Amber Archive Sep 2009: by date

Monday, 31 August 2009
- [AMBER] ACE and NME patch: VMD ??? Siddharth Rastogi
- Re: [AMBER] Docking with Amber case
- [AMBER] how to pull a dna balaji nagarajan
- Re: [AMBER] ATP/GTP parameters E.M.
- Re: [AMBER] problem with 4-Hydroxyl-Proline tutorial Jia Xu
- Re: [AMBER] ATP/GTP parameters wang
- Re: [AMBER] ATP/GTP parameters FyD
Tuesday, 1 September 2009
- [AMBER] symbol lookup error Bala subramanian
- Re: [AMBER] How to derive charges from the output bharat lakhani
- [AMBER] How to remove Hydrogen using ptraj Mannan
- Re: [AMBER] how to pull a dna Sam Danziger
- RE: [AMBER] ATP/GTP parameters Steve Seibold
- Re: [AMBER] momentum in MD simulation case
- Re: [AMBER] cpin error case
- Re: [AMBER] Changing pH of the system nicholus bhattacharjee
- [AMBER] how to pull a dna balaji nagarajan
- [AMBER] How to use AMBER 10 for PCA analysis. Catein Catherine
- Re: [AMBER] How to remove Hydrogen using ptraj Thomas Cheatham III
- RE: [AMBER] ATP/GTP parameters FyD
- RE: [AMBER] ATP/GTP parameters Steve Seibold
- [AMBER] Reg. snapshot_statistics.out.snap Rose Tamil
- Re: [AMBER] How to remove Hydrogen using ptraj case
- Re: [AMBER] How to remove Hydrogen using ptraj Thomas Cheatham III
- RE: [AMBER] ACE and NME patch: VMD ??? Ross Walker
- RE: [AMBER] symbol lookup error Ross Walker
- Re: [AMBER] Creating new counterions Bill Ross
- Re: [AMBER] Creating new counterions case
- [AMBER] Simulation short peptide and protein interaction Rilei Yu
- [AMBER] Question regarding PCA analysis. Catein Catherine
Wednesday, 2 September 2009
- [AMBER] question about ptraj Jeffrey
- [AMBER] how to give force values in TMD balaji nagarajan
- Re: [AMBER] Simulation short peptide and protein interaction case
- [AMBER] How to find water-mediated hydrogen bond? Catein Catherine
- RE: [AMBER] question about ptraj Niel Henriksen
- [AMBER] Active site - Ion - Search engine s. Bill
- [AMBER] What is dual topology Ashish Runthala
- [AMBER] How to consider the off centre charges Ashish Runthala
- Re: [AMBER] What is dual topology case
- Re: [AMBER] How to consider the off centre charges case
- [AMBER] unit of force constant balaji nagarajan
- [AMBER] antechamber bug: output of incorrect bond character Matthew Walsh
- [AMBER] Question about the debug forces Faezeh Salehi
- [AMBER] how to deal with aromatic nitro group with antechamber Lin Xu
- Re: [AMBER] antechamber bug: output of incorrect bond character case
- Re: [AMBER] how to deal with aromatic nitro group with antechamber case
- [AMBER] Heme + Fe(II) + O2 + histidine parameter Haining Liu
- Re: [AMBER] antechamber bug: output of incorrect bond character Matthew Walsh
- [AMBER] ATP and GTP parameters E.M.
- Re: [AMBER] ATP and GTP parameters FyD
- Re: [AMBER] ATP and GTP parameters E.M.
- Re: [AMBER] ATP and GTP parameters Sergey Samsonov
Thursday, 3 September 2009
- Re: [AMBER] Heme + Fe(II) + O2 + histidine parameter FyD
- [AMBER] What should be the standard input file when imin=5 Ashish Runthala
- Re: [AMBER] How to find water-mediated hydrogen bond? Hannes Loeffler
- Re: [AMBER] ATP and GTP parameters FyD
- Re: [AMBER] ATP and GTP parameters FyD
- Re: [AMBER] antechamber bug: output of incorrect bond character case
- Re: [AMBER] ATP and GTP parameters Carlos Simmerling
- Re: [AMBER] What should be the standard input file when imin=5 Carlos Simmerling
- Re: [AMBER] Simulation short peptide and protein interaction Rilei Yu
- Re: [AMBER] Simulation short peptide and protein interaction Carlos Simmerling
- Re: [AMBER] Question regarding PCA analysis. Chris Moth
- Re: [AMBER] antechamber bug: output of incorrect bond character Matthew Walsh
- Re: [AMBER] antechamber bug: output of incorrect bond character case
- [AMBER] QM/MM simulation gaurav panwar
- RE: [AMBER] QM/MM simulation Ross Walker
- Re: [AMBER] Heme + Fe(II) + O2 + histidine parameter Haining Liu
- Re: [AMBER] ATP and GTP parameters E.M.
- RE: [AMBER] Question regarding PCA analysis. Catein Catherine
- [AMBER] Problem about adding a small residue to DNA Yikan Chen
- 回复： [AMBER] Problem about adding a small residue to DNA Rilei Yu
- [AMBER] Kinetics Soumya Lipsa Rath
Friday, 4 September 2009
- Re: [AMBER] Heme + Fe(II) + O2 + histidine parameter FyD
- [AMBER] prep file Jio M
- [AMBER] MM-GBAS decomp error Catein Catherine
- Re: [AMBER] prep file case
- [AMBER] Dummy atoms and MM-PBSA Alireza Shaneh
- [AMBER] nmropt option Jio M
- Re: [AMBER] nmropt option Carlos Simmerling
- Re: [AMBER] Dummy atoms and MM-PBSA Ray Luo
- [AMBER] Provisional Support for AMBER 10 PMEMD on NVIDIA GPUs Ross Walker
- Re: [AMBER] Kinetics case
- Re: [AMBER] Problem about adding a small residue to DNA case
- Re: 回复： [AMBER] Problem about adding a small residue to DNA Yikan Chen
- Re: 回复： [AMBER] Problem about adding a small residue to DNA Yikan Chen
- Re: 回复： [AMBER] Problem about adding a small residue to DNA case
- Re: 回复： [AMBER] Problem about adding a small residue to DNA Yikan Chen
- Re: [AMBER] nmropt option Jio M
Saturday, 5 September 2009
- Re: [AMBER] nmropt option Carlos Simmerling
- [AMBER] Antechamber generate a prep file in a wrong order... Yikan Chen
- [AMBER] How to find a protein's energy Ashish Runthala
Sunday, 6 September 2009
- Re: [AMBER] How to find a protein's energy Carlos Simmerling
- Re: [AMBER] Antechamber generate a prep file in a wrong order... case
- Re: 回复： [AMBER] Problem about adding a small residue to DNA case
- Re: [AMBER] How to find a protein's energy Ashish Runthala
- Re: 回复： [AMBER] Problem about adding a small residue to DNA Yikan Chen
- [AMBER] R.E.D. : Gaussian Error manoj singh
- Re: [AMBER] R.E.D. : Gaussian Error FyD
- Re: [AMBER] R.E.D. : Gaussian Error manoj singh
- Re: [AMBER] R.E.D. : Gaussian Error FyD
- Re: [AMBER] R.E.D. : Gaussian Error manoj singh
Monday, 7 September 2009
- [AMBER] (no subject) gunajyoti das
- Re: [AMBER] Problem about adding a small residue to DNA FyD
- [AMBER] problem in QM/MM input file gaurav panwar
- [AMBER] loadpdb Jagdeesh C
- Re: [AMBER] loadpdb Carlos Simmerling
- Re: [AMBER] loadpdb Jagdeesh C
- Re: [AMBER] loadpdb Ashish Runthala
- [AMBER] problem of PBCAL/GB Qinghua Liao
- Re: [AMBER] problem of PBCAL/GB Ray Luo
- Re: [AMBER] Kinetics Soumya Lipsa Rath
Tuesday, 8 September 2009
- [AMBER] Enquiry about MM/GBSA output file. Catein Catherine
- Re: [AMBER] problem of PBCAL/GB Qinghua Liao
- [AMBER] general query: implicit solvation Jio M
- Re: [AMBER] general query: implicit solvation Carlos Simmerling
- [AMBER] loading PDB of a RNA sequence gunajyoti das
- Re: [AMBER] loading PDB of a RNA sequence Carlos Simmerling
- Re: [AMBER] loading PDB of a RNA sequence case
- [AMBER] No sp2 improper torsion term for NB-CA-CB-CB qiaoyan
- Re: [AMBER] loadpdb Tom Joseph
- Re: [AMBER] problem in QM/MM input file Tom Joseph
- Re: [AMBER] No sp2 improper torsion term for NB-CA-CB-CB case
- [AMBER] unit of force constant balaji nagarajan
- Re: [AMBER] unit of force constant Carlos Simmerling
- Re: [AMBER] loadpdb Carlos Simmerling
- RE: [AMBER] unit of force constant balaji nagarajan
- Re: [AMBER] Problem with loading PDB into tleap Kamali Sripathi
- [AMBER] How to denature DNA balaji nagarajan
- Re: [AMBER] How to denature DNA Adrian Roitberg
- [AMBER] AmberTools 1.3 / CHAMBER Mag. Thomas Taylor
- [AMBER] amoeba.prm problem? Ivan Gladich
- Re: [AMBER] Problem with loading PDB into tleap Ashish Runthala
- [AMBER] TI in Amber9/10 Alessandro S. Nascimento
- RE: [AMBER] How to denature DNA balaji nagarajan
- Re: [AMBER] How to denature DNA Adrian Roitberg
- Re: [AMBER] loadpdb Bill Ross
- [AMBER] logdvdl does not work helde010.umn.edu
- Re: [AMBER] loadpdb Bill Ross
- RE: [AMBER] How to denature DNA balaji nagarajan
- [AMBER] loading a following attached protein in amber 10 albert albert
- Re: [AMBER] How to denature DNA Adrian Roitberg
- Re: [AMBER] loading a following attached protein in amber 10 David Watson
- Re: [AMBER] loading a following attached protein in amber 10 case
- RE: [AMBER] How to denature DNA Bill Ross
- Re: [AMBER] logdvdl does not work steinbrt.rci.rutgers.edu
- Re: [AMBER] TI in Amber9/10 steinbrt.rci.rutgers.edu
- Re: [AMBER] loading a following attached protein in amber 10 albert albert
- Re: [AMBER] TI in Amber9/10 Ilyas Yildirim
- [AMBER] QMMM NEB with PM3-PDDG fails with ASSERTion 'ierr.eq.0' pimd_init.f line 320 Keith Van Nostrand
- [AMBER] Hbond analysis: Direction of the hydrogen Age.Skjevik.biomed.uib.no
- Re: [AMBER] Hbond analysis: Direction of the hydrogen Shulin Zhuang
- Re: [AMBER] Hbond analysis: Direction of the hydrogen Age.Skjevik.biomed.uib.no
- Re: [AMBER] loadpdb Jagdeesh C
- Re: [AMBER] loadpdb Bill Ross
- RE: [AMBER] How to denature DNA balaji nagarajan
- [AMBER] Leap warning manoj singh
Wednesday, 9 September 2009
- Re: [AMBER] Leap warning Ashish Runthala
- [AMBER] about the number of residues after MD Qinghua Liao
- Re: [AMBER] PK zero for specific dihedral and parmchk Carlos Simmerling
- Re: [AMBER] Leap warning case
- Re: [AMBER] PK zero for specific dihedral and parmchk case
- Re: [AMBER] loadpdb Carlos Simmerling
- [AMBER] gaff.dat questions gilbert.bluemarble.net
- Re: [AMBER] gaff.dat questions case
- [AMBER] parameterization of protein-ligand complex cc cc
- RE: [AMBER] How to denature DNA Bill Ross
- Re: [AMBER] parameterization of protein-ligand complex case
- Re: [AMBER] Leap warning Bill Ross
- Re: [AMBER] parameterization of protein-ligand complex Bill Ross
- RE: [AMBER] How to denature DNA balaji nagarajan
- RE: [AMBER] parameterization of protein-ligand complex cc cc
- RE: [AMBER] parameterization of protein-ligand complex cc cc
- [AMBER] Any tutorial on the proper way to merge a ligand and protein? Dean Cuebas
- Re: [AMBER] Any tutorial on the proper way to merge a ligand and protein? case
- Re: [AMBER] Any tutorial on the proper way to merge a ligand and protein? Dean Cuebas
- Re: [AMBER] amoeba.prm problem? case
Thursday, 10 September 2009
- [AMBER] Solvate in an alkaline solution vallespardojl.chem.leidenuniv.nl
- [AMBER] input file Mag. Thomas Taylor
- Re: [AMBER] input file Carlos Simmerling
- Re: [AMBER] Solvate in an alkaline solution case
- Re: [AMBER] input file Jenny Iskrenova
- Re: [AMBER] input file Ashish Runthala
- [AMBER] QM/MM minimization gaurav panwar
- Re: [AMBER] QM/MM minimization Pansy Patel
- Re: [AMBER] input file Bill Ross
- [AMBER] question with radial distribution function Ganesh Kamath
- [AMBER] periodic boundary condition for implicit solvent simulation and SHORT command Workalemahu Berhanu
- Re: [AMBER] periodic boundary condition for implicit solvent simulation and SHORT command case
- [AMBER] DMF solvent box Abhishek Banerjee
- [AMBER] PBSA for gp41 binding free energy shuqing wang
Friday, 11 September 2009
- [AMBER] dihedral force calculation Germain Vallverdu
- Re: [AMBER] DMF solvent box Jio M
- RE: [AMBER] Any tutorial on the proper way to merge a ligand and protein? cc cc
- [AMBER] RESP RED s. Bill
- Re: [AMBER] Any tutorial on the proper way to merge a ligand and protein? case
- [AMBER] charge consideration Jio M
- [AMBER] "nan" in gaussian input files generated by antechamber Yikan Chen
- Re: [AMBER] amoeba.prm problem? Ivan Gladich
- Re: [AMBER] PBSA for gp41 binding free energy Ray Luo
Saturday, 12 September 2009
- [AMBER] What is the unit of RMSF? Catein Catherine
- Re: [AMBER] What is the unit of RMSF? case
- Re: [AMBER] amoeba.prm problem? case
- Re: [AMBER] "nan" in gaussian input files generated by antechamber case
- Re: [AMBER] charge consideration case
- Re: [AMBER] dihedral force calculation case
- Re: [AMBER] DMF solvent box FyD
- Re: [AMBER] QMMM NEB with PM3-PDDG fails with ASSERTion 'ierr.eq.0' pimd_init.f line 320 case
- Re: [AMBER] RESP RED FyD
- Re: [AMBER] "nan" in gaussian input files generated by antechamber FyD
- Re: [AMBER] DMF solvent box Abhishek Banerjee
Sunday, 13 September 2009
- Re: [AMBER] DMF solvent box Abhishek Banerjee
- Re: [AMBER] DMF solvent box FyD
- [AMBER] What is the Optimum Ph for solvating a protein Ashish Runthala
- [AMBER] load .crd & .top in xleap vallespardojl.chem.leidenuniv.nl
- Re: [AMBER] DMF solvent box Abhishek Banerjee
- [AMBER] re: charge interaction Jio M
- Re: [AMBER] DMF solvent box FyD
- Re: [AMBER] load .crd & .top in xleap oguz gurbulak
- Re: [AMBER] re: charge interaction case
- Re: [AMBER] What is the Optimum Ph for solvating a protein case
- Re: [AMBER] re: charge interaction case
- [AMBER] variable header for ABMD stephane acoca
Monday, 14 September 2009
- [AMBER] re: charge consideration Jio M
- [AMBER] How to prepare the coordinate and toplogy files in leap ? xuemeiwang1103
- [AMBER] error xleap: XaLeap_wcl is empty Mari Carmen Pérez
- [AMBER] how to calculate correct RMSF? Catein Catherine
- [AMBER] Ki and G s. Bill
- Re: [AMBER] How to prepare the coordinate and toplogy files in leap ? case
- Re: [AMBER] Ki and G steinbrt.rci.rutgers.edu
- Re: [AMBER] error xleap: XaLeap_wcl is empty case
- Re: [AMBER] how to calculate correct RMSF? case
- Re: [AMBER] DMF solvent box Abhishek Banerjee
- [AMBER] Carbon Nanotube Library file (CNT) Christopher Stiles
- Re: [AMBER] Ki and G Adrian Roitberg
- [AMBER] radial distribution function in amber Ganesh Kamath
- RE: [AMBER] parameterization of protein-ligand complex Jeff Yeo
- Re: [AMBER] DMF solvent box FyD
- [AMBER] Question on ECAVITY term of MM_PBSA Gianluca Degliesposti
- Re: [AMBER] Ki and G Marek Maly
- Re: [AMBER] Ki and G case
- Re: [AMBER] Ki and G Marek Maly
- [AMBER] makeDIST_RST: no map function Workalemahu Berhanu
- Re: [AMBER] Ki and G steinbrt.rci.rutgers.edu
- Re: [AMBER] Ki and G case
- RE: [AMBER] how to calculate correct RMSF? Catein Catherine
- [AMBER] Problem on PMEMD zyxism
- Re: [AMBER] Problem on PMEMD Tom Joseph
- Re: [AMBER] Problem on PMEMD Adrian Roitberg
- Re: Re: [AMBER] Problem on PMEMD zyxism
- Re: [AMBER] Problem on PMEMD Robert Duke
Tuesday, 15 September 2009
- [AMBER] Error in minimal xuemeiwang1103
- Re: [AMBER] Ki and G Marek Maly
- Re: [AMBER] Error in minimal case
- RE: [AMBER] makeDIST_RST: no map function Duggan, Brendan M.
- Re:Re: [AMBER] Error in minimal xuemeiwang1103
- Re: [AMBER] makeDIST_RST: no map function case
- Re: [AMBER] makeDIST_RST: no map function Workalemahu Berhanu
- Re: [AMBER] makeDIST_RST: no map function Workalemahu Berhanu
- [AMBER] problem running pmemd gbrna tests wong105.llnl.gov
- [AMBER] can antechamber convert a prep file from cartesian to internal coordinates? Paul Ledbetter
- Re: [AMBER] can antechamber convert a prep file from cartesian to internal coordinates? case
- Re: Re: [AMBER] Error in minimal case
- Re: [AMBER] can antechamber convert a prep file from cartesian to internal coordinates? Bill Ross
- Re: [AMBER] can antechamber convert a prep file from cartesian to internal coordinates? Paul Ledbetter
- Re: [AMBER] can antechamber convert a prep file from cartesian to internal coordinates? Paul Ledbetter
- Re: [AMBER] DMF solvent box Abhishek Banerjee
- Re: [AMBER] DMF solvent box FyD
- [AMBER] About the PMEMD compiling for CUDA wang
- [AMBER] About the PMEMD compiling for CUDA Ross Walker
- RE: [AMBER] About the PMEMD compiling for CUDA Ross Walker
Wednesday, 16 September 2009
- Re: [AMBER] input file / skinnb Mag. Thomas Taylor
- Re: [AMBER] input file / skinnb case
- Re: [AMBER] input file / skinnb Robert Duke
- [AMBER] database Steve Seibold
- Re: [AMBER] database case
- [AMBER] RDC analysis: "No restraint defined" Michael Durney
- RE: [AMBER] database Steve Seibold
- Re: [AMBER] RDC analysis: "No restraint defined" case
- Re: [AMBER] database case
- RE: [AMBER] database FyD
- RE: [AMBER] database Steve Seibold
- RE: [AMBER] database Bill Ross
- [AMBER] antechamber error Taufik Al-Sarraj
- Re: [AMBER] antechamber error case
- Re: [AMBER] antechamber error Taufik Al-Sarraj
- RE: [AMBER] database FyD
- RE: [AMBER] database FyD
- Re: [AMBER] antechamber error Taufik Al-Sarraj
- [AMBER] question with hbond Ganesh Kamath
- Re: [AMBER] input file / skinnb Mag. Thomas Taylor
- Re: [AMBER] DMF solvent box Abhishek Banerjee
Thursday, 17 September 2009
- Re: [AMBER] DMF solvent box FyD
- [AMBER] loading RNA sequence in xleap gunajyoti das
- Re: [AMBER] loading RNA sequence in xleap FyD
- [AMBER] PES QM and MM s. Bill
- [AMBER] Force Field Fitting s. Bill
- Re: [AMBER] loading RNA sequence in xleap case
- [AMBER] install ambertools Karl Kirschner
- Re: [AMBER] install ambertools case
- RE: [AMBER] database Steve Seibold
- [AMBER] NAB syntax Michael Durney
- [AMBER] pH calculations Michael Durney
- Re: [AMBER] NAB syntax Andreas Svrcek-Seiler
- Re: [AMBER] NAB syntax case
- RE: [AMBER] database FyD
- Re: [AMBER] PES QM and MM Bill Ross
- Re: [AMBER] Force Field Fitting manoj singh
- [AMBER] how to ouput the electrostatic potential at a single atomic position? Jose Borreguero
- [AMBER] Discrepancy between AMBER and VMD calculation Sunita Patel
- Re: [AMBER] Force Field Fitting s. Bill
- Re: [AMBER] Force Field Fitting manoj singh
- RE: [AMBER] database Steve Seibold
- RE: [AMBER] database Jeff Yeo
- RE: [AMBER] database FyD
- Re: [AMBER] database case
Friday, 18 September 2009
- Re: [AMBER] database FyD
- [AMBER] LINMIN failure notice Jio M
- Re: [AMBER] LINMIN failure notice Ashish Runthala
- Re: [AMBER] LINMIN failure notice case
- [AMBER] PROBLEM WITH CHCL3BOX pdb Silvia Carlotto
- Re: [AMBER] PROBLEM WITH CHCL3BOX pdb case
- [AMBER] how to make 50% aqueous TFE box? parul sharma
- RE: [AMBER] database Steve Seibold
- Re: [AMBER] PROBLEM WITH CHCL3BOX pdb Hannes Loeffler
- Re: [AMBER] LINMIN failure notice Bill Ross
- Re: [AMBER] database case
- [AMBER] Cygwin Home Directory Wallace Kunin
- Re: [AMBER] Cygwin Home Directory Bill Ross
- RE: [AMBER] database Steve Seibold
- Re: [AMBER] Cygwin Home Directory Wallace Kunin
- Re: [AMBER] Cygwin Home Directory manoj singh
- Re: [AMBER] amoeba.prm problem? Ivan Gladich
- Re: [AMBER] Cygwin Home Directory Bill Ross
- Re: [AMBER] PROBLEM WITH CHCL3BOX pdb case
- RE: [AMBER] LINMIN failure notice Ross Walker
- Re: [AMBER] how to make 50% aqueous TFE box? FyD
- RE: [AMBER] database FyD
- Re: [AMBER] database case
- Re: [AMBER] DMF solvent box Abhishek Banerjee
- Re: [AMBER] DMF solvent box FyD
Saturday, 19 September 2009
- Re: [AMBER] Cygwin Home Directory Wallace Kunin
- Re: [AMBER] Cygwin Home Directory Bill Ross
- Re: [AMBER] Cygwin Home Directory case
- Re: [AMBER] Cygwin Home Directory Ashish Runthala
Sunday, 20 September 2009
- [AMBER] warning in dispatchToken Jeff Yeo
- Re: [AMBER] warning in dispatchToken case
- [AMBER] combining MD runs for post-MD analysis Jeff Yeo
- Re: [AMBER] combining MD runs for post-MD analysis Qinghua Liao
- Re: [AMBER] combining MD runs for post-MD analysis case
Monday, 21 September 2009
- [AMBER] Regarding united atom force field aneesh cna
- [AMBER] problem building sander.apbs Oliver Kuhn
- [AMBER] Question on ECAVITY term of MM_PBSA Gianluca Degliesposti
- Re: [AMBER] problem building sander.apbs case
- Re: [AMBER] problem building sander.apbs Oliver Kuhn
- [AMBER] generate prmtop file from CHARMM psf file Jeffrey
- Re: [AMBER] problem building sander.apbs case
- Re: [AMBER] Cygwin Home Directory Wallace Kunin
- Re: [AMBER] Cygwin Home Directory case
- Re: [AMBER] Question on ECAVITY term of MM_PBSA Ray Luo
- Re: [AMBER] combining MD runs for post-MD analysis Bill Ross
- Re: [AMBER] Regarding united atom force field Ray Luo
- Re: [AMBER] Cygwin Home Directory Bill Ross
- [AMBER] ACS COMP division awards- Oct 19th deadline Carlos Simmerling
- [AMBER] Installing AmberTools and Amber10 in Ubuntu - Instructions. David Dubins
- Re: [AMBER] Question on ECAVITY term of MM_PBSA Ray Luo
- Re: [AMBER] Regarding united atom force field FyD
- [AMBER] Pentane UA model aneesh cna
- Re: [AMBER] Installing AmberTools and Amber10 in Ubuntu - Instructions. oguz gurbulak
Tuesday, 22 September 2009
- Re: [AMBER] Pentane UA model FyD
- Re: [AMBER] problem building sander.apbs Oliver Kuhn
- [AMBER] RMSDf of heavy atoms Syed Tarique Moin
- [AMBER] MM_PBSA decomp problem B. Nandy
- [AMBER] Compiling Amber10 Williams, John
- [AMBER] ambertools and Snow Leopard 64 bits kernel Alan
- [AMBER] Installation issue Ashveen Seenauth
- Re: [AMBER] Installation issue Bill Ross
- Re: [AMBER] Installation issue Ashveen Seenauth
- Re: [AMBER] Installation issue Tom Joseph
- Re: [AMBER] Installation issue Ashveen Seenauth
- Re: [AMBER] Installation issue Tom Joseph
- Re: [AMBER] Installation issue Bill Ross
- Re: [AMBER] Installation issue Bill Ross
- Re: [AMBER] Installation issue Bill Ross
- Re: [AMBER] Installation issue Ashveen Seenauth
- Re: [AMBER] ambertools and Snow Leopard 64 bits kernel Tom Joseph
- Re: [AMBER] Installation issue Tom Joseph
- Re: [AMBER] Installation issue Bill Ross
- Re: [AMBER] problem building sander.apbs case
- [AMBER] Parameter Problem manoj singh
- [AMBER] group distance restraint XIAOHUICANG
- [AMBER] Problem regarding Hbond analysis Abhishek Singh
- [AMBER] Parameter Problem manoj singh
- Re: [AMBER] problem building sander.apbs Robert Konecny
- Re: [AMBER] Problem regarding Hbond analysis Bill Ross
- Re: [AMBER] ambertools and Snow Leopard 64 bits kernel Alan
- [AMBER] parameter for manganese Yuqin Cai
- [AMBER] apbs-amber Rilei Yu
- Re: [AMBER] apbs-amber Robert Konecny
- Re: [AMBER] ambertools and Snow Leopard 64 bits kernel Tom Joseph
- Re: [AMBER] apbs-amber Rilei Yu
- Re: [AMBER] ambertools and Snow Leopard 64 bits kernel gilbert.bluemarble.net
Wednesday, 23 September 2009
- Re: [AMBER] Parameter Problem FyD
- Re: [AMBER] Parameter Problem Manish Kumar
- Re: [AMBER] ambertools and Snow Leopard 64 bits kernel Alan
- Re: [AMBER] Installation issue Ashveen Seenauth
- Re: [AMBER] Installation issue Tom Joseph
- Re: [AMBER] Installation issue Ashveen Seenauth
- Re: [AMBER] Installation issue Tom Joseph
- Re: [AMBER] Installation issue Ashveen Seenauth
- Re: [AMBER] Installation issue Tom Joseph
- Re: [AMBER] Installation issue Bill Ross
- Re: [AMBER] Installation issue Bill Ross
- [AMBER] solvent accessible surface area Ganesh Kamath
- Re: [AMBER] solvent accessible surface area Carlos Simmerling
- Re: [AMBER] solvent accessible surface area Ganesh Kamath
- Re: [AMBER] solvent accessible surface area Carlos Simmerling
- Re: [AMBER] ambertools and Snow Leopard 64 bits kernel case
- [AMBER] fatal "does not have a type" error in tleap for a protein-ligand complex Jeff Yeo
Thursday, 24 September 2009
- [AMBER] Teragrid Beale, John
- Re: [AMBER] Teragrid Carlos Simmerling
- Re: [AMBER] parameter for manganese Mahmoud A. A. Ibrahim
- [AMBER] CH3Hg+ parameters babak minoofar
- Re: [AMBER] fatal "does not have a type" error in tleap for a protein-ligand complex case
- [AMBER] Ewald error estimated xuemeiwang1103
- [AMBER] Ewald error estimated xuemeiwang1103
Friday, 25 September 2009
- Re: [AMBER] Ewald error estimated Qinghua Liao
- Re: [AMBER] Ewald error estimated case
- [AMBER] pmemd and internal dielectric Serguei Vassiliev
- Re: [AMBER] Ewald error estimated Robert Duke
- Re: [AMBER] pmemd and internal dielectric Robert Duke
- Re: [AMBER] pmemd and internal dielectric Adrian Roitberg
- Re: [AMBER] pmemd and internal dielectric Serguei Vassiliev
- Re: [AMBER] pmemd and internal dielectric Robert Duke
- [AMBER] Attaching a ligand to a protein residue. Kipras Redeckas
- Re: [AMBER] pmemd and internal dielectric case
- Re: [AMBER] pmemd and internal dielectric Robert Duke
Saturday, 26 September 2009
- Re: [AMBER] Attaching a ligand to a protein residue. case
Sunday, 27 September 2009
- Re: [AMBER] Attaching a ligand to a protein residue. Kipras Redeckas
- [AMBER] problem when doing mm/pbsa: bad atom type Br Baifan Wang
- Re: [AMBER] problem when doing mm/pbsa: bad atom type Br Ray Luo
- [AMBER] How to obtain amber top and crd from pdb file with POPE lipids? decastro.physics.usyd.edu.au
Monday, 28 September 2009
- Re: [AMBER] problem when doing mm/pbsa: bad atom type Br Baifan Wang
- Re: [AMBER] How to obtain amber top and crd from pdb file with POPE lipids? Hannes Loeffler
- [AMBER] Your help about ptraj in AmberTools!]] Rosina Noto
- [AMBER] trouble using iAPBS Oliver Kuhn
- Re: [AMBER] trouble using iAPBS Robert Konecny
- [AMBER] Gap in rst file Katrina Lexa
- [AMBER] LJ-partial charges and force field parameters for ethylene glycol and glycerol Ganesh Kamath
- [AMBER] partial charges in Amber force field Jihang Wang
- Re: [AMBER] LJ-partial charges and force field parameters for ethylene glycol and glycerol FyD
- [AMBER] why should one restrain the position of the counterions? Jose Borreguero
- Re: [AMBER] partial charges in Amber force field FyD
Tuesday, 29 September 2009
- [AMBER] Problem in compiling AMBER9 in parallel ! Pradipta Bandyopadhyay
- [AMBER] Problem in test run Kshatresh Dutta Dubey
- Re: [AMBER] Problem in test run Carlos Simmerling
- Re: [AMBER] Problem in test run Kshatresh Dutta Dubey
- Re: [AMBER] Problem in test run Carlos Simmerling
- Re: [AMBER] Problem in test run Kshatresh Dutta Dubey
- Re: [AMBER] Problem in test run Kshatresh Dutta Dubey
- Re: [AMBER] Problem in test run case
- Re: [AMBER] Problem in compiling AMBER9 in parallel ! Abhishek Banerjee
- Re: [AMBER] Problem in compiling AMBER9 in parallel ! case
- [AMBER] Zinc Sel Ercan
- Re: [AMBER] Zinc Rubben Torella
- [AMBER] Compiling Amber with gfortran-4.5.0 on a mac Ben Roberts
- Re: [AMBER] Zinc Roman Osman
- [AMBER] MM_PBSA Zhongjie Liang
Wednesday, 30 September 2009
- [AMBER] too many missing parameters in frcmod for the prep of my ligand xueqin pang
- [AMBER] No restrt file xuemeiwang1103
- Re: [AMBER] No restrt file case
- Re: [AMBER] too many missing parameters in frcmod for the prep of my ligand FyD
- Re:Re: [AMBER] No restrt file null
- Re: Re: [AMBER] No restrt file case

Last message date: Wed Sep 30 2009 - 05:30:02 PDT
Archived on: Fri Nov 15 2024 - 05:53:58 PST

Amber Archive Sep 2009 by date