AMBER] addition of massless particle to benzene that interacts only with massless particles in other benzene molecules Tan Yaw Sing
- Re: [AMBER] MMPBSA.py - Entropy: Error message George Tzotzos
- Re: [AMBER] Failure kReduceSoluteCOM with GPU Scott Le Grand
- Re: [AMBER] Failure kReduceSoluteCOM with GPU Jason Swails
- Re: [AMBER] addition of massless particle to benzene that interacts only with massless particles in other benzene molecules Jason Swails
- Re: [AMBER] addition of massless particle to benzene that interacts only with massless particles in other benzene molecules Carlos Simmerling
- Re: [AMBER] Failure kReduceSoluteCOM with GPU Scott Le Grand
- [AMBER] Questions regarding Clustering in ptraj. Catein Catherine
- [AMBER] What is the physical meaning and good parameters for EXTDIEL and INDIEL and SURFTEN and SURFOFF in GBSA calculations? Catein Catherine
- Re: [AMBER] Failure kReduceSoluteCOM with GPU Ismail, Mohd F.
- [AMBER] trouble compiling AmberTools 1.5 Jennifer L. Muzyka
- Re: [AMBER] Failure kReduceSoluteCOM with GPU Scott Le Grand
- Re: [AMBER] trouble compiling AmberTools 1.5 Jason Swails
- Re: [AMBER] GBSA calculations for protein-protein complexes Carlos Simmerling
- Re: [AMBER] GBSA calculations with MgATP ligand Irene Newhouse
- Re: [AMBER] trouble compiling AmberTools 1.5 Jennifer L. Muzyka
- Re: [AMBER] GBSA calculations with MgATP ligand Jason Swails
- [AMBER] mutating a residue to another residue on a protein structure George A. Khoury
- Re: [AMBER] GBSA calculations with MgATP ligand Irene Newhouse
- Re: [AMBER] mutating a residue to another residue on a protein structure Jason Swails
- [AMBER] mol2 to PREP David Cantu
- Re: [AMBER] mol2 to PREP tdo.chem.ucsb.edu
- Re: [AMBER] mol2 to PREP Jason Swails
- Re: [AMBER] GBSA calculations with MgATP ligand filip fratev
- Re: [AMBER] GBSA calculations with MgATP ligand Irene Newhouse
- Re: [AMBER] mol2 to PREP David Cantu
- Re: [AMBER] GBSA calculations with MgATP ligand Jason Swails
Wednesday, 10 August 2011
- [AMBER] PMEMD installation hari krishna
- Re: [AMBER] PMEMD installation Ismail, Mohd F.
- [AMBER] Question about Tutorial 8 section 6: How to convert mdcrd to specific PDB files for clustering analysis with MMTSB? Catein Catherine
- Re: [AMBER] Question about Tutorial 8 section 6: How to convert mdcrd to specific PDB files for clustering analysis with MMTSB? Carlos Simmerling
- [AMBER] How to calculate the electrostatic contribution to "solvation free energy"? Jan-Philip Gehrcke
- [AMBER] problem running with restraints Sangeetha B
- [AMBER] Xleap installation problem kureeckal ramesh
- [AMBER] coordination number DEBOSTUTI GHOSHDASTIDAR
- [AMBER] Problem related to the correlation function Sindrila Dutta banik
- [AMBER] Proble related to the correlation function Sindrila Dutta banik
- [AMBER] MMPBSA.py: Effect on ionic strength concentration on Delta G George Tzotzos
- Re: [AMBER] Problem related to the correlation function David Case
- [AMBER] questions about calculating thermodynamics properties of water model zhouhaibin2008.ok
- [AMBER] Can I use ptraj to cluster proteins based on residue contact map? Catein Catherine
- [AMBER] Cholesterol and Cholesteryl hemisuccinate TAEJIN KIM
- Re: [AMBER] Amoeba seems not work with free energy calculation li he
- Re: [AMBER] MMPBSA.py: Effect on ionic strength concentration on Delta G Jason Swails
- [AMBER] could not find amber atom type F in forcefield 10 Rajesh Raju
- Re: [AMBER] Xleap installation problem Jason Swails
- Re: [AMBER] Cholesterol and Cholesteryl hemisuccinate Jason Swails
- Re: [AMBER] How to calculate the electrostatic contribution to "solvation free energy"? Jason Swails
- Re: [AMBER] Proble related to the correlation function Jason Swails
- Re: [AMBER] Proble related to the correlation function Adrian Roitberg
- Re: [AMBER] could not find amber atom type F in forcefield 10 Rajesh Raju
- Re: [AMBER] MMPBSA.py: Effect on ionic strength concentration on Delta G George Tzotzos
- Re: [AMBER] coordination number Bruno Rodrigues
- [AMBER] rst to mdcrd Anglea A.
- Re: [AMBER] QUASI-HARMONIC APPROXIMATION belal najjar
- Re: [AMBER] rst to mdcrd Ozen, Aysegul
- [AMBER] How to extract selected residues from mdcrd to PDB file using ptraj? Catein Catherine
- [AMBER] How to extract every 10th snapshot from mdcrd to PDB format? Catein Catherine
- [AMBER] trying to make parallel Amber on Centos Irene Newhouse
- Re: [AMBER] MMPBSA.py: Effect on ionic strength concentration on Delta G Jason Swails
- Re: [AMBER] trying to make parallel Amber on Centos Jason Swails
- Re: [AMBER] How to extract every 10th snapshot from mdcrd to PDB format? Jason Swails
- Re: [AMBER] How to extract selected residues from mdcrd to PDB file using ptraj? Jason Swails
- Re: [AMBER] rst to mdcrd waqasuddin.khan.iccs.edu
- Re: [AMBER] How to extract selected residues from mdcrd to PDB file using ptraj? Catein Catherine
- Re: [AMBER] rst to mdcrd Ross Walker
- [AMBER] nothing wtitten in .out file after heating Nyla Zaman
Thursday, 11 August 2011
- [AMBER] calculating distance between two atoms clwg
- [AMBER] espgen cannot generate esp file Reza Aditama
- Re: [AMBER] calculating distance between two atoms steinbrt.rci.rutgers.edu
- Re: [AMBER] How to calculate the electrostatic contribution to "solvation free energy"? Jan-Philip Gehrcke
- Re: [AMBER] MMPBSA.py: Effect on ionic strength concentration on Delta G George Tzotzos
- Re: [AMBER] rst to mdcrd waqasuddin.khan.iccs.edu
- Re: [AMBER] MMPBSA.py: Effect on ionic strength concentration on Delta G Jason Swails
- Re: [AMBER] rst to mdcrd Jason Swails
- Re: [AMBER] How to calculate the electrostatic contribution to "solvation free energy"? Jason Swails
- Re: [AMBER] MMPBSA.py: Effect on ionic strength concentration on Delta G George Tzotzos
- [AMBER] Inpcrd file problem David Cantu
- [AMBER] Fwd: problem running with restraints Sangeetha B
- Re: [AMBER] MMPBSA.py: Effect on ionic strength concentration on Delta G Jason Swails
- Re: [AMBER] MMPBSA.py: Effect on ionic strength concentration on Delta G George Tzotzos
- Re: [AMBER] Inpcrd file problem Daniel Roe
- Re: [AMBER] What is the physical meaning and good parameters for EXTDIEL and INDIEL and SURFTEN and SURFOFF in GBSA calculations? case
- Re: [AMBER] nothing wtitten in .out file after heating case
- Re: [AMBER] Inpcrd file problem David Cantu
- Re: [AMBER] nothing wtitten in .out file after heating M. L. Dodson
- Re: [AMBER] nothing wtitten in .out file after heating Jason Swails
- Re: [AMBER] Inpcrd file problem Daniel Roe
- [AMBER] leaprc Charles Johnson
- Re: [AMBER] Inpcrd file problem David Cantu
- Re: [AMBER] Inpcrd file problem Bill Ross
- Re: [AMBER] Inpcrd file problem David Cantu
- Re: [AMBER] Inpcrd file problem Daniel Roe
- Re: [AMBER] Inpcrd file problem Bill Ross
- [AMBER] leaprc Charles Johnson
- Re: [AMBER] leaprc Ismail, Mohd F.
- Re: [AMBER] Inpcrd file problem Ismail, Mohd F.
- Re: [AMBER] Inpcrd file problem Ismail, Mohd F.
- Re: [AMBER] calculating distance between two atoms Dean Cuebas
- Re: [AMBER] leaprc Charles Johnson
- Re: [AMBER] Inpcrd file problem David Cantu
- Re: [AMBER] leaprc Ismail, Mohd F.
- Re: [AMBER] leaprc Charles Johnson
- Re: [AMBER] Inpcrd file problem David Cantu
- Re: [AMBER] Inpcrd file problem Carlos Simmerling
- Re: [AMBER] Inpcrd file problem David Cantu
- Re: [AMBER] Inpcrd file problem Daniel Roe
- Re: [AMBER] Inpcrd file problem David Cantu
- Re: [AMBER] Inpcrd file problem David Cantu
- Re: [AMBER] Inpcrd file problem Jason Swails
- [AMBER] GBSA E. Nihal Korkmaz
- Re: [AMBER] Inpcrd file problem Jason Swails
- Re: [AMBER] GBSA Jason Swails
- Re: [AMBER] Inpcrd file problem Thomas Cheatham
- Re: [AMBER] Inpcrd file problem David Cantu
- Re: [AMBER] leaprc case
- [AMBER] unspecified launch failure launching kernel kCalculateMolecularVirial arikcohen
- Re: [AMBER] unspecified launch failure launching kernel kCalculateMolecularVirial Scott Le Grand
- Re: [AMBER] unspecified launch failure launching kernel kCalculateMolecularVirial arikcohen
- Re: [AMBER] unspecified launch failure launching kernel kCalculateMolecularVirial Ross Walker
- Re: [AMBER] unspecified launch failure launching kernel kCalculateMolecularVirial arikcohen
- Re: [AMBER] unspecified launch failure launching kernel kCalculateMolecularVirial Ross Walker
- Re: [AMBER] unspecified launch failure launching kernel kCalculateMolecularVirial arikcohen
- Re: [AMBER] unspecified launch failure launching kernel kCalculateMolecularVirial arikcohen
- Re: [AMBER] unspecified launch failure launching kernel kCalculateMolecularVirial Ross Walker
- [AMBER] QM runs Maura Catherine Mooney
- Re: [AMBER] QM runs Ross Walker
- Re: [AMBER] unspecified launch failure launching kernel kCalculateMolecularVirial arikcohen
- Re: [AMBER] unspecified launch failure launching kernel kCalculateMolecularVirial Ross Walker
- [AMBER] loadpdb with GLYCAM_06 ? Yun Shi
- Re: [AMBER] unspecified launch failure launching kernel kCalculateMolecularVirial Sangeetha B
- Re: [AMBER] loadpdb with GLYCAM_06 ? Sushil Mishra
- [AMBER] PTRAJ; how to extract selected atoms from mdcrd to PDB file. Catein Catherine
Friday, 12 August 2011
- [AMBER] Hot to compare to contact map instead of visually? Catein Catherine
- Re: [AMBER] QM runs Maura Catherine Mooney
- Re: [AMBER] PTRAJ; how to extract selected atoms from mdcrd to PDB file. Jason Swails
- [AMBER] Non-identical prmtop files for PNEB William Cantara
- Re: [AMBER] leaprc Charles Johnson
- Re: [AMBER] QM runs case
- Re: [AMBER] questions about calculating thermodynamics properties of water model case
- Re: [AMBER] DNA-22mer case
- Re: [AMBER] DNA-22mer Jason Swails
- Re: [AMBER] unspecified launch failure launching kernel kCalculateMolecularVirial Ross Walker
- Re: [AMBER] loadpdb with GLYCAM_06 ? Oliver Grant
- Re: [AMBER] Non-identical prmtop files for PNEB Daniel Roe
- Re: [AMBER] loadpdb with GLYCAM_06 ? Yun Shi
- Re: [AMBER] loadpdb with GLYCAM_06 ? Lachele Foley (Lists)
- Re: [AMBER] loadpdb with GLYCAM_06 ? Yun Shi
- Re: [AMBER] loadpdb with GLYCAM_06 ? Lachele Foley (Lists)
- Re: [AMBER] Non-identical prmtop files for PNEB William Cantara
- Re: [AMBER] DNA-22mer manikanthan bhavaraju
- [AMBER] residue list E. Nihal Korkmaz
- Re: [AMBER] DNA-22mer Bruno Rodrigues
- Re: [AMBER] residue list Jason Swails
- Re: [AMBER] loadpdb with GLYCAM_06 ? Yun Shi
- Re: [AMBER] loadpdb with GLYCAM_06 ? Lachele Foley (Lists)
- Re: [AMBER] loadpdb with GLYCAM_06 ? Yun Shi
- [AMBER] Binding energy with ff02ep Anglea A.
Saturday, 13 August 2011
- [AMBER] Xmgr download link souvik sur
- Re: [AMBER] Xmgr download link Marc van der Kamp
- [AMBER] error running mmpbsa.py Siavoush Dastmalchi
- [AMBER] question about the output of H-bond analysis by ptraj Ying Yang
- Re: [AMBER] leaprc case
- Re: [AMBER] error running mmpbsa.py Jason Swails
- Re: [AMBER] DNA-22mer Daniel Roe
- [AMBER] Amber11 re-compiling Anglea A.
- Re: [AMBER] Amber11 re-compiling Jason Swails
- Re: [AMBER] loadpdb with GLYCAM_06 ? Lachele Foley (Lists)
- [AMBER] nmpimd heating Andrew Petersen
- Re: [AMBER] loadpdb with GLYCAM_06 ? Yun Shi
- Re: [AMBER] loadpdb with GLYCAM_06 ? Lachele Foley (Lists)
- Re: [AMBER] DNA-22mer Jason Swails
- Re: [AMBER] nmpimd heating Francesco Paesani
- [AMBER] Randomize trajectory frames Tai Chi For Me
Sunday, 14 August 2011
- Re: [AMBER] Randomize trajectory frames Daniel Sindhikara
- [AMBER] _mmpbsa_py_energy error durint PB calculations HIromichi Tsurui
- [AMBER] inter & intra-molecular interaction energies clwg
- Re: [AMBER] _mmpbsa_py_energy error durint PB calculations Jason Swails
- Re: [AMBER] loadpdb with GLYCAM_06 ? Bill Ross
- Re: [AMBER] _mmpbsa_py_energy error durint PB calculations Hiromichi Tsurui
- [AMBER] Get access to my pictures and more Navanath Kumbhar
Monday, 15 August 2011
- [AMBER] No data for 0+2 PB PB 0 problem in Amber10 mm_pbsa sribone.fcq.unc.edu.ar
- [AMBER] Amber Minimization MUSTAFA BUGHIO
- Re: [AMBER] DNA-22mer manikanthan bhavaraju
- Re: [AMBER] loadpdb with GLYCAM_06 ? Yun Shi
- Re: [AMBER] loadpdb with GLYCAM_06 ? Yun Shi
- [AMBER] Software announcement: Release of PUPIL 1.4 Joan Torras
- Re: [AMBER] loadpdb with GLYCAM_06 ? Lachele Foley (Lists)
- [AMBER] Can one preserve heavy atom / hydrogen atom ordering in LEaP? Fenley, Andrew
- Re: [AMBER] No data for 0+2 PB PB 0 problem in Amber10 mm_pbsa Ray Luo, Ph.D.
- [AMBER] pm6 parametes Anglea A.
- [AMBER] Old problem with restart Bruno Rodrigues
- Re: [AMBER] _mmpbsa_py_energy error durint PB calculations 鶴井博理
- Re: [AMBER] Randomize trajectory frames Dean Cuebas
- Re: [AMBER] _mmpbsa_py_energy error durint PB calculations Ray Luo, Ph.D.
Tuesday, 16 August 2011
- Re: [AMBER] Old problem with restart Jason Swails
- Re: [AMBER] _mmpbsa_py_energy error durint PB calculations Jason Swails
- [AMBER] Fwd: simulating Modified residue of Cysteine attached to mercury madhumita das
- Re: [AMBER] Old problem with restart Marc van der Kamp
- Re: [AMBER] Old problem with restart Bruno Rodrigues
- Re: [AMBER] Old problem with restart Marc van der Kamp
- Re: [AMBER] Old problem with restart case
- Re: [AMBER] No data for 0+2 PB PB 0 problem in Amber10 mm_pbsa sribone.fcq.unc.edu.ar
- Re: [AMBER] No data for 0+2 PB PB 0 problem in Amber10 mm_pbsa Jason Swails
- Re: [AMBER] loadpdb with GLYCAM_06 ? Yun Shi
- [AMBER] again GLYCAM06 + 99SB + GAFF ? Yun Shi
- [AMBER] Widom Method with amber Matias Factorovich
- Re: [AMBER] again GLYCAM06 + 99SB + GAFF ? Lachele Foley (Lists)
- Re: [AMBER] Can one preserve heavy atom / hydrogen atom ordering in LEaP? case
- Re: [AMBER] Fwd: simulating Modified residue of Cysteine attached to mercury case
- Re: [AMBER] Widom Method with amber case
- [AMBER] Problems with MMPBSA and steered molecular dynamics Márcio Souza Damaso
- Re: [AMBER] Old problem with restart Bruno Rodrigues
- Re: [AMBER] Old problem with restart Bruno Rodrigues
- [AMBER] Amberlite error Irene Newhouse
- Re: [AMBER] Old problem with restart Jason Swails
- Re: [AMBER] Problems with MMPBSA and steered molecular dynamics Jason Swails
- Re: [AMBER] Can one preserve heavy atom / hydrogen atom ordering in LEaP? Bill Ross
- Re: [AMBER] Widom Method with amber Bill Ross
- Re: [AMBER] Old problem with restart Bill Ross
- Re: [AMBER] Can one preserve heavy atom / hydrogen atom ordering in LEaP? Bill Ross
- Re: [AMBER] _mmpbsa_py_energy error durint PB calculations 鶴井博理
- Re: [AMBER] _mmpbsa_py_energy error durint PB calculations 鶴井博理
- [AMBER] partial atomic charges parametarization in ff10 manikanthan bhavaraju
- Re: [AMBER] partial atomic charges parametarization in ff10 Jason Swails
Wednesday, 17 August 2011
- [AMBER] General questions about POL3 and AMOEBA timings D.G. Sprous, PhD
- [AMBER] comments format within .mdin files Yun Shi
- [AMBER] strategies to terminate and continue a MD run Yun Shi
- [AMBER] Iron in CHAMBER: chemicalSymbolToZ() cannot map symbol: FE, to a Z value Patrick von Glehn
- [AMBER] problem with NPT equilibration stage Jurica Novak
- Re: [AMBER] problem with NPT equilibration stage Ross Walker
- Re: [AMBER] Iron in CHAMBER: chemicalSymbolToZ() cannot map symbol: FE, to a Z value Ross Walker
- Re: [AMBER] comments format within .mdin files Ross Walker
- [AMBER] How to specify a quantum region of a system Aimin
- Re: [AMBER] How to specify a quantum region of a system Jason Swails
- Re: [AMBER] strategies to terminate and continue a MD run Jason Swails
- Re: [AMBER] Iron in CHAMBER: chemicalSymbolToZ() cannot map symbol: FE, to a Z value Mark Williamson
- Re: [AMBER] strategies to terminate and continue a MD run Yun Shi
- Re: [AMBER] strategies to terminate and continue a MD run sribone.fcq.unc.edu.ar
- Re: [AMBER] strategies to terminate and continue a MD run Bill Ross
- [AMBER] AmberTools installation difficulties on Mac OSX Jennifer L. Muzyka
- Re: [AMBER] How to specify a quantum region of a system Ross Walker
- Re: [AMBER] AmberTools installation difficulties on Mac OSX Jason Swails
- [AMBER] How to interpret GLYCAM prep file? Yun Shi
- [AMBER] Problem with AT 1.5 installation Emmanuel Baribefe Naziga
- Re: [AMBER] How to interpret GLYCAM prep file? Bill Ross
- Re: [AMBER] Problem with AT 1.5 installation David Case
- Re: [AMBER] How to interpret GLYCAM prep file? Lachele Foley (Lists)
- [AMBER] Coordinate resetting cannot be accomplished, deviation is too large Danny Xu
- Re: [AMBER] Problem with AT 1.5 installation Emmanuel Baribefe Naziga
- Re: [AMBER] Coordinate resetting cannot be accomplished, deviation is too large Jason Swails
- Re: [AMBER] Problem with AT 1.5 installation Daniel Roe
- Re: [AMBER] Problem with AT 1.5 installation Emmanuel Baribefe Naziga
- Re: [AMBER] Coordinate resetting cannot be accomplished, deviation is too large Danny Xu
- Re: [AMBER] Coordinate resetting cannot be accomplished, deviation is too large Daniel Roe
- [AMBER] pm6 parameters Anglea A.
- Re: [AMBER] Coordinate resetting cannot be accomplished, deviation is too large Danny Xu
Thursday, 18 August 2011
- [AMBER] Xleap installation problem kureeckal ramesh
- Re: [AMBER] Xleap installation problem Mark Williamson
- [AMBER] Executing Parmchk madhumita das
- [AMBER] NOE constraints labeling marco.bartoloni.students.unibe.ch
- Re: [AMBER] NOE constraints labeling David A Case
- Re: [AMBER] strategies to terminate and continue a MD run Bruno Rodrigues
- Re: [AMBER] Executing Parmchk Jason Swails
- Re: [AMBER] Coordinate resetting cannot be accomplished, deviation is too large Jason Swails
- Re: [AMBER] Iron in CHAMBER: chemicalSymbolToZ() cannot map symbol: FE, to a Z value Jason Swails
- [AMBER] test of the mailing list server David A Case
- Re: [AMBER] pm6 parameters Andreas Goetz
- Re: [AMBER] How to interpret GLYCAM prep file? Yun Shi
- Re: [AMBER] How to interpret GLYCAM prep file? Lachele Foley (Lists)
- Re: [AMBER] How to interpret GLYCAM prep file? Yun Shi
- Re: [AMBER] How to interpret GLYCAM prep file? Lachele Foley (Lists)
- [AMBER] molecule out box after reimage mirage .
- Re: [AMBER] molecule out box after reimage Jason Swails
- [AMBER] Using iwrap with harmonic restraints Ozen, Aysegul
- Re: [AMBER] Using iwrap with harmonic restraints Jason Swails
- [AMBER] Fwd: _mmpbsa_py_energy error durint PB calculations Ray Luo, Ph.D.
- [AMBER] Questions about Amber Tutorials - A7 - Replica Exchange Simulations with AMBER 10 Catein Catherine
- Re: [AMBER] Questions about Amber Tutorials - A7 - Replica Exchange Simulations with AMBER 10 Daniel Sindhikara
Friday, 19 August 2011
- [AMBER] Problem installing AmverTools 1.5 on Mac Alexej Grjasnow
- [AMBER] ntr=1 nmropt=1 Fernando Martín García
- Re: [AMBER] ntr=1 nmropt=1 Mark Williamson
- Re: [AMBER] ntr=1 nmropt=1 Fernando Martín García
- Re: [AMBER] ntr=1 nmropt=1 Mark Williamson
- Re: [AMBER] ntr=1 nmropt=1 Fernando Martín García
- Re: [AMBER] ntr=1 nmropt=1 David A Case
- Re: [AMBER] ntr=1 nmropt=1 Fernando Martín García
- [AMBER] Any tutorial on 3D-RISM calculation with AMBER10? Catein Catherine
- [AMBER] Amber 11 bugfix Jennifer L. Muzyka
- Re: [AMBER] Amber 11 bugfix David A Case
- Re: [AMBER] Amber 11 bugfix Jennifer L. Muzyka
- [AMBER] pmemd.cuda error Oliver Kuhn
- Re: [AMBER] Amber 11 bugfix Jason Swails
- [AMBER] Major GPU Update Released Ross Walker
- Re: [AMBER] Problem installing AmverTools 1.5 on Mac Daniel Roe
- Re: [AMBER] again GLYCAM06 + 99SB + GAFF ? Yun Shi
- [AMBER] antechamber + CNT parameter Jagur Lambix
- Re: [AMBER] Major GPU Update Released filip fratev
- Re: [AMBER] antechamber + CNT parameter David A Case
- [AMBER] nmropt and restraint_wt Danny Xu
- Re: [AMBER] Major GPU Update Released Ismail, Mohd F.
- Re: [AMBER] antechamber + CNT parameter Nadine Utz
- Re: [AMBER] antechamber + CNT parameter Jagur Lambix
- Re: [AMBER] Major GPU Update Released Ross Walker
- Re: [AMBER] Amber 11 bugfix/Cuda update filip fratev
- Re: [AMBER] Amber 11 bugfix/Cuda update Ismail, Mohd F.
- Re: [AMBER] Amber 11 bugfix/Cuda update Ross Walker
- Re: [AMBER] Amber 11 bugfix/cuda update filip fratev
- Re: [AMBER] again GLYCAM06 + 99SB + GAFF ? Lachele Foley (Lists)
- Re: [AMBER] Major GPU Update Released Ye MEI
- Re: [AMBER] Major GPU Update Released Ross Walker
- Re: [AMBER] Major GPU Update Released Ismail, Mohd F.
- Re: [AMBER] Major GPU Update Released Ross Walker
- Re: [AMBER] Major GPU Update Released Ismail, Mohd F.
- Re: [AMBER] Any tutorial on 3D-RISM calculation with AMBER10? Tyler Luchko
- [AMBER] TUTORIAL B3 - SECTION 6 George Tzotzos
- Re: [AMBER] nmropt and restraint_wt David A Case
- Re: [AMBER] again GLYCAM06 + 99SB + GAFF ? Yun Shi
- Re: [AMBER] again GLYCAM06 + 99SB + GAFF ? Lachele Foley (Lists)
- Re: [AMBER] TUTORIAL B3 - SECTION 6 George Tzotzos
- Re: [AMBER] TUTORIAL B3 - SECTION 6 Jason Swails
- Re: [AMBER] Problem installing AmverTools 1.5 on Mac Jason Swails
- Re: [AMBER] Major GPU Update Released filip fratev
- [AMBER] hbond atom mask in cpptraj mirage .
- Re: [AMBER] Major GPU Update Released Scott Le Grand
- [AMBER] Creating new reaction coordinates Michael F. Bruist
Saturday, 20 August 2011
- Re: [AMBER] again GLYCAM06 + 99SB + GAFF ? FyD
- Re: [AMBER] Fwd: simulating Modified residue of Cysteine attached to mercury FyD
- Re: [AMBER] Major GPU Update Released Levi Pierce
- Re: [AMBER] [q4md-fft] General Question about Charge Derivation using RESP FyD
- Re: [AMBER] Major GPU Update Released Santosh Mogurampelly
- [AMBER] ptraj cluster George Tzotzos
- Re: [AMBER] TUTORIAL B3 - SECTION 6 George Tzotzos
- Re: [AMBER] Major GPU Update Released filip fratev
- Re: [AMBER] Major GPU Update Released filip fratev
- Re: [AMBER] Major GPU Update Released filip fratev
- Re: [AMBER] nmropt and restraint_wt Danny Xu
- Re: [AMBER] Major GPU Update Released Ross Walker
- Re: [AMBER] nmropt and restraint_wt case
- Re: [AMBER] Major GPU Update Released filip fratev
- Re: [AMBER] hbond atom mask in cpptraj mirage .
- Re: [AMBER] nmropt and restraint_wt Danny Xu
- Re: [AMBER] Major GPU Update Released Ismail, Mohd F.
- Re: [AMBER] nmropt and restraint_wt Jason Swails
- Re: [AMBER] hbond atom mask in cpptraj Jason Swails
- Re: [AMBER] Major GPU Update Released Danny Xu
- Re: [AMBER] Major GPU Update Released filip fratev
- Re: [AMBER] Major GPU Update Released filip fratev
- Re: [AMBER] Major GPU Update Released Scott Le Grand
- Re: [AMBER] hbond atom mask in cpptraj mirage .
- Re: [AMBER] Major GPU Update Released filip fratev
- Re: [AMBER] Major GPU Update Released Ross Walker
- Re: [AMBER] Major GPU Update Released Scott Le Grand
- Re: [AMBER] Major GPU Update Released Santosh Mogurampelly
Sunday, 21 August 2011
- Re: [AMBER] Major GPU Update Released filip fratev
- Re: [AMBER] Problem with MMPBSA.py Osman, Roman
- [AMBER] fftw-2.1.5 and Fedora Dmitry Mukha
- Re: [AMBER] Major GPU Update Released Dmitry Mukha
- Re: [AMBER] Major GPU Update Released Jason Swails
- Re: [AMBER] Major GPU Update Released Dmitry Mukha
- Re: [AMBER] Major GPU Update Released Scott Le Grand
- Re: [AMBER] Major GPU Update Released Dmitry Mukha
- Re: [AMBER] Major GPU Update Released Scott Le Grand
- Re: [AMBER] Major GPU Update Released filip fratev
- Re: [AMBER] Major GPU Update Released Scott Le Grand
- [AMBER] Analysing the result after simulation souvik sur
- Re: [AMBER] Analysing the result after simulation Kshatresh Dutta Dubey
- Re: [AMBER] Analysing the result after simulation TH Chew
- Re: [AMBER] Analysing the result after simulation souvik sur
- Re: [AMBER] Analysing the result after simulation souvik sur
Monday, 22 August 2011
- [AMBER] Error in mm_pbsa Esam Tolba
- Re: [AMBER] Error in mm_pbsa Ray Luo, Ph.D.
- Re: [AMBER] Error in mm_pbsa Ray Luo, Ph.D.
- [AMBER] problem with decomposition in mm-pbsa.pl moitrayee.mbu.iisc.ernet.in
- Re: [AMBER] Problem with MMPBSA.py Seungyeul Yoo
- Re: [AMBER] Using iwrap with harmonic restraints Ozen, Aysegul
- Re: [AMBER] hbond atom mask in cpptraj Daniel Roe
- Re: [AMBER] ptraj cluster Daniel Roe
- Re: [AMBER] Problem with MMPBSA.py Osman, Roman
- Re: [AMBER] hbond atom mask in cpptraj mirage .
- Re: [AMBER] Problem with MMPBSA.py Jan-Philip Gehrcke
- Re: [AMBER] Problem with MMPBSA.py Osman, Roman
- Re: [AMBER] Using iwrap with harmonic restraints Ross Walker
- Re: [AMBER] ptraj cluster George Tzotzos
- Re: [AMBER] again GLYCAM06 + 99SB + GAFF ? Marek Maly
- [AMBER] compilation problem with bugfix 1 to 17 Hongyu Miao
- Re: [AMBER] Analysing the result after simulation Bruno Rodrigues
- Re: [AMBER] compilation problem with bugfix 1 to 17 Jason Swails
- [AMBER] Is GB solvation possible with AT 1.5 sqm? Emmanuel Baribefe Naziga
- Re: [AMBER] compilation problem with bugfix 1 to 17 Hongyu Miao
- Re: [AMBER] Xleap problem William Wei
- [AMBER] ESPGEN William Wei
- Re: [AMBER] ESPGEN Jason Swails
- [AMBER] problem with mm_pbsa moitrayee.mbu.iisc.ernet.in
- Re: [AMBER] Xleap problem Ross Walker
- Re: [AMBER] Old problem with restart Bruno Rodrigues
- Re: [AMBER] Using iwrap with harmonic restraints Ozen, Aysegul
- Re: [AMBER] Using iwrap with harmonic restraints Ross Walker
- Re: [AMBER] Error in mm_pbsa Mengjuei Hsieh
- [AMBER] Error: Amber 11 and CUDA4.0 c00jsw00.nchc.narl.org.tw
- [AMBER] Error: Amber 11 and CUDA4.0 c00jsw00.nchc.narl.org.tw
- Re: [AMBER] Error: Amber 11 and CUDA4.0 Ismail, Mohd F.
- Re: [AMBER] Error: Amber 11 and CUDA4.0 Ross Walker
- Re: [AMBER] Error: Amber 11 and CUDA4.0 c00jsw00.nchc.narl.org.tw
- Re: [AMBER] Error: Amber 11 and CUDA4.0 Ross Walker
Tuesday, 23 August 2011
- [AMBER] MMPBSA not installed in amber11 vaibhav dixit
- [AMBER] MD output files George Tzotzos
- Re: [AMBER] MMPBSA not installed in amber11 Jason Swails
- Re: [AMBER] MD output files Jason Swails
- Re: [AMBER] MMPBSA not installed in amber11 vaibhav dixit
- Re: [AMBER] MMPBSA not installed in amber11 Jason Swails
- Re: [AMBER] MMPBSA not installed in amber11 vaibhav dixit
- Re: [AMBER] Major GPU Update Released Dmitry Mukha
- Re: [AMBER] nmpimd heating Andrew Petersen
- Re: [AMBER] Using iwrap with harmonic restraints Ozen, Aysegul
- Re: [AMBER] Using iwrap with harmonic restraints Ozen, Aysegul
- Re: [AMBER] Using iwrap with harmonic restraints Jason Swails
- Re: [AMBER] fftw-2.1.5 and Fedora Dmitry Mukha
- Re: [AMBER] Major GPU Update Released Scott Le Grand
- Re: [AMBER] [q4md-fft] General Question about Charge Derivation using RESP Ismail, Mohd F.
- [AMBER] AMBER11 GPGPU question Carlos Sosa
- [AMBER] Is it possible to do REMD for a 12000 atom molecule? Catein Catherine
- Re: [AMBER] Is it possible to do REMD for a 12000 atom molecule? Carlos Simmerling
- Re: [AMBER] Is it possible to do REMD for a 12000 atom molecule? Adrian Roitberg
- Re: [AMBER] problem with mm_pbsa Bill Miller III
- [AMBER] GPGPU AMBER11 question Carlos P Sosa
- [AMBER] libstdc++, Fedora14, Amber11, pmemd.cuda Dmitry Mukha
- [AMBER] Fwd: Is it possible to do REMD for a 12000 atom molecule? Dmitry Mukha
- Re: [AMBER] Fwd: Is it possible to do REMD for a 12000 atom molecule? Carlos Simmerling
- Re: [AMBER] Fwd: Is it possible to do REMD for a 12000 atom molecule? Adrian Roitberg
- Re: [AMBER] Fwd: Is it possible to do REMD for a 12000 atom molecule? Dmitry Mukha
- Re: [AMBER] Fwd: Is it possible to do REMD for a 12000 atom molecule? Carlos Simmerling
- Re: [AMBER] Fwd: Is it possible to do REMD for a 12000 atom molecule? Dmitry Mukha
- Re: [AMBER] Fwd: Is it possible to do REMD for a 12000 atom molecule? Carlos Simmerling
- Re: [AMBER] Fwd: Is it possible to do REMD for a 12000 atom molecule? Dmitry Mukha
- Re: [AMBER] ESPGEN William Wei
- Re: [AMBER] Fwd: Is it possible to do REMD for a 12000 atom molecule? Adrian Roitberg
- Re: [AMBER] Fwd: Is it possible to do REMD for a 12000 atom molecule? Carlos Simmerling
- [AMBER] ptraj invalid writes Ben Gamari
- Re: [AMBER] Fwd: Is it possible to do REMD for a 12000 atom molecule? Carlos Simmerling
- Re: [AMBER] Fwd: Is it possible to do REMD for a 12000 atom molecule? Dmitry Mukha
- Re: [AMBER] Fwd: Is it possible to do REMD for a 12000 atom molecule? Carlos Simmerling
- [AMBER] About sudden simulation box twist Bin Wu
- Re: [AMBER] About sudden simulation box twist Carlos Simmerling
- Re: [AMBER] Fwd: Is it possible to do REMD for a 12000 atom molecule? Ross Walker
- Re: [AMBER] About sudden simulation box twist Bin Wu
- Re: [AMBER] About sudden simulation box twist Adrian Roitberg
- Re: [AMBER] ESPGEN Jason Swails
- Re: [AMBER] ESPGEN Niel Henriksen
- Re: [AMBER] libstdc++, Fedora14, Amber11, pmemd.cuda Jason Swails
- Re: [AMBER] About sudden simulation box twist Bin Wu
- Re: [AMBER] About sudden simulation box twist Adrian Roitberg
- Re: [AMBER] ptraj invalid writes Daniel Roe
- Re: [AMBER] About sudden simulation box twist Jason Swails
- Re: [AMBER] ESPGEN Jason Swails
- Re: [AMBER] Fwd: Is it possible to do REMD for a 12000 atom molecule? Jason Swails
- Re: [AMBER] About sudden simulation box twist Bin Wu
- Re: [AMBER] About sudden simulation box twist Jason Swails
- Re: [AMBER] About sudden simulation box twist Bin Wu
- Re: [AMBER] Is it possible to do REMD for a 12000 atom molecule? Catein Catherine
- Re: [AMBER] Is it possible to do REMD for a 12000 atom molecule? Carlos Simmerling
- [AMBER] antechamber error vaibhav dixit
- Re: [AMBER] [q4md-fft] General Question about Charge Derivation using RESP FyD
Wednesday, 24 August 2011
- Re: [AMBER] antechamber error Jason Swails
- [AMBER] How to make a graph of secondary structure? qiao xue
- [AMBER] Amber Shesh Nath
- Re: [AMBER] libstdc++, Fedora14, Amber11, pmemd.cuda Dmitry Mukha
- Re: [AMBER] Amber David A Case
- Re: [AMBER] antechamber error vaibhav dixit
- Re: [AMBER] libstdc++, Fedora14, Amber11, pmemd.cuda Jason Swails
- Re: [AMBER] libstdc++, Fedora14, Amber11, pmemd.cuda Dmitry Mukha
- Re: [AMBER] antechamber error David A Case
- Re: [AMBER] libstdc++, Fedora14, Amber11, pmemd.cuda Jason Swails
- [AMBER] question about creating phantom residues moitrayee.mbu.iisc.ernet.in
- Re: [AMBER] question about creating phantom residues Jason Swails
- Re: [AMBER] GPGPU AMBER11 question Carlos Sosa
- [AMBER] mmgbsa.py energy decomposition problem Yi An
- Re: [AMBER] About sudden simulation box twist Bin Wu
- Re: [AMBER] About sudden simulation box twist Thomas Cheatham III
- Re: [AMBER] mmgbsa.py energy decomposition problem Bill Miller III
- Re: [AMBER] mmgbsa.py energy decomposition problem Jason Swails
- Re: [AMBER] About sudden simulation box twist Bin Wu
- [AMBER] MMPBSA free energy decomposition values and total binding free energy values Rajesh Raju
- Re: [AMBER] again GLYCAM06 + 99SB + GAFF ? Yun Shi
- Re: [AMBER] again GLYCAM06 + 99SB + GAFF ? FyD
Thursday, 25 August 2011
- Re: [AMBER] antechamber error vaibhav dixit
- Re: [AMBER] antechamber error Daniel Roe
- [AMBER] Technical problems with running steered MD Sergey Samsonov
- Re: [AMBER] antechamber error David A Case
- Re: [AMBER] Technical problems with running steered MD David A Case
- Re: [AMBER] Technical problems with running steered MD Sergey Samsonov
- [AMBER] Dihedral of quadruple of centres of mass Massimiliano Porrini
- Re: [AMBER] Dihedral of quadruple of centres of mass Daniel Roe
- Re: [AMBER] Dihedral of quadruple of centres of mass Massimiliano Porrini
- Re: [AMBER] Technical problems with running steered MD David A Case
- Re: [AMBER] nmpimd heating Francesco Paesani
- Re: [AMBER] dodecahedron box ? Brian Radak
- Re: [AMBER] Technical problems with running steered MD Jason Swails
- Re: [AMBER] Dihedral of quadruple of centres of mass Daniel Roe
- [AMBER] Jarzynski and PMEMD Sai Kumar Ramadugu
- Re: [AMBER] again GLYCAM06 + 99SB + GAFF ? Yun Shi
- [AMBER] Potential problem with CUDA version in release 18? Carlos P Sosa
- Re: [AMBER] Potential problem with CUDA version in release 18? Ismail, Mohd F.
- [AMBER] Potential problem with CUDA version in release 18? Carlos P Sosa
- Re: [AMBER] again GLYCAM06 + 99SB + GAFF ? Yun Shi
- Re: [AMBER] Potential problem with CUDA version in release 18? David A Case
- [AMBER] GPGPU AMBER11 question Carlos P Sosa
- Re: [AMBER] ptraj invalid writes Ben Gamari
- Re: [AMBER] Potential problem with CUDA version in release 18? Ismail, Mohd F.
- Re: [AMBER] Potential problem with CUDA version in release 18? Carlos Sosa
- Re: [AMBER] About sudden simulation box twist Thomas Cheatham III
- Re: [AMBER] About sudden simulation box twist Bin Wu
- Re: [AMBER] ESPGEN Niel Henriksen
- [AMBER] Ptraj and wrapping water molecules Sai Kumar Ramadugu
- [AMBER] Calculating Cpu hours from output file Chris Bryant
- Re: [AMBER] Ptraj and wrapping water molecules Thomas Cheatham III
- [AMBER] Amber11 on SGI Altix Bruno Rodrigues
- Re: [AMBER] Calculating Cpu hours from output file Jason Swails
- Re: [AMBER] Jarzynski and PMEMD Jason Swails
- Re: [AMBER] Calculating Cpu hours from output file Chris Bryant
- Re: [AMBER] GPGPU AMBER11 question Ross Walker
- Re: [AMBER] Potential problem with CUDA version in release 18? Ross Walker
- Re: [AMBER] Potential problem with CUDA version in release 18? Carlos Sosa
- Re: [AMBER] again GLYCAM06 + 99SB + GAFF ? Yun Shi
- Re: [AMBER] antechamber error vaibhav dixit
- Re: [AMBER] again GLYCAM06 + 99SB + GAFF ? FyD
- Re: [AMBER] again GLYCAM06 + 99SB + GAFF ? FyD
- Re: [AMBER] again GLYCAM06 + 99SB + GAFF ? FyD
Friday, 26 August 2011
- Re: [AMBER] Technical problems with running steered MD Sergey Samsonov
- [AMBER] folding/unfolding or just local minimum trap? Chinh Su Tran To
- Re: [AMBER] folding/unfolding or just local minimum trap? Carlos Simmerling
- Re: [AMBER] Amber11 on SGI Altix Bruno Rodrigues
- Re: [AMBER] antechamber error David A Case
- Re: [AMBER] folding/unfolding or just local minimum trap? Chinh Su Tran To
- Re: [AMBER] libstdc++, Fedora14, Amber11, pmemd.cuda Dmitry Mukha
- Re: [AMBER] problem with ZAFF Hashem Taha
- [AMBER] postdoc positions in chemical physics Dr. Vitaly V. Chaban
- [AMBER] problem with Cadmium parameters and running minimization Hashem Taha
- Re: [AMBER] problem with Cadmium parameters and running minimization Ben Roberts
- Re: [AMBER] problem with Cadmium parameters and running minimization Hashem Taha
- Re: [AMBER] problem with Cadmium parameters and running minimization Ben Roberts
- Re: [AMBER] GPGPU AMBER11 question Carlos Sosa
- [AMBER] problem with TI calculation, help!! Victor Ma
- Re: [AMBER] problem with TI calculation, help!! InSuk Joung
- Re: [AMBER] problem with TI calculation, help!! Niel Henriksen
- Re: [AMBER] problem with TI calculation, help!! Victor Ma
- Re: [AMBER] Major GPU Update Released Dmitry Mukha
- Re: [AMBER] again GLYCAM06 + 99SB + GAFF ? Yun Shi
- [AMBER] how to fill in missing parameters in tleap? Yun Shi
- Re: [AMBER] again GLYCAM06 + 99SB + GAFF ? Yun Shi
- Re: [AMBER] how to fill in missing parameters in tleap? Jason Swails
- Re: [AMBER] _mmpbsa_py_energy error durint PB calculations Jason Swails
- Re: [AMBER] antechamber error vaibhav dixit
- Re: [AMBER] how to fill in missing parameters in tleap? FyD
- Re: [AMBER] again GLYCAM06 + 99SB + GAFF ? FyD
Saturday, 27 August 2011
- Re: [AMBER] again GLYCAM06 + 99SB + GAFF ? FyD
- Re: [AMBER] folding/unfolding or just local minimum trap? Carlos Simmerling
- Re: [AMBER] folding/unfolding or just local minimum trap? Chinh Su Tran To
- [AMBER] NaN Error in mdout, restrt, mdcrd, mdvel files with pmemd.cuda Ismail, Mohd F.
- Re: [AMBER] NaN Error in mdout, restrt, mdcrd, mdvel files with pmemd.cuda Ross Walker
Sunday, 28 August 2011
- [AMBER] Error in pmemd.cuda: test.pmemd.cuda.pme zhenquan hu
- Re: [AMBER] how to fill in missing parameters in tleap? case
- Re: [AMBER] antechamber error case
- Re: [AMBER] Error in pmemd.cuda: test.pmemd.cuda.pme Ross Walker
- Re: [AMBER] NaN Error in mdout, restrt, mdcrd, mdvel files with pmemd.cuda Ismail, Mohd F.
- Re: [AMBER] Error in pmemd.cuda: test.pmemd.cuda.pme Zhenquan Hu
- Re: [AMBER] Error in pmemd.cuda: test.pmemd.cuda.pme Scott Le Grand
Monday, 29 August 2011
- Re: [AMBER] antechamber error vaibhav dixit
- [AMBER] ntf parameters in energy minimization Qin Zhang
- Re: [AMBER] ntf parameters in energy minimization Jason Swails
- [AMBER] PBS script Bruno Rodrigues
- Re: [AMBER] PBS script Jason Swails
- Re: [AMBER] PBS script Bruno Rodrigues
- Re: [AMBER] PBS script Jason Swails
- Re: [AMBER] PBS script Bruno Rodrigues
- Re: [AMBER] PBS script Bruno Rodrigues
- Re: [AMBER] How to interpret GLYCAM prep file? Yun Shi
- [AMBER] MMPBSA.py parallel Jesper Sørensen
- Re: [AMBER] MMPBSA.py parallel Bill Miller III
- Re: [AMBER] MMPBSA.py parallel Jesper Sørensen
- Re: [AMBER] How to interpret GLYCAM prep file? Lachele Foley (Lists)
- Re: [AMBER] MMPBSA.py parallel Jason Swails
- Re: [AMBER] MMPBSA.py parallel Jesper Sørensen
- [AMBER] two planes' dihedral angle caobb0214
- Re: [AMBER] PBS script Bruno Rodrigues
- Re: [AMBER] two planes' dihedral angle Andrew Jewett
- [AMBER] mmpbsa issues Neha Gandhi
Tuesday, 30 August 2011
- [AMBER] How to patch phosphate at the 3'-end Indrajit Deb
- Re: [AMBER] mmpbsa issues sribone.fcq.unc.edu.ar
- [AMBER] LEaP for organic molecule Chidambar Kulkarni
- Re: [AMBER] LEaP for organic molecule Daniel Roe
- Re: [AMBER] PBS script Ross Walker
- [AMBER] cpptraj: 1) align using a certain region 2) calc rmsd for another region Jan-Philip Gehrcke
- Re: [AMBER] PBS script Carlos Sosa
- Re: [AMBER] mmpbsa issues Jason Swails
- Re: [AMBER] cpptraj: 1) align using a certain region 2) calc rmsd for another region Jason Swails
- Re: [AMBER] Ptraj and wrapping water molecules Ozen, Aysegul
- Re: [AMBER] ntf parameters in energy minimization Qin Zhang
- Re: [AMBER] How to patch phosphate at the 3'-end David A Case
- Re: [AMBER] How to interpret GLYCAM prep file? Yun Shi
- Re: [AMBER] How to interpret GLYCAM prep file? Lachele Foley (Lists)
- [AMBER] sander compiled by which compiler can show full error mesage? xiaodong huang
- Re: [AMBER] sander compiled by which compiler can show full error mesage? Ray Luo, Ph.D.
- Re: [AMBER] sander compiled by which compiler can show full error mesage? xiaodong huang
- Re: [AMBER] How to patch phosphate at the 3'-end Hugh Heldenbrand
- Re: [AMBER] sander compiled by which compiler can show full error mesage? Jason Swails
Wednesday, 31 August 2011
- [AMBER] problem in installing xleap sonali dhindwal
- Re: [AMBER] problem in installing xleap Hirdesh Kumar
- Re: [AMBER] cpptraj: 1) align using a certain region 2) calc rmsd for another region Jan-Philip Gehrcke
- [AMBER] flip command in leap Peter Varnai
- Re: [AMBER] problem in installing xleap David A Case
- Re: [AMBER] problem in installing xleap Chirag Vora
- Re: [AMBER] problem in installing xleap sonali dhindwal
- Re: [AMBER] addition of massless particle to benzene that interacts only with massless particles in other benzene molecules Dean Cuebas
- Re: [AMBER] flip command in leap FyD
- Re: [AMBER] problem in installing xleap David A Case
- Re: [AMBER] Ptraj and wrapping water molecules Sai Kumar Ramadugu
- Re: [AMBER] Ptraj and wrapping water molecules InSuk Joung
- [AMBER] Calculation of Force during SMD Sai Kumar Ramadugu
- Re: [AMBER] Calculation of Force during SMD Adrian Roitberg
- Re: [AMBER] Calculation of Force during SMD Sai Kumar Ramadugu

Last message date: Wed Aug 31 2011 - 20:30:02 PDT
Archived on: Fri Nov 22 2024 - 05:54:20 PST

Amber Archive Aug 2011 by date