Amber Archive Oct 2013: by date

Monday, 30 September 2013
- [AMBER] RED-VIII.52 Problem--cannot find scratch file and punch file Dongshan Wei
- [AMBER] MMPBSA.py MPI problem on TACC Stampede Sorensen, Jesper
- Re: [AMBER] RED-VIII.52 Problem--cannot find scratch file and punch file Dongshan Wei
- Re: [AMBER] RED-VIII.52 Problem--cannot find scratch file and punch file FyD
Tuesday, 1 October 2013
- Re: [AMBER] Erro in the Thermodynamic Intergration using soft core potentials" 冉挺
- [AMBER] Ambiguity in PMF calculated from umbrella sampling of a dihedral angle Mohan Pradhan
- Re: [AMBER] Use of Langevin Thermostat with Amoeba force field David A Case
- [AMBER] Modified Cysteine Devlina Chakravarty
- Re: [AMBER] MMPBSA.py MPI problem on TACC Stampede Jason Swails
- Re: [AMBER] Erro in the Thermodynamic Intergration using soft core potentials" David A Case
- Re: [AMBER] Generating topology files for two proteins in a single input pdb David A Case
- Re: [AMBER] problem with addIons in tleap David A Case
- Re: [AMBER] Generating topology files for two proteins in a single input pdb George Green
- Re: [AMBER] Generating topology files for two proteins in a single input pdb George Green
- Re: [AMBER] Ambiguity in PMF calculated from umbrella sampling of a dihedral angle Jason Swails
- Re: [AMBER] Generating topology files for two proteins in a single input pdb George Green
- Re: [AMBER] Generating topology files for two proteins in a single input pdb Jason Swails
- Re: [AMBER] Generating topology files for two proteins in a single input pdb George Green
- Re: [AMBER] Erro in the Thermodynamic Intergration using soft core potentials" 冉挺
- Re: [AMBER] Ambiguity in PMF calculated from umbrella sampling of a dihedral angle Mohan Pradhan
- [AMBER] Problem in antechamber execution Problem in antechamber execution problem in antechamber execution Tanmoy Paul
- Re: [AMBER] Modified Cysteine FyD
- [AMBER] about error with "Must have more residues than processors!" Biao Ma
- Re: [AMBER] Fwd: DMPC GAFF lipid membrane is freezing at 303 K. Ross Walker
- Re: [AMBER] Problem in antechamber execution Problem in antechamber execution problem in antechamber execution Daniel Roe
- Re: [AMBER] Ambiguity in PMF calculated from umbrella sampling of a dihedral angle Jason Swails
- Re: [AMBER] about error with "Must have more residues than processors!" Jason Swails
- Re: [AMBER] MMPBSA.py MPI problem on TACC Stampede Sorensen, Jesper
- Re: [AMBER] Generating topology files for two proteins in a single input pdb George Green
- Re: [AMBER] Fwd: DMPC GAFF lipid membrane is freezing at 303 K. Subbarao Kanchi
- Re: [AMBER] rotational diffusion error Vijay Manickam Achari
- Re: [AMBER] rotational diffusion error Vijay Manickam Achari
Wednesday, 2 October 2013
- Re: [AMBER] Temperature based trajectory in REMD Gargi Borgohai
- [AMBER] Predicting druggable hotspots anu chandra
- Re: [AMBER] Erro in the Thermodynamic Intergration using soft core potentials" 冉挺
- Re: [AMBER] rotational diffusion error David A Case
- Re: [AMBER] Erro in the Thermodynamic Intergration using soft core potentials" David A Case
- [AMBER] PROBLEM USING ANTECHAMBER Tanmoy Paul
- Re: [AMBER] PROBLEM USING ANTECHAMBER Daniel Roe
- Re: [AMBER] Temperature based trajectory in REMD Daniel Roe
- Re: [AMBER] rotational diffusion error Vijay Manickam Achari
- Re: [AMBER] about error with "Must have more residues than processors!" Biao Ma
- [AMBER] About INP in case of MS=1 Hiromasa WATANABE
- [AMBER] The Error when I run MdoutAnalysizer.py Biao Ma
Thursday, 3 October 2013
- Re: [AMBER] The Error when I run MdoutAnalysizer.py Jason Swails
- [AMBER] Questions about VDW process of thermodynamic integration method 袁丹丹
- [AMBER] Questions about VDW process of thermodynamic integration method‏ 袁丹丹
- Re: [AMBER] Erro in the Thermodynamic Intergration using soft core potentials" 冉挺
- Re: [AMBER] The Error when I run MdoutAnalysizer.py Jason Swails
- Re: [AMBER] Erro in the Thermodynamic Intergration using soft core potentials" David A Case
- Re: [AMBER] About INP in case of MS=1 Ray Luo, Ph.D.
- Re: [AMBER] The Error when I run MdoutAnalysizer.py Biao Ma
Friday, 4 October 2013
- [AMBER] Replica exchange umbrella sampling Fabrício Bracht
- [AMBER] QM/MM MMPBSA Jacopo Sgrignani
- [AMBER] ITN Marie Curie positions available for early-stage researchers Paolo Ruggerone
- [AMBER] About the Mg charge in AMBER FF George Patargias
- Re: [AMBER] About the Mg charge in AMBER FF Jacopo Sgrignani
- Re: [AMBER] QM/MM MMPBSA Jason Swails
- Re: [AMBER] Replica exchange umbrella sampling Jason Swails
- [AMBER] changeLJ14Pair CHAMI F.
- Re: [AMBER] About the Mg charge in AMBER FF FyD
- Re: [AMBER] QM/MM MMPBSA Jacopo Sgrignani
- [AMBER] Regarding addition of DL_Poly Inversion potential in Amber MOHD HOMAIDUR RAHMAN
- Re: [AMBER] QM/MM MMPBSA Jason Swails
- Re: [AMBER] About the Mg charge in AMBER FF George Patargias
- Re: [AMBER] About the Mg charge in AMBER FF Jason Swails
- [AMBER] Reading NetCDF file Uday Midya
- Re: [AMBER] Reading NetCDF file Jason Swails
- Re: [AMBER] QM/MM MMPBSA Jacopo Sgrignani
- Re: [AMBER] QM/MM MMPBSA Jason Swails
- Re: [AMBER] QM/MM MMPBSA Jason Swails
- Re: [AMBER] changeLJ14Pair Jason Swails
- Re: [AMBER] Reading NetCDF file Daniel Roe
- Re: [AMBER] rotational diffusion error Daniel Roe
- [AMBER] Regarding addition of DL_Poly Inversion and three body potential in Amber MOHD HOMAIDUR RAHMAN
- [AMBER] A problem with a specific input in pmemd.cuda.MPI. 4 GPU fails, 2 GPU works fine. Jeremy Hallum
- [AMBER] NAB : Orienting a molecule HIMANSHU JOSHI
- Re: [AMBER] A problem with a specific input in pmemd.cuda.MPI. 4 GPU fails, 2 GPU works fine. Ross Walker
- [AMBER] Generating reservoirs for non-Boltzmann T-RREMD Eugene Yedvabny
- Re: [AMBER] NAB : Orienting a molecule Aldo Segura
- Re: [AMBER] Generating reservoirs for non-Boltzmann T-RREMD Niel Henriksen
- Re: [AMBER] NAB : Orienting a molecule Daniel Roe
- Re: [AMBER] Generating reservoirs for non-Boltzmann T-RREMD Eugene Yedvabny
- Re: [AMBER] About the Mg charge in AMBER FF Andreas Goetz
- Re: [AMBER] Reading NetCDF file Uday Midya
Saturday, 5 October 2013
- Re: [AMBER] Replica exchange umbrella sampling Fabrício Bracht
- [AMBER] MPI install with openmpi Makoto Chikira
- Re: [AMBER] NAB : Orienting a molecule case
- Re: [AMBER] MPI install with openmpi case
- Re: [AMBER] MPI install with openmpi Makoto Chikira
- Re: [AMBER] MPI install with openmpi case
- [AMBER] sumit.saurav.jain.gmail.com has indicated you're a friend. Accept? sumit.saurav.jain.gmail.com
- Re: [AMBER] Regarding addition of DL_Poly Inversion potential in Amber Jason Swails
- Re: [AMBER] MPI install with openmpi Makoto Chikira
- [AMBER] Error in antechamber Installation Vijayalaxmi Sahoo
Sunday, 6 October 2013
- Re: [AMBER] Error in antechamber Installation Jason Swails
- Re: [AMBER] MPI install with openmpi Makoto Chikira
- Re: [AMBER] MPI install with openmpi Jason Swails
- [AMBER] Hydrogen Bond Term in Amber ff99SB forcefield Asmit Bhowmick
- [AMBER] Phenyl-boronic acid derivatives lacking of parameter in Mol2 file 陈发生
- [AMBER] Generation of melting curves Gargi Borgohai
- Re: [AMBER] Generating reservoirs for non-Boltzmann T-RREMD Niel Henriksen
- Re: [AMBER] Generating reservoirs for non-Boltzmann T-RREMD Eugene Yedvabny
- Re: [AMBER] Fwd: DMPC GAFF lipid membrane is freezing at 303 K. Subbarao Kanchi
Monday, 7 October 2013
- [AMBER] Soft-core questions for TI method yuandandan
- [AMBER] Soft-core questions for TI method yuandandan
- Re: [AMBER] MPI install with openmpi David A Case
- Re: [AMBER] Hydrogen Bond Term in Amber ff99SB forcefield David A Case
- Re: [AMBER] Soft-core questions for TI method David A Case
- Re: [AMBER] Generation of melting curves Brian Radak
- [AMBER] problem in creating .mol2 and .frcmod files Vijayalaxmi Sahoo
- Re: [AMBER] Generation of melting curves Daniel Roe
- Re: [AMBER] problem in creating .mol2 and .frcmod files Jason Swails
- Re: [AMBER] Generation of melting curves Carlos Simmerling
- [AMBER] ambertools patch 19 fails Matthew Wampole
- Re: [AMBER] problem in creating .mol2 and .frcmod files Vijayalaxmi Sahoo
- Re: [AMBER] ambertools patch 19 fails Jason Swails
- Re: [AMBER] Generating reservoirs for non-Boltzmann T-RREMD Niel Henriksen
- Re: [AMBER] Reading NetCDF file Daniel Roe
- [AMBER] Parameter Discrepancy in Walker Tutorial B1? Robert Molt
- Re: [AMBER] Soft-core questions for TI method yuandandan
Tuesday, 8 October 2013
- Re: [AMBER] Parameter Discrepancy in Walker Tutorial B1? Jason Swails
- Re: [AMBER] Generating reservoirs for non-Boltzmann T-RREMD Jason Swails
- [AMBER] Block Averaging of Trajectory Mathias Gruber
- [AMBER] GAFF angle term constants with phosphor or sulphur Igor Marques
- Re: [AMBER] RED-VIII.52 Problem--cannot find scratch file and punch file Dongshan Wei
- [AMBER] ERROR in DISTANCE RESTRAINT Sourav Purohit
- Re: [AMBER] ERROR in DISTANCE RESTRAINT Brian Radak
- Re: [AMBER] ERROR in DISTANCE RESTRAINT Ross Walker
- [AMBER] Scaling of multi GPU runs peter.stauffert.boehringer-ingelheim.com
- Re: [AMBER] Scaling of multi GPU runs Ross Walker
- Re: [AMBER] Scaling of multi GPU runs Scott Le Grand
- Re: [AMBER] Scaling of multi GPU runs Ross Walker
- [AMBER] Amber99SB force field Shomesankar Bhunia
- Re: [AMBER] Amber99SB force field Carlos Simmerling
- Re: [AMBER] Scaling of multi GPU runs Scott Le Grand
- Re: [AMBER] Amber99SB force field Shomesankar Bhunia
- Re: [AMBER] ERROR in DISTANCE RESTRAINT David A Case
- Re: [AMBER] Amber99SB force field Shomesankar Bhunia
- Re: [AMBER] RED-VIII.52 Problem--cannot find scratch file and punch file Dongshan Wei
- Re: [AMBER] About INP in case of MS=1 Hiromasa WATANABE
Wednesday, 9 October 2013
- Re: [AMBER] RED-VIII.52 Problem--cannot find scratch file and punch file FyD
- Re: [AMBER] RED-VIII.52 Problem--cannot find scratch file and punch file FyD
- Re: [AMBER] Fwd: DMPC GAFF lipid membrane is freezing at 303 K. Dickson, Callum
- Re: [AMBER] Fwd: DMPC GAFF lipid membrane is freezing at 303 K. Subbarao Kanchi
- Re: [AMBER] Fwd: DMPC GAFF lipid membrane is freezing at 303 K. Ross Walker
- Re: [AMBER] Fwd: DMPC GAFF lipid membrane is freezing at 303 K. Dickson, Callum
- Re: [AMBER] RED-VIII.52 Problem--cannot find scratch file and punch file Dongshan Wei
- Re: [AMBER] Problem in creating .mol2 and .frcmod files Vijayalaxmi Sahoo
- [AMBER] AMBER ff99Sbildn Shomesankar Bhunia
- Re: [AMBER] Problem in creating .mol2 and .frcmod files David A Case
- [AMBER] Shifting molecules by a box length Heribert Reis
- Re: [AMBER] Shifting molecules by a box length Jason Swails
- Re: [AMBER] AMBER ff99Sbildn Jason Swails
- Re: [AMBER] AMBER ff99Sbildn Shomesankar Bhunia
- Re: [AMBER] AMBER ff99Sbildn Jason Swails
- Re: [AMBER] AMBER ff99Sbildn Shomesankar Bhunia
- Re: [AMBER] About INP in case of MS=1 Ray Luo, Ph.D.
Thursday, 10 October 2013
- [AMBER] Distributions of the phi and psi torsion angles during MD simulations Baptiste Legrand
- Re: [AMBER] RED-VIII.52 Problem--cannot find scratch file and punch file FyD
- Re: [AMBER] RED-VIII.52 Problem--cannot find scratch file and punch file FyD
- [AMBER] Questions about softcore part yuandandan
- Re: [AMBER] Questions about softcore part David A Case
- [AMBER] High energy in per-residue MMPBSA calculation anu chandra
- [AMBER] How to run npt simulation if IFBOX=0 in .prmtop file? Dongshan Wei
- Re: [AMBER] How to run npt simulation if IFBOX=0 in .prmtop file? Jason Swails
- Re: [AMBER] Distributions of the phi and psi torsion angles during MD simulations Jason Swails
- Re: [AMBER] How to run npt simulation if IFBOX=0 in .prmtop file? Dongshan Wei
- [AMBER] Fwd: Shifting molecules by a box length Heribert Reis
- Re: [AMBER] Fwd: Shifting molecules by a box length Daniel Roe
- [AMBER] solvate box Rasha Alqus
- Re: [AMBER] solvate box Jason Swails
- [AMBER] SHAKE flucatuation Zhiye Tang
- Re: [AMBER] SHAKE flucatuation Thomas Cheatham
- Re: [AMBER] SHAKE flucatuation Jason Swails
- [AMBER] MMPBSA error Symon Gathiaka
- Re: [AMBER] SHAKE flucatuation Zhiye Tang
- Re: [AMBER] SHAKE flucatuation Thomas Cheatham
- Re: [AMBER] MMPBSA error Ray Luo, Ph.D.
- Re: [AMBER] Distributions of the phi and psi torsion angles during MD simulations Baptiste Legrand
- [AMBER] Stuck on AmberTools bugfix.23 Terry M. Gray
- [AMBER] I/O errors while using CHARMM psf with CHAMBER Debayan Chakraborty
- [AMBER] Segmentation fault in tleap mmalett.nmt.edu
- Re: [AMBER] Segmentation fault in tleap Jason Swails
- Re: [AMBER] Segmentation fault in tleap mmalett.nmt.edu
- [AMBER] Protein-DNA covalent bond John Gehman
- [AMBER] Stuck on AmberTools12 bug fix.23 Terry M. Gray
- [AMBER] How to calculate the free energy change of a chemical reaction by the thermodynamic integration approach? cwt
Friday, 11 October 2013
- Re: [AMBER] Stuck on AmberTools12 bug fix.23 Jason Swails
- Re: [AMBER] How to calculate the free energy change of a chemical reaction by the thermodynamic integration approach? Brian Radak
- Re: [AMBER] [Amber]Question about softcore yuandandan
- Re: [AMBER] Segmentation fault in tleap David A Case
- Re: [AMBER] Protein-DNA covalent bond David A Case
- [AMBER] AmberTools13 and Amber11 Alan
- Re: [AMBER] AmberTools13 and Amber11 Jason Swails
- Re: [AMBER] Segmentation fault in tleap mmalett.nmt.edu
- Re: [AMBER] AmberTools13 and Amber11 Alan
- [AMBER] tleap cannot handle dummies in the middle? Hannes Loeffler
- Re: [AMBER] Segmentation fault in tleap David A Case
- Re: [AMBER] MMPSA: PB Bomb in pb_aaradi(): ... psu4.uic.edu
- Re: [AMBER] MMPSA: PB Bomb in pb_aaradi(): ... Ray Luo, Ph.D.
- Re: [AMBER] Segmentation fault in tleap mmalett.nmt.edu
- Re: [AMBER] Segmentation fault in tleap case
Saturday, 12 October 2013
- Re: [AMBER] Protein-DNA covalent bond John Gehman
- [AMBER] running MMPBSA.py on an NMR ensemble Thomas Evangelidis
- [AMBER] Questions regarding AMBER Kamali Sripathi
- Re: [AMBER] Questions regarding AMBER Jiri Sponer
- Re: [AMBER] running MMPBSA.py on an NMR ensemble Jason Swails
- Re: [AMBER] Questions regarding AMBER David Case
- Re: [AMBER] How do I use MMPBSA.py for namd .dcd file? sudipta
- Re: [AMBER] How do I use MMPBSA.py for namd .dcd file? Jason Swails
- [AMBER] Iron(III)Hydroxide complexing with Enterobactin (quantum chemistry calculations?) Jonathan Saboury
- [AMBER] Problem in deriving RESP charges with RED-3.52 tools Sajeewa Pemasinghe
Sunday, 13 October 2013
- Re: [AMBER] Problem in deriving RESP charges with RED-3.52 tools FyD
- Re: [AMBER] Iron(III)Hydroxide complexing with Enterobactin (quantum chemistry calculations?) FyD
- Re: [AMBER] Problem in deriving RESP charges with RED-3.52 tools Sajeewa Pemasinghe
- Re: [AMBER] Questions regarding AMBER Kamali Sripathi
- Re: [AMBER] Problem in deriving RESP charges with RED-3.52 tools FyD
- Re: [AMBER] Questions regarding AMBER FyD
- [AMBER] Problem about water Cap with igb=10 Tong ZHU
- Re: [AMBER] Questions regarding AMBER Kamali Sripathi
- Re: [AMBER] Questions regarding AMBER FyD
- Re: [AMBER] Questions regarding AMBER Kamali Sripathi
- [AMBER] DNA with NAB Jio M
- [AMBER] PMEMD trajectory and MMPBSA Sangita Kachhap
Monday, 14 October 2013
- Re: [AMBER] inquiry Vaibhav Dixit
- [AMBER] about rms atomic fluctuation for protein crystal .thank you very much! Yongxiu Li
- Re: [AMBER] DNA with NAB David A Case
- Re: [AMBER] PMEMD trajectory and MMPBSA Bill Miller III
- Re: [AMBER] How do I use MMPBSA.py for namd .dcd file? sudipta
- Re: [AMBER] GAFF angle term constants with phosphor or sulphur James Murdock
- Re: [AMBER] How do I use MMPBSA.py for namd .dcd file? Jason Swails
- Re: [AMBER] PMEMD trajectory and MMPBSA Sangita Kachhap
- Re: [AMBER] about rms atomic fluctuation for protein crystal .thank you very much! Pawel
Tuesday, 15 October 2013
- Re: [AMBER] about rms atomic fluctuation for protein crystal .thank you very much! Yongxiu Li
- [AMBER] Exceed character limit in bellyrestraint mask selection Mike Limb
- Re: [AMBER] Exceed character limit in bellyrestraint mask selection Jason Swails
- Re: [AMBER] Problem in deriving RESP charges with RED-3.52 tools Sajeewa Pemasinghe
- [AMBER] Constant pH with ligand Nicole Ippolito
- Re: [AMBER] about rms atomic fluctuation for protein crystal .thank you very much! Pawel
- Re: [AMBER] Problem in deriving RESP charges with RED-3.52 tools Sajeewa Pemasinghe
- Re: [AMBER] Constant pH with ligand Jason Swails
- [AMBER] PMF for 2 Arginines Nihal Korkmaz
- Re: [AMBER] Problem in deriving RESP charges with RED-3.52 tools FyD
- Re: [AMBER] Constant pH with ligand FyD
Wednesday, 16 October 2013
- [AMBER] PTRAJ - Problem with inserting TER card anu chandra
- Re: [AMBER] Constant pH with ligand Nicole Ippolito
- [AMBER] RESP charge calculation problem for SO4 -2 group Bajarang Kumbhar
- Re: [AMBER] PMF for 2 Arginines Brian Radak
- Re: [AMBER] RESP charge calculation problem for SO4 -2 group FyD
- Re: [AMBER] PTRAJ - Problem with inserting TER card Daniel Roe
- [AMBER] strange behavior of MCPB houcemeddine
- Re: [AMBER] PMF for 2 Arginines Nihal Korkmaz
- Re: [AMBER] strange behavior of MCPB Jia Xu
- Re: [AMBER] PMF for 2 Arginines Brian Radak
- Re: [AMBER] PMF for 2 Arginines Carlos Simmerling
- [AMBER] Error message from pmemd.cuda Brian Radak
- Re: [AMBER] Error message from pmemd.cuda Niel Henriksen
- Re: [AMBER] Error message from pmemd.cuda Niel Henriksen
- [AMBER] ratio between frames for MM/PBSA and frames for normal mode calculations Thomas Evangelidis
- [AMBER] Python script to reweight aMD simulations filip fratev
- Re: [AMBER] PTRAJ - Problem with inserting TER card anu chandra
Thursday, 17 October 2013
- [AMBER] unique atoms in TI softcore Hannes Loeffler
- Re: [AMBER] unique atoms in TI softcore David Case
- Re: [AMBER] unique atoms in TI softcore Hannes Loeffler
- [AMBER] Doubt regarding the metadynamics simulation Ravi Tripathi
- Re: [AMBER] Doubt regarding the metadynamics simulation Adrian Roitberg
- [AMBER] CYM residue problem(MCPB) houcemeddine
- Re: [AMBER] CYM residue problem(MCPB) Jason Swails
- Re: [AMBER] Doubt regarding the metadynamics simulation Ravi Tripathi
- Re: [AMBER] Doubt regarding the metadynamics simulation Adrian Roitberg
- Re: [AMBER] Doubt regarding the metadynamics simulation Robert Molt
- Re: [AMBER] Doubt regarding the metadynamics simulation Jason Swails
- Re: [AMBER] PTRAJ - Problem with inserting TER card Daniel Roe
- Re: [AMBER] CYM residue problem(MCPB) FyD
- Re: [AMBER] PTRAJ - Problem with inserting TER card anu chandra
- [AMBER] problem for prmtop and inpcrd file generation Bajarang Kumbhar
Friday, 18 October 2013
- [AMBER] How to deal with duplicate frames during MD? rohitarora10.gmail.com
- [AMBER] problem with heme parameters bound to HIS moitrayee.mbu.iisc.ernet.in
- [AMBER] Running simultaneously AMBER jobs in CPU and GPU Muthukumaran R
- [AMBER] parmchk doesn't recognize the changes made in leaprc.ff99SB and parm.99 Sajeewa Pemasinghe
- Re: [AMBER] CYM residue problem(MCPB) houcemeddine
- Re: [AMBER] Running simultaneously AMBER jobs in CPU and GPU Jan-Philip Gehrcke
- Re: [AMBER] PTRAJ - Problem with inserting TER card Daniel Roe
- Re: [AMBER] parmchk doesn't recognize the changes made in leaprc.ff99SB and parm.99 Jason Swails
- Re: [AMBER] How to deal with duplicate frames during MD? Daniel Roe
- Re: [AMBER] CYM residue problem(MCPB) Jason Swails
- Re: [AMBER] How to deal with duplicate frames during MD? rohitarora10.gmail.com
- [AMBER] Fwd: FW: Fwd: DMPC GAFF lipid membrane is freezing at 303 K. Subbarao Kanchi
- Re: [AMBER] unique atoms in TI softcore case
- Re: [AMBER] problem with heme parameters bound to HIS case
- Re: [AMBER] problem with heme parameters bound to HIS moitrayee.mbu.iisc.ernet.in
- Re: [AMBER] Exceed character limit in bellyrestraint mask selection Mike Limb
- Re: [AMBER] Exceed character limit in bellyrestraint mask selection Jason Swails
- Re: [AMBER] CYM residue problem(MCPB) FyD
- Re: [AMBER] How to deal with duplicate frames during MD? rohitarora10.gmail.com
Saturday, 19 October 2013
- [AMBER] PROBLEM IN QM/MM RUN Tanmoy Paul
- [AMBER] output of diffusion data doesn't show two columns for big number values Vijay Manickam Achari
- Re: [AMBER] How to deal with duplicate frames during MD? Jason Swails
- Re: [AMBER] PROBLEM IN QM/MM RUN Gustavo Seabra
- Re: [AMBER] output of diffusion data doesn't show two columns for big number values Daniel Roe
- Re: [AMBER] parmchk doesn't recognize the changes made in leaprc.ff99SB and parm.99 Sajeewa Pemasinghe
Sunday, 20 October 2013
- Re: [AMBER] Problem in deriving RESP charges with RED-3.52 tools Sajeewa Pemasinghe
Monday, 21 October 2013
- [AMBER] problem using the R.E.D server output Bajarang Kumbhar
- [AMBER] optimization using gaussian and RESP using antechamber Bajarang Kumbhar
- Re: [AMBER] problem using the R.E.D server output Jason Swails
- [AMBER] example of MTKpp on Ambertools 13 setyanto md
- Re: [AMBER] example of MTKpp on Ambertools 13 Daniel Roe
- Re: [AMBER] example of MTKpp on Ambertools 13 Jason Swails
- [AMBER] MMPBSA problem with CHAMBER generated topology file Uday Midya
- Re: [AMBER] MMPBSA problem with CHAMBER generated topology file Bill Miller III
- [AMBER] Fwd: requesting in executing CHAMBER Soumya Lipsa Rath
- Re: [AMBER] example of MTKpp on Ambertools 13 setyanto md
Tuesday, 22 October 2013
- [AMBER] PCA analysis and amber prmtop file Neha Gandhi
- [AMBER] namelist input > 80 columns thomas.fox.boehringer-ingelheim.com
- Re: [AMBER] Exceed character limit in bellyrestraint mask selection Mike Limb
- Re: [AMBER] namelist input > 80 columns thomas.fox.boehringer-ingelheim.com
- Re: [AMBER] Exceed character limit in bellyrestraint mask selection Jason Swails
- Re: [AMBER] MMPBSA problem with CHAMBER generated topology file Jason Swails
- Re: [AMBER] PCA analysis and amber prmtop file Jason Swails
- [AMBER] High Temperature at NSTEP = 0 Alessandra Lacetera
- Re: [AMBER] DNA with NAB Jio M
- Re: [AMBER] High Temperature at NSTEP = 0 Brian Radak
- Re: [AMBER] High Temperature at NSTEP = 0 Carlos Simmerling
- [AMBER] Script? Beale, John
- Re: [AMBER] Script? Daniel Roe
- [AMBER] Update 21 for Amber 12: EXTERN QM/MM interface Andreas Goetz
- [AMBER] MMPBSA calculation Mary Varughese
Wednesday, 23 October 2013
- [AMBER] Terachem tests with trial version Fabrício Bracht
- [AMBER] MMPBSA.py error Rasha Alqus
- Re: [AMBER] MMPBSA.py error Rasha Alqus
- Re: [AMBER] MMPBSA.py error Jason Swails
- Re: [AMBER] Terachem tests with trial version Andreas Goetz
- Re: [AMBER] namelist input > 80 columns case
- Re: [AMBER] Terachem tests with trial version Fabrício Bracht
- Re: [AMBER] Terachem tests with trial version Ross Walker
- [AMBER] Leap ff10 and Sodium ion Johannes Zuegg
Thursday, 24 October 2013
- Re: [AMBER] Terachem tests with trial version Fabrício Bracht
- [AMBER] AMBERTOOLS13 test error: 01_Generalized_Born and 03_Alanine_Scanning marco.molinari
- Re: [AMBER] Leap ff10 and Sodium ion case
- [AMBER] Regarding radial distribution function MOHD HOMAIDUR RAHMAN
- Re: [AMBER] AMBERTOOLS13 test error: 01_Generalized_Born and 03_Alanine_Scanning Jason Swails
- [AMBER] MMPBSA.py problem Indrajit Deb
- [AMBER] MMGBSA, Generalized Born, protein-nucleic acid complex Vlad Cojocaru
- Re: [AMBER] MMPBSA.py error Rasha Alqus
- Re: [AMBER] Regarding radial distribution function Daniel Roe
- Re: [AMBER] MMPBSA.py error Jason Swails
- Re: [AMBER] MMPBSA.py problem Jason Swails
- Re: [AMBER] MMPBSA.py error Rasha Alqus
- Re: [AMBER] igb=7, 8 incompatible with the ILDN modifications of ff99SB Vlad Cojocaru
- Re: [AMBER] MMPBSA.py error Jason Swails
- Re: [AMBER] igb=7, 8 incompatible with the ILDN modifications of ff99SB Jason Swails
- [AMBER] parmed.py bug when using the "parmout" command ? Vlad Cojocaru
- Re: [AMBER] parmed.py bug when using the "parmout" command ? Brian Radak
- Re: [AMBER] parmed.py bug when using the "parmout" command ? Vlad Cojocaru
- Re: [AMBER] parmed.py bug when using the "parmout" command ? Jason Swails
- Re: [AMBER] parmed.py bug when using the "parmout" command ? Vlad Cojocaru
- Re: [AMBER] parmed.py bug when using the "parmout" command ? Vlad Cojocaru
- Re: [AMBER] parmed.py bug when using the "parmout" command ? Jason Swails
- Re: [AMBER] parmed.py bug when using the "parmout" command ? Vlad Cojocaru
- Re: [AMBER] parmed.py bug when using the "parmout" command ? Vlad Cojocaru
- Re: [AMBER] parmed.py bug when using the "parmout" command ? Jan-Philip Gehrcke
- Re: [AMBER] parmed.py bug when using the "parmout" command ? Jason Swails
- Re: [AMBER] parmed.py bug when using the "parmout" command ? Vlad Cojocaru
- Re: [AMBER] parmed.py bug when using the "parmout" command ? Jason Swails
- Re: [AMBER] MMGBSA, Generalized Born, protein-nucleic acid complex Hai Nguyen
- Re: [AMBER] DNA with NAB Jio M
- Re: [AMBER] parmed.py bug when using the "parmout" command ? Vlad Cojocaru
- Re: [AMBER] problem with heme parameters bound to HIS case
- Re: [AMBER] DNA with NAB case
- Re: [AMBER] Problem about water Cap with igb=10 case
Friday, 25 October 2013
- [AMBER] MMPBSA, ligand sequence maghtar
- Re: [AMBER] MMPBSA, ligand sequence Jason Swails
- Re: [AMBER] AMBERTOOLS13 test error: 01_Generalized_Born and, 03_Alanine_Scanning (Jason Swails) marco.molinari
- Re: [AMBER] DNA with NAB Jio M
- Re: [AMBER] MMPBSA, ligand sequence maghtar
- [AMBER] ionic strength conversion between MMPBSA.py and PBSA Vlad Cojocaru
- [AMBER] About foundations of T-REMD Francesco Pietra
- Re: [AMBER] About foundations of T-REMD Adrian Roitberg
- Re: [AMBER] About foundations of T-REMD Brian Radak
- Re: [AMBER] ionic strength conversion between MMPBSA.py and PBSA Jason Swails
- [AMBER] Making Au surface using xleap Hoshin Kim
- [AMBER] why are pres_X, pres_Y, and pres_Z different? Jose Borreguero
- Re: [AMBER] ionic strength conversion between MMPBSA.py and PBSA Vlad Cojocaru
- Re: [AMBER] ionic strength conversion between MMPBSA.py and PBSA Jason Swails
- [AMBER] mmpbsa_py_energy and PBSA options Vlad Cojocaru
- Re: [AMBER] mmpbsa_py_energy and PBSA options Ray Luo, Ph.D.
- Re: [AMBER] mmpbsa_py_energy and PBSA options Vlad Cojocaru
- Re: [AMBER] mmpbsa_py_energy and PBSA options Ray Luo, Ph.D.
- [AMBER] Constant pH with enzyme and substrate Nicole Ippolito
- Re: [AMBER] mmpbsa_py_energy and PBSA options Vlad Cojocaru
- Re: [AMBER] Making Au surface using xleap Brian Radak
- Re: [AMBER] mmpbsa_py_energy and PBSA options Ray Luo, Ph.D.
- [AMBER] Single quotes in AMBER manual Jonathan Sheehan
- Re: [AMBER] Constant pH with enzyme and substrate Daniel Roe
- [AMBER] AmberTools13 Concha, Monica
- Re: [AMBER] AmberTools13 Jason Swails
- Re: [AMBER] AmberTools13 Daniel Roe
- Re: [AMBER] AmberTools13 Concha, Monica
- Re: [AMBER] Constant pH with enzyme and substrate Nicole Ippolito
- Re: [AMBER] why are pres_X, pres_Y, and pres_Z different? case
- [AMBER] How to use TIP4P/2005 water model Deborah Howe
Saturday, 26 October 2013
- [AMBER] Difference between the .crd file format in AMBER-7 and AMBER-12 anu chandra
- [AMBER] QM/MM interfacing Gaussian Ahmed Ayoub
- Re: [AMBER] How to use TIP4P/2005 water model case
- Re: [AMBER] Difference between the .crd file format in AMBER-7 and AMBER-12 case
- Re: [AMBER] QM/MM interfacing Gaussian case
- Re: [AMBER] Single quotes in AMBER manual case
- Re: [AMBER] DNA with NAB case
- Re: [AMBER] How to use TIP4P/2005 water model Deborah Howe
- Re: [AMBER] How to use TIP4P/2005 water model James Maier
- [AMBER] ptraj - loading list of frames Mark Healey
- Re: [AMBER] ptraj - loading list of frames Daniel Roe
- [AMBER] idecomp does not work for canonical-residues kurisaki
Sunday, 27 October 2013
- Re: [AMBER] idecomp does not work for canonical-residues Jason Swails
- Re: [AMBER] idecomp does not work for canonical-residues kurisaki
- Re: [AMBER] idecomp does not work for canonical-residues Jason Swails
- Re: [AMBER] FW: Fwd: DMPC GAFF lipid membrane is freezing at 303 K. Subbarao Kanchi
- Re: [AMBER] idecomp does not work for canonical-residues kurisaki
- [AMBER] problem after minimization of pure DMF Sohag Biswas
- Re: [AMBER] Difference between the .crd file format in AMBER-7 and AMBER-12 anu chandra
Monday, 28 October 2013
- Re: [AMBER] idecomp does not work for canonical-residues Jason Swails
- Re: [AMBER] idecomp does not work for canonical-residues kurisaki
- [AMBER] Error - PMEMD.MPI cannot understand line in rst file rohitarora10.gmail.com
- Re: [AMBER] problem after minimization of pure DMF David A Case
- Re: [AMBER] FW: Fwd: DMPC GAFF lipid membrane is freezing at 303 K. Dickson, Callum
- Re: [AMBER] Error - PMEMD.MPI cannot understand line in rst file Daniel Roe
- [AMBER] problem in saving prmtop file in ff12SB force field Subrata Paul
- Re: [AMBER] problem in saving prmtop file in ff12SB force field Daniel Roe
- Re: [AMBER] problem in saving prmtop file in ff12SB force field Subrata Paul
- Re: [AMBER] why are pres_X, pres_Y, and pres_Z different? Jose Borreguero
- Re: [AMBER] why are pres_X, pres_Y, and pres_Z different? David A Case
- Re: [AMBER] why are pres_X, pres_Y, and pres_Z different? Jose Borreguero
Tuesday, 29 October 2013
- Re: [AMBER] about rms atomic fluctuation for protein crystal .thank you very much! Yongxiu Li
- [AMBER] huge values for the vibrational entropy from ptraj Vlad Cojocaru
- Re: [AMBER] huge values for the vibrational entropy from ptraj David A Case
- Re: [AMBER] huge values for the vibrational entropy from ptraj Vlad Cojocaru
- Re: [AMBER] huge values for the vibrational entropy from ptraj David A Case
- Re: [AMBER] huge values for the vibrational entropy from ptraj Vlad Cojocaru
- [AMBER] acclerated molecular dynamics alphaP Nicole Ippolito
- Re: [AMBER] huge values for the vibrational entropy from ptraj Jason Swails
- Re: [AMBER] huge values for the vibrational entropy from ptraj Jason Swails
- Re: [AMBER] huge values for the vibrational entropy from ptraj Daniel Roe
- Re: [AMBER] acclerated molecular dynamics alphaP Daniel Roe
- Re: [AMBER] huge values for the vibrational entropy from ptraj Vlad Cojocaru
- [AMBER] Sander error Concha, Monica
- Re: [AMBER] Sander error Jason Swails
- [AMBER] calculatie the energy between two groups of atoms from an MD trajectory, is it possible? Jose Borreguero
- Re: [AMBER] Sander error Concha, Monica
- Re: [AMBER] Sander error Jason Swails
- Re: [AMBER] calculatie the energy between two groups of atoms from an MD trajectory, is it possible? Brian Radak
Wednesday, 30 October 2013
- Re: [AMBER] Soft-core questions for TI method Ying-Chieh Sun
- [AMBER] Installation error Dhananjay
- Re: [AMBER] Trajectory determination and directionality in TI with softcore potentials Ying-Chieh Sun
- [AMBER] Free binding energy calculations for Zinc dependent ligands Tivani Mashamba
- [AMBER] Amber 12 Updater error on Arch linux M. Reza Ganjalikhany
- Re: [AMBER] Amber 12 Updater error on Arch linux Jason Swails
- Re: [AMBER] Installation error Jason Swails
- Re: [AMBER] Installation error David A Case
- Re: [AMBER] problem after minimization of pure DMF FyD
- Re: [AMBER] Free binding energy calculations for Zinc dependent ligands Jason Swails
- Re: [AMBER] calculatie the energy between two groups of atoms from an MD trajectory, is it possible? Jose Borreguero
- Re: [AMBER] about rms atomic fluctuation for protein crystal .thank you very much! Pawel
- Re: [AMBER] optimization using gaussian and RESP using antechamber Tanmoy Paul
- [AMBER] Hbond analysis Fabrício Bracht
- Re: [AMBER] Hbond analysis Daniel Roe
- Re: [AMBER] Hbond analysis Fabrício Bracht
- Re: [AMBER] Hbond analysis Daniel Roe
- Re: [AMBER] Hbond analysis Fabrício Bracht
- Re: [AMBER] Hbond analysis Fabrício Bracht
- Re: [AMBER] Hbond analysis Daniel Roe
- Re: [AMBER] AMBER Digest, Vol 659, Issue 1 Sohag Biswas
Thursday, 31 October 2013
- Re: [AMBER] huge values for the vibrational entropy from ptraj Vlad Cojocaru
- [AMBER] Monte Carlo Method/Simulation in AMBER 12 Emmanuel Oluwatobi SALAWU
- Re: [AMBER] Installation error Dhananjay
- Re: [AMBER] Installation error Jason Swails
- Re: [AMBER] Monte Carlo Method/Simulation in AMBER 12 Jason Swails
- [AMBER] About calculating entropy Olayide Arodola
- Re: [AMBER] Installation error Dhananjay
- Re: [AMBER] Installation error Jason Swails
- [AMBER] mdcrd to dcd 石坪江梨花
- Re: [AMBER] Installation error Dhananjay
- Re: [AMBER] huge values for the vibrational entropy from ptraj David A Case
- Re: [AMBER] Monte Carlo Method/Simulation in AMBER 12 David A Case
- Re: [AMBER] mdcrd to dcd kurisaki
- Re: [AMBER] huge values for the vibrational entropy from ptraj Vlad Cojocaru
- Re: [AMBER] About calculating entropy Jason Swails
- Re: [AMBER] Installation error Jason Swails
- Re: [AMBER] mdcrd to dcd Daniel Roe
- Re: [AMBER] Installation error David A Case
- Re: [AMBER] About calculating entropy Tivani Mashamba
- Re: [AMBER] About calculating entropy Hannes Loeffler
- [AMBER] Sander error (AmberTools 13 & Amber10) Concha, Monica
- Re: [AMBER] Sander error (AmberTools 13 & Amber10) Daniel Roe
- Re: [AMBER] About calculating entropy Tivani Mashamba
- Re: [AMBER] calculatie the energy between two groups of atoms from an MD trajectory, is it possible? Jose Borreguero
- Re: [AMBER] calculatie the energy between two groups of atoms from an MD trajectory, is it possible? Daniel Roe
- Re: [AMBER] Sander error (AmberTools 13 & Amber10) Concha, Monica
- Re: [AMBER] Installation error Jason Swails
- Re: [AMBER] Sander error (AmberTools 13 & Amber10) Daniel Roe
- [AMBER] TI soft-core parameters Hamed S. Hayatshahi
- Re: [AMBER] Sander error (AmberTools 13 & Amber10) Concha, Monica
- Re: [AMBER] Sander error (AmberTools 13 & Amber10) Daniel Roe

Last message date: Thu Oct 31 2013 - 15:00:03 PDT
Archived on: Wed Dec 25 2024 - 05:54:53 PST

Amber Archive Oct 2013 by date