Amber Archive Sep 2017: by date

Friday, 1 September 2017
- Re: [AMBER] An equilibration of the membrane protein prepared by charmm-gui James Starlight
- [AMBER] Pressure tensor Sonata Kvedaravičiūtė
- Re: [AMBER] An equilibration of the membrane protein prepared by charmm-gui ABEL Stephane
- [AMBER] ACE and NME capping protein is essential for protein simulation jacky zhao
- [AMBER] significance of iwrap Saikat Pal
- Re: [AMBER] significance of iwrap Daniel Roe
- [AMBER] H++ salinity Andreas Tosstorff
- Re: [AMBER] ACE and NME capping protein is essential for protein simulation David A Case
- Re: [AMBER] An equilibration of the membrane protein prepared by charmm-gui James Starlight
- Re: [AMBER] Calculation the Area per lipids using cpptraj Daniel Roe
- Re: [AMBER] ACE and NME capping protein is essential for protein simulation Carlos Simmerling
- Re: [AMBER] An equilibration of the membrane protein prepared by charmm-gui ABEL Stephane
- Re: [AMBER] ACE and NME capping protein is essential for protein simulation jacky zhao
- Re: [AMBER] ACE and NME capping protein is essential for protein simulation jacky zhao
- [AMBER] Missing amino acids preparation for long-term simulation jacky zhao
- [AMBER] Cpptraj and parmwrite and strip Khabiri, Morteza
- Re: [AMBER] Cpptraj and parmwrite and strip Daniel Roe
- Re: [AMBER] Cpptraj and parmwrite and strip Khabiri, Morteza
- Re: [AMBER] Cpptraj and parmwrite and strip Khabiri, Morteza
- Re: [AMBER] Cpptraj and parmwrite and strip Daniel Roe
- Re: [AMBER] How to add the charged sphere (ion) with arbitrary charge to my PDB file. Parviz Seifpanahi Shabane
- Re: [AMBER] How to add the charged sphere (ion) with arbitrary charge to my PDB file. Bill Ross
- Re: [AMBER] How to add the charged sphere (ion) with arbitrary charge to my PDB file. Bill Ross
Saturday, 2 September 2017
- [AMBER] Explicit solvent CpHMD: seeking clarifications George Tzotzos
Sunday, 3 September 2017
- Re: [AMBER] Explicit solvent CpHMD: seeking clarifications Jason Swails
- Re: [AMBER] Explicit solvent CpHMD: seeking clarifications George Tzotzos
- Re: [AMBER] Explicit solvent CpHMD: seeking clarifications Cruzeiro,Vinicius Wilian D
- [AMBER] amberlite p38 tutorial: Failure of final step of "pymdpbsa" in amberlite Bartberger, Michael
- [AMBER] Error bad atom Br Fábio Jorge
- Re: [AMBER] Error bad atom Br James Kress
- Re: [AMBER] How to add the charged sphere (ion) with arbitrary charge to my PDB file. Parviz Seifpanahi Shabane
- Re: [AMBER] How to add the charged sphere (ion) with arbitrary charge to my PDB file. Bill Ross
- Re: [AMBER] How to add the charged sphere (ion) with arbitrary charge to my PDB file. Parviz Seifpanahi Shabane
- Re: [AMBER] How to add the charged sphere (ion) with arbitrary charge to my PDB file. Bill Ross
- Re: [AMBER] How to add the charged sphere (ion) with arbitrary charge to my PDB file. Parviz Seifpanahi Shabane
- Re: [AMBER] How to add the charged sphere (ion) with arbitrary charge to my PDB file. Bill Ross
- Re: [AMBER] How to add the charged sphere (ion) with arbitrary charge to my PDB file. Parviz Seifpanahi Shabane
- Re: [AMBER] amberlite p38 tutorial: Failure of final step of "pymdpbsa" in amberlite David A Case
- [AMBER] Binding Free Energy Calculation in Ionic Liquid Debasish Mandal
- Re: [AMBER] Binding Free Energy Calculation in Ionic Liquid Bill Ross
Monday, 4 September 2017
- [AMBER] Moldeling with MCPB.py Lê Ngọc Chính
- Re: [AMBER] Binding Free Energy Calculation in Ionic Liquid David A Case
- Re: [AMBER] Explicit solvent CpHMD: seeking clarifications George Tzotzos
- Re: [AMBER] Explicit solvent CpHMD: seeking clarifications George Tzotzos
- [AMBER] Question about MM/PBSA idecomp=1: Eelec from receptor and ligand don't add up Guqin Shi
- [AMBER] Residue wise energy decomposition via MM-PBSA Rajarshi Roy
- [AMBER] Rebuilt missing amino acid gap is critical for long-time MD simulation by Amber jacky zhao
Tuesday, 5 September 2017
- Re: [AMBER] Moldeling with MCPB.py Pengfei Li
- [AMBER] .crd file format error Thakur, Abhishek
- Re: [AMBER] .crd file format error Daniel Roe
- Re: [AMBER] Question about MM/PBSA idecomp=1: decomposed Eelec stays the same when internal dielec constant increases. Is this a bug? Guqin Shi
- [AMBER] Zinc dummy atom error in MMPBSA calculation Sharon D. Morris
- Re: [AMBER] Residue wise energy decomposition via MM-PBSA Elvis Martis
Wednesday, 6 September 2017
- Re: [AMBER] Residue wise energy decomposition via MM-PBSA Rajarshi Roy
- [AMBER] MD terminate in HPC Garima Singh
- [AMBER] Oct 2 deadline for awards applications, Computers in Chemistry Division of ACS Carlos Simmerling
- Re: [AMBER] MD terminate in HPC Elvis Martis
- Re: [AMBER] MD terminate in HPC David A Case
- Re: [AMBER] Zinc dummy atom error in MMPBSA calculation Bill Ross
Thursday, 7 September 2017
- [AMBER] Error in MM-PBSA -- BondError: Cannot exclude an atom from itself 康宁
- Re: [AMBER] Error in MM-PBSA -- BondError: Cannot exclude an atom from itself Bill Ross
- [AMBER] Error after using Parmed: A residue defined as "fast 3-point water"... David Sáez
- Re: [AMBER] Error after using Parmed: A residue defined as "fast 3-point water"... Bill Ross
- [AMBER] Fixed links and files: Error in parmed: A residue defined as "fast 3-point water"... David Adrian Saez San Martin
- Re: [AMBER] Fixed links and files: Error in parmed: A residue defined as "fast 3-point water"... Bill Ross
Friday, 8 September 2017
- [AMBER] umbrella sampling - restraint problem Nisha Amarnath Jonniya
- [AMBER] Problem in restarting pH-REMD CpHMD Elisa Pieri
- Re: [AMBER] umbrella sampling - restraint problem diego.soler.uam.es
- Re: [AMBER] Rebuilt missing amino acid gap is critical for long-time MD simulation by Amber jacky zhao
- Re: [AMBER] Rebuilt missing amino acid gap is critical for long-time MD simulation by Amber Carlos Simmerling
- [AMBER] Frcmod file for ionic liquids guptashilpa_91.yahoo.com
- Re: [AMBER] umbrella sampling - restraint problem Nisha Amarnath Jonniya
- Re: [AMBER] umbrella sampling - restraint problem Carlos Simmerling
- Re: [AMBER] Problem in restarting pH-REMD CpHMD Daniel Roe
- Re: [AMBER] Frcmod file for ionic liquids Bill Ross
- Re: [AMBER] Fixed links and files: Error in parmed: A residue defined as "fast 3-point water"... David Adrian Saez San Martin
- [AMBER] I only receive a digest, but not specific answers to my posts David Adrian Saez San Martin
- Re: [AMBER] I only receive a digest, but not specific answers to my posts David Adrian Saez San Martin
- Re: [AMBER] Fixed links and files: Error in parmed: A residue defined as "fast 3-point water"... David Adrian Saez San Martin
- Re: [AMBER] Error in MM-PBSA -- BondError: Cannot exclude an atom from itself 康宁
- [AMBER] Frcmod file for ionic liquids Shilpa Gupta
Saturday, 9 September 2017
- Re: [AMBER] Rebuilt missing amino acid gap is critical for long-time MD simulation by Amber jacky zhao
- Re: [AMBER] Problem in restarting pH-REMD CpHMD Elisa Pieri
- Re: [AMBER] Rebuilt missing amino acid gap is critical for long-time MD simulation by Amber Carlos Simmerling
- [AMBER] Regarding Glucose naming Aashish Bhatt
- Re: [AMBER] amberlite p38 tutorial: Failure of final step of "pymdpbsa" in amberlite Bartberger, Michael
- Re: [AMBER] Error in MM-PBSA -- BondError: Cannot exclude an atom from itself Jason Swails
- [AMBER] Error in quasiharmonic calculation: prmtop file? Nada Afiva
- Re: [AMBER] Error in quasiharmonic calculation: prmtop file? Hai Nguyen
- Re: [AMBER] Regarding Glucose naming Elvis Martis
- Re: [AMBER] Error in quasiharmonic calculation: prmtop file? Nada Afiva
- [AMBER] Obtaining AM1-BCC charges in Antechamber Zachary Smithline
Sunday, 10 September 2017
- Re: [AMBER] Regarding Glucose naming Aashish Bhatt
- [AMBER] index error -reg Jeyaram R A
- Re: [AMBER] index error -reg David A Case
- Re: [AMBER] Moldeling with MCPB.py Lê Ngọc Chính
- Re: [AMBER] Regarding Glucose naming Hector A. Baldoni
- [AMBER] tleap atom numbering Neha Gandhi
- [AMBER] CNT hongping zhang
- Re: [AMBER] umbrella sampling - restraint problem Nisha Amarnath Jonniya
Monday, 11 September 2017
- [AMBER] rmsf < 5A colvin
- [AMBER] MMPBSA.py failing with topologies Sebastian Franco Ulloa
- [AMBER] MMPBSA error Sebastian Franco Ulloa
- [AMBER] gamd.log for multiple runs Battocchio, Giovanni
- [AMBER] TLEAP generation of ionized amino acid residue? Michael Shokhen
- Re: [AMBER] tleap atom numbering David A Case
- Re: [AMBER] Obtaining AM1-BCC charges in Antechamber David A Case
- Re: [AMBER] umbrella sampling - restraint problem Daniel Roe
- Re: [AMBER] rmsf < 5A Daniel Roe
- Re: [AMBER] Minimization error due to modified residue Bill Ross
- Re: [AMBER] Minimization error due to modified residue Lizelle Lubbe
- Re: [AMBER] Minimization error due to modified residue Lizelle Lubbe
- [AMBER] How to use two different force fields for a molecule? Anhui Wang
- Re: [AMBER] Minimization error due to modified residue Lizelle Lubbe
- Re: [AMBER] Minimization error due to modified residue Bill Ross
- Re: [AMBER] Minimization error due to modified residue Lizelle Lubbe
- Re: [AMBER] Minimization error due to modified residue Bill Ross
- Re: [AMBER] Minimization error due to modified residue Lizelle Lubbe
- Re: [AMBER] Minimization error due to modified residue Bill Ross
- Re: [AMBER] Minimization error due to modified residue Bill Ross
- Re: [AMBER] Minimization error due to modified residue Shafaq Muzammal
- Re: [AMBER] Minimization error due to modified residue Lizelle Lubbe
- [AMBER] Atom does not have file type -reg. Jeyaram R A
- Re: [AMBER] Atom does not have file type -reg. Bill Ross
- Re: [AMBER] Minimization error due to modified residue Shafaq Muzammal
- Re: [AMBER] Minimization error due to modified residue Bill Ross
- Re: [AMBER] Minimization error due to modified residue Lizelle Lubbe
- Re: [AMBER] Error in quasiharmonic calculation: prmtop file? Daniel Roe
- Re: [AMBER] How to use two different force fields for a molecule? Hai Nguyen
- Re: [AMBER] TIP3p lennard jones parameters Pengfei Li
- [AMBER] pmemd and sander simulations different - sander equilibration crashes Chayya Bhargac
- Re: [AMBER] Minimization error due to modified residue Ross Walker
- Re: [AMBER] pmemd and sander simulations different - sander equilibration crashes Chayya Bhargac
- Re: [AMBER] tleap atom numbering Neha Gandhi
- Re: [AMBER] tleap atom numbering Bill Ross
- [AMBER] Can we specify the length and width of the water box in LEaP ? Xing
- Re: [AMBER] Can we specify the length and width of the water box in LEaP ? Robin Betz
- Re: [AMBER] Can we specify the length and width of the water box in LEaP ? Xing
- [AMBER] NEW machine need help with GPU choice. Mohit Mazumder
- Re: [AMBER] NEW machine need help with GPU choice. David Cerutti
- [AMBER] Could not import Amber Python modules when using mdout_analyzer.py jacky zhao
- Re: [AMBER] Could not import Amber Python modules when using mdout_analyzer.py Hai Nguyen
Tuesday, 12 September 2017
- Re: [AMBER] Could not import Amber Python modules when using mdout_analyzer.py jacky zhao
- Re: [AMBER] How to use two different force fields for a molecule? David A Case
- Re: [AMBER] Atom does not have file type -reg. David A Case
- Re: [AMBER] pmemd and sander simulations different - sander equilibration crashes David A Case
- Re: [AMBER] Minimization error due to modified residue Lizelle Lubbe
- Re: [AMBER] Could not import Amber Python modules when using mdout_analyzer.py Hai Nguyen
- Re: [AMBER] Could not import Amber Python modules when using mdout_analyzer.py jacky zhao
- Re: [AMBER] Could not import Amber Python modules when using mdout_analyzer.py jacky zhao
- Re: [AMBER] Could not import Amber Python modules when using mdout_analyzer.py Hai Nguyen
- Re: [AMBER] Could not import Amber Python modules when using mdout_analyzer.py jacky zhao
- Re: [AMBER] Could not import Amber Python modules when using mdout_analyzer.py jacky zhao
- Re: [AMBER] Could not import Amber Python modules when using mdout_analyzer.py Hai Nguyen
- [AMBER] GPU-accelerated thermodynamic integration available in Amber Darrin York
- Re: [AMBER] NEW machine need help with GPU choice. Ross Walker
- Re: [AMBER] GPU-accelerated thermodynamic integration available in Amber Ross Walker
- Re: [AMBER] Atom does not have file type -reg. Jeyaram R A
- Re: [AMBER] Minimization error due to modified residue Lizelle Lubbe
- Re: [AMBER] Regarding Glucose naming Aashish Bhatt
- Re: [AMBER] Atom does not have file type -reg. Aashish Bhatt
- Re: [AMBER] Atom does not have file type -reg. Jeyaram R A
- Re: [AMBER] Atom does not have file type -reg. Aashish Bhatt
- Re: [AMBER] gamd.log for multiple runs Ross Walker
- [AMBER] Etot and TEMP become NaN during a simulation on commodity GPUs Chris Neale
- Re: [AMBER] Etot and TEMP become NaN during a simulation on commodity GPUs Ross Walker
- Re: [AMBER] Etot and TEMP become NaN during a simulation on commodity GPUs Chris Neale
- [AMBER] Creation of unusual bonding via pdb4amber. Rajarshi Roy
- Re: [AMBER] gamd.log for multiple runs Yinglong Miao
- Re: [AMBER] Creation of unusual bonding via pdb4amber. Hai Nguyen
- Re: [AMBER] Could not import Amber Python modules when using mdout_analyzer.py jacky zhao
- Re: [AMBER] Could not import Amber Python modules when using mdout_analyzer.py Hai Nguyen
- Re: [AMBER] Could not import Amber Python modules when using mdout_analyzer.py Hai Nguyen
- Re: [AMBER] Could not import Amber Python modules when using mdout_analyzer.py jacky zhao
- Re: [AMBER] Creation of unusual bonding via pdb4amber. Hai Nguyen
- Re: [AMBER] Could not import Amber Python modules when using mdout_analyzer.py Hai Nguyen
- Re: [AMBER] Could not import Amber Python modules when using mdout_analyzer.py Hai Nguyen
- Re: [AMBER] Could not import Amber Python modules when using mdout_analyzer.py jacky zhao
- Re: [AMBER] Could not import Amber Python modules when using mdout_analyzer.py Hai Nguyen
- Re: [AMBER] Could not import Amber Python modules when using mdout_analyzer.py Hai Nguyen
- Re: [AMBER] Could not import Amber Python modules when using mdout_analyzer.py jacky zhao
- Re: [AMBER] Could not import Amber Python modules when using mdout_analyzer.py Hai Nguyen
- Re: [AMBER] Could not import Amber Python modules when using mdout_analyzer.py jacky zhao
- Re: [AMBER] Creation of unusual bonding via pdb4amber. Rajarshi Roy
- [AMBER] How to calculate RDF with 'radial' 杨满意
- Re: [AMBER] Creation of unusual bonding via pdb4amber. Hai Nguyen
- Re: [AMBER] Creation of unusual bonding via pdb4amber. Rajarshi Roy
Wednesday, 13 September 2017
- Re: [AMBER] gamd.log for multiple runs Battocchio, Giovanni
- [AMBER] tleap error jacky zhao
- [AMBER] Amber16 archive corrupted? Casalini Tommaso
- Re: [AMBER] Amber16 archive corrupted? Elvis Martis
- Re: [AMBER] Amber16 archive corrupted? Casalini Tommaso
- Re: [AMBER] Rebuilt missing amino acid gap is critical for long-time MD simulation by Amber jacky zhao
- Re: [AMBER] tleap error jacky zhao
- [AMBER] REMD one long or many short runs? Andreas Tosstorff
- Re: [AMBER] tleap error David A Case
- Re: [AMBER] REMD one long or many short runs? Carlos Simmerling
- Re: [AMBER] How to calculate RDF with 'radial' Daniel Roe
- Re: [AMBER] tleap error jacky zhao
- Re: [AMBER] pmemd and sander simulations different - sander equilibration crashes Chayya Bhargac
- Re: [AMBER] pmemd and sander simulations different - sander equilibration crashes Chayya Bhargac
- [AMBER] Deprotonated SER side residue by AMBER? Michael Shokhen
- Re: [AMBER] GPU-accelerated thermodynamic integration available in Amber Hadházi Ádám
- Re: [AMBER] GPU-accelerated thermodynamic integration available in Amber Daniel Mermelstein
- Re: [AMBER] GPU-accelerated thermodynamic integration available in Amber Hadházi Ádám
- Re: [AMBER] How to calculate RDF with 'radial' 杨满意
- Re: [AMBER] GPU-accelerated thermodynamic integration available in Amber Jason Swails
- Re: [AMBER] MMPBSA.py failing with topologies Dwight McGee
- Re: [AMBER] MMPBSA.py failing with topologies Sebastian Franco Ulloa
Thursday, 14 September 2017
- Re: [AMBER] MMPBSA.py failing with topologies Sebastian Franco Ulloa
- [AMBER] TI where charges change David A Case
- Re: [AMBER] Deprotonated SER side residue by AMBER? David A Case
- Re: [AMBER] TI where charges change Adrian Roitberg
- [AMBER] Total energy of peptide simulation is positive Chetna Tyagi
- Re: [AMBER] TI where charges change Hadházi Ádám
- Re: [AMBER] Deprotonated SER side residue by AMBER? Michael Shokhen
- Re: [AMBER] TI where charges change David A Case
- Re: [AMBER] Total energy of peptide simulation is positive David A Case
- [AMBER] cpptraj SPAM error George Tzotzos
- Re: [AMBER] cpptraj SPAM error Daniel Roe
- Re: [AMBER] cpptraj SPAM error George Tzotzos
- Re: [AMBER] Total energy of peptide simulation is positive Chetna Tyagi
- Re: [AMBER] cpptraj SPAM error George Tzotzos
- Re: [AMBER] cpptraj SPAM error Daniel Roe
- Re: [AMBER] cpptraj SPAM error George Tzotzos
- Re: [AMBER] cpptraj SPAM error Daniel Roe
- Re: [AMBER] cpptraj SPAM error George Tzotzos
- Re: [AMBER] TI where charges change Hadházi Ádám
- [AMBER] Installing Compiling Errors Timothy Schutt
- Re: [AMBER] Installing Compiling Errors Hai Nguyen
- Re: [AMBER] Installing Compiling Errors Timothy Schutt
- Re: [AMBER] Installing Compiling Errors David A Case
Friday, 15 September 2017
- [AMBER] New Phospho Amino Acids Parameters? martin.lepsik.uochb.cas.cz
- [AMBER] cpptraj volmap: some questions George Tzotzos
- Re: [AMBER] New Phospho Amino Acids Parameters? Carlos Simmerling
- Re: [AMBER] Installing Compiling Errors Timothy Schutt
- Re: [AMBER] Etot and TEMP become NaN during a simulation on commodity GPUs Chris Neale
Saturday, 16 September 2017
- [AMBER] Is geometric center of atoms same as center of mass ? Saikat Pal
- Re: [AMBER] Is geometric center of atoms same as center of mass ? Daniel Roe
- Re: [AMBER] Etot and TEMP become NaN during a simulation on commodity GPUs Ross Walker
- [AMBER] simulation time Rana Rehan Khalid
- [AMBER] Mcpb.py for bay60 compound Rana Rehan Khalid
- Re: [AMBER] simulation time Elvis Martis
- Re: [AMBER] simulation time Rana Rehan Khalid
- Re: [AMBER] simulation time Elvis Martis
- Re: [AMBER] simulation time Hai Nguyen
- Re: [AMBER] simulation time Rana Rehan Khalid
- [AMBER] MCPB.py hbay.in input (system does not have metal ion) Rana Rehan Khalid
- Re: [AMBER] Mcpb.py for bay60 compound Rana Rehan Khalid
- Re: [AMBER] MCPB.py hbay.in input (system does not have metal ion) Rana Rehan Khalid
- Re: [AMBER] MCPB.py hbay.in input (system does not have metal ion) Bill Ross
- Re: [AMBER] simulation time Elvis Martis
- Re: [AMBER] MCPB.py hbay.in input (system does not have metal ion) Rana Rehan Khalid
Sunday, 17 September 2017
- Re: [AMBER] MCPB.py hbay.in input (system does not have metal ion) Bill Ross
- [AMBER] cpptraj: modification of topologies/trajectories George Tzotzos
- Re: [AMBER] MCPB.py hbay.in input (system does not have metal ion) David A Case
- [AMBER] Manually set residues Protonation states for HIS and CYS Rana Rehan Khalid
- Re: [AMBER] Manually set residues Protonation states for HIS and CYS Rana Rehan Khalid
- Re: [AMBER] Error in MM-PBSA -- BondError: Cannot exclude an atom from itself 康宁
Monday, 18 September 2017
- [AMBER] How to specify the liquid-liquid interface 鲁俊波
- [AMBER] CpHMD and cys residues Angus Voice
- [AMBER] AmberTools 17 incomplete compilation D L S Dinuka
- Re: [AMBER] cpptraj: modification of topologies/trajectories Daniel Roe
- Re: [AMBER] AmberTools 17 incomplete compilation Daniel Roe
- Re: [AMBER] cpptraj: modification of topologies/trajectories George Tzotzos
- Re: [AMBER] cpptraj: modification of topologies/trajectories Daniel Roe
- Re: [AMBER] cpptraj: modification of topologies/trajectories George Tzotzos
- Re: [AMBER] Manually set residues Protonation states for HIS and CYS David A Case
- [AMBER] improper torsion terms Lizelle Lubbe
- [AMBER] Problem with parallel install Maria Clelia Milletti
- Re: [AMBER] Manually set residues Protonation states for HIS and CYS Rana Rehan Khalid
- Re: [AMBER] Is geometric center of atoms same as center of mass ? Daniel Roe
- [AMBER] cpptraj: usage of strip and parmstrip George Tzotzos
- Re: [AMBER] How to calculate RDF with 'radial' Daniel Roe
- Re: [AMBER] cpptraj: usage of strip and parmstrip Daniel Roe
- Re: [AMBER] cpptraj: modification of topologies/trajectories Daniel Roe
- Re: [AMBER] Problem with parallel install David A Case
- [AMBER] How tleap read a Ruthenium complex solvent box generated by packmol? Sanaa ALAbbad
- Re: [AMBER] AmberTools 17 incomplete compilation Hai Nguyen
Tuesday, 19 September 2017
- Re: [AMBER] How tleap read a Ruthenium complex solvent box generated by packmol? David A Case
- [AMBER] Hoogsteen base pair using "useboundsfrom" Mandar Kulkarni
- [AMBER] Pytraj Gyration Tensor Domenico Marson
- Re: [AMBER] Pytraj Gyration Tensor Hai Nguyen
- [AMBER] angle between two subdomains Sowmya Indrakumar
- Re: [AMBER] Problem with parallel install Maria Clelia Milletti
- Re: [AMBER] Problem with parallel install Daniel Roe
- Re: [AMBER] angle between two subdomains Daniel Roe
- [AMBER] reduce command warnings Rana Rehan Khalid
- Re: [AMBER] Problem with parallel install Maria Clelia Milletti
- [AMBER] converting crd to pdb Rana Rehan Khalid
- Re: [AMBER] converting crd to pdb Bill Ross
- Re: [AMBER] converting crd to pdb Hai Nguyen
- Re: [AMBER] converting crd to pdb Rana Rehan Khalid
- Re: [AMBER] Problem with parallel install Daniel Roe
- [AMBER] ambertools install issue Eric Smoll
- Re: [AMBER] ambertools install issue Hai Nguyen
- [AMBER] Restart Simulation Rana Rehan Khalid
- Re: [AMBER] Restart Simulation Daniel Roe
- Re: [AMBER] ambertools install issue (Eric Smoll) Eric Smoll
- [AMBER] .com file creation Rana Rehan Khalid
- Re: [AMBER] ambertools install issue (Eric Smoll) Hai Nguyen
- Re: [AMBER] How tleap read a Ruthenium complex solvent box generated by packmol? Sanaa ALAbbad
- Re: [AMBER] .com file creation pancham lal Gupta
- Re: [AMBER] improper torsion terms Pengfei Li
- Re: [AMBER] simulation time Pengfei Li
- Re: [AMBER] simulation time Pengfei Li
- Re: [AMBER] simulation time Chris Neale
- Re: [AMBER] Mcpb.py for bay60 compound Pengfei Li
- [AMBER] Error in pmemd.cuda David Sáez
Wednesday, 20 September 2017
- Re: [AMBER] improper torsion terms Lizelle Lubbe
- [AMBER] Protein drifts out of the periodic cell Michael Shokhen
- Re: [AMBER] Protein drifts out of the periodic cell Daniel Roe
- [AMBER] Distance restraint Lizelle Lubbe
- Re: [AMBER] ambertools install issue (Eric Smoll) David A Case
- Re: [AMBER] Protein drifts out of the periodic cell Michael Shokhen
- Re: [AMBER] Protein drifts out of the periodic cell Daniel Roe
- [AMBER] protein-membrane visualize in VMD Kanin Wichapong
- Re: [AMBER] Protein drifts out of the periodic cell Michael Shokhen
- [AMBER] simulation of docked domains of protein Rana Rehan Khalid
- Re: [AMBER] cpptraj volmap: some questions Daniel Roe
- Re: [AMBER] simulation of docked domains of protein Elvis Martis
- [AMBER] Antechamber Rana Rehan Khalid
- Re: [AMBER] Antechamber Rana Rehan Khalid
- Re: [AMBER] Antechamber Rana Rehan Khalid
- Re: [AMBER] Antechamber Bill Ross
- Re: [AMBER] Antechamber Robin Betz
- Re: [AMBER] Antechamber Rana Rehan Khalid
- Re: [AMBER] cpptraj volmap: some questions George Tzotzos
- Re: [AMBER] Problem with parallel install Maria Clelia Milletti
- Re: [AMBER] Problem with parallel install Bill Ross
- Re: [AMBER] simulation of docked domains of protein Rana Rehan Khalid
- Re: [AMBER] simulation of docked domains of protein Bill Ross
- Re: [AMBER] Problem with parallel install Maria Clelia Milletti
- Re: [AMBER] Problem with parallel install Bill Ross
- [AMBER] Inverting a selection in NAB atom expression? Istvan Kolossvary
- Re: [AMBER] Problem with parallel install Maria Clelia Milletti
- Re: [AMBER] Problem with parallel install Bill Ross
- Re: [AMBER] simulation of docked domains of protein Elvis Martis
Thursday, 21 September 2017
- [AMBER] Question about MCPB.py Lê Ngọc Chính
- [AMBER] Amber16 electric field parameters Alessandro Mariani
- Re: [AMBER] Pytraj Gyration Tensor Domenico Marson
- Re: [AMBER] Pytraj Gyration Tensor Hai Nguyen
- [AMBER] simulation stop due to size limit exceed Rana Rehan Khalid
- Re: [AMBER] Pytraj Gyration Tensor Domenico Marson
- Re: [AMBER] Problem with parallel install Maria Clelia Milletti
- [AMBER] Antechamber error Rana Rehan Khalid
- Re: [AMBER] Antechamber error Elvis Martis
- Re: [AMBER] Problem with parallel install Daniel Roe
- [AMBER] Quasi-Harmonic Analysis and Entropy Calculations in cpptraj - Help Requested Mo Rahman
- Re: [AMBER] Quasi-Harmonic Analysis and Entropy Calculations in cpptraj - Help Requested Daniel Roe
- Re: [AMBER] Antechamber error Scott Brozell
- Re: [AMBER] Antechamber error Rana Rehan Khalid
- [AMBER] Setting water box with fix dimension Ashutosh Shandilya
- Re: [AMBER] simulation stop due to size limit exceed Chris Neale
- Re: [AMBER] simulation stop due to size limit exceed Rana Rehan Khalid
- [AMBER] Question about MCPB.py Lê Ngọc Chính
- [AMBER] MCPB.py AmberTools17 Amani Eshtiwi
- Re: [AMBER] Question about MCPB.py Hai Nguyen
- Re: [AMBER] Problem with parallel install Bill Ross
- Re: [AMBER] Question about MCPB.py Lê Ngọc Chính
- Re: [AMBER] Pytraj Gyration Tensor Domenico Marson
- Re: [AMBER] Quasi-Harmonic Analysis and Entropy Calculations in cpptraj - Help Requested Mo Rahman
- Re: [AMBER] Pytraj Gyration Tensor Hai Nguyen
- Re: [AMBER] Problem with parallel install Maria Clelia Milletti
- [AMBER] Reduce command warnings Skipped hydrogen Rana Rehan Khalid
- [AMBER] Is it possible to compile without linking C++ and fortran? Timothy Schutt
- Re: [AMBER] Reduce command warnings Skipped hydrogen Rana Rehan Khalid
- Re: [AMBER] Is it possible to compile without linking C++ and fortran? Daniel Roe
- Re: [AMBER] Pytraj Gyration Tensor Daniel Roe
- Re: [AMBER] Pytraj Gyration Tensor Hai Nguyen
- Re: [AMBER] Quasi-Harmonic Analysis and Entropy Calculations in cpptraj - Help Requested Daniel Roe
- [AMBER] cpinutil.py Pacheco, Sayuri
- Re: [AMBER] Setting water box with fix dimension Daniel Roe
- [AMBER] Split the image to run in the string method Chunli Yan
- Re: [AMBER] Setting water box with fix dimension Ashutosh Shandilya
- Re: [AMBER] Setting water box with fix dimension Bill Ross
- Re: [AMBER] Setting water box with fix dimension Daniel Roe
- Re: [AMBER] Setting water box with fix dimension Bill Ross
- Re: [AMBER] Quasi-Harmonic Analysis and Entropy Calculations in cpptraj - Help Requested Mo Rahman
- Re: [AMBER] simulation of docked domains of protein David A Case
- Re: [AMBER] Antechamber David A Case
- Re: [AMBER] cpinutil.py Adrian Roitberg
- Re: [AMBER] Setting water box with fix dimension David A Case
- Re: [AMBER] Problem regarding Chamber and psf file David Sáez
- [AMBER] [david.case.rutgers.edu: Re: Is it possible to compile without linking C++ and fortran?] David A Case
- Re: [AMBER] cpinutil.py Pacheco, Sayuri
- Re: [AMBER] Antechamber Rana Rehan Khalid
- Re: [AMBER] [david.case.rutgers.edu: Re: Is it possible to compile without linking C++ and fortran?] Timothy Schutt
- Re: [AMBER] Split the image to run in the string method Feng Pan
- Re: [AMBER] Is it possible to compile without linking C++ and fortran? Timothy Schutt
- Re: [AMBER] Is it possible to compile without linking C++ and fortran? Daniel Roe
- Re: [AMBER] Problem regarding Chamber and psf file Jason Swails
- Re: [AMBER] Quasi-Harmonic Analysis and Entropy Calculations in cpptraj - Help Requested Celeste Saguí
- Re: [AMBER] Problem regarding Chamber and psf file David Sáez
- Re: [AMBER] cpinutil.py Hai Nguyen
- Re: [AMBER] Pytraj Gyration Tensor Hai Nguyen
Friday, 22 September 2017
- [AMBER] simulations crash Ana Luisa Novo de Oliveira
- Re: [AMBER] simulations crash Carlos Simmerling
- Re: [AMBER] simulations crash Ana Luisa Novo de Oliveira
- [AMBER] SHAKE failure Lizelle Lubbe
- Re: [AMBER] simulations crash Carlos Simmerling
- Re: [AMBER] [david.case.rutgers.edu: Re: Is it possible to compile without linking C++ and fortran?] Daniel Roe
- Re: [AMBER] simulations crash Daniel Roe
- Re: [AMBER] SHAKE failure Daniel Roe
- Re: [AMBER] SHAKE failure Bill Ross
- [AMBER] PMEMD TERMINATED ABNORMALLY (But simulation run with sander command) Rana Rehan Khalid
- Re: [AMBER] PMEMD TERMINATED ABNORMALLY (But simulation run with sander command) Bill Ross
- [AMBER] cluster analysis of protein complex simulation jacky zhao
- Re: [AMBER] cluster analysis of protein complex simulation Hai Nguyen
- Re: [AMBER] PMEMD TERMINATED ABNORMALLY (But simulation run with sander command) Rana Rehan Khalid
- Re: [AMBER] cluster analysis of protein complex simulation Daniel Roe
- [AMBER] mdcrd file not open in vmd Rana Rehan Khalid
- Re: [AMBER] mdcrd file not open in vmd Daniel Roe
- Re: [AMBER] mdcrd file not open in vmd Rana Rehan Khalid
- Re: [AMBER] SHAKE failure Lizelle Lubbe
- Re: [AMBER] SHAKE failure Lizelle Lubbe
- Re: [AMBER] .com file creation Rana Rehan Khalid
- Re: [AMBER] cluster analysis of protein complex simulation jacky zhao
- [AMBER] How to compare the difference between two trajectories with two very similar parm files jacky zhao
Saturday, 23 September 2017
- [AMBER] Antechamber RESP calculation error Rana Rehan Khalid
- Re: [AMBER] Antechamber RESP calculation error Pengfei Li
- Re: [AMBER] PMEMD TERMINATED ABNORMALLY (But simulation run with sander command) David A Case
- Re: [AMBER] SHAKE failure Pengfei Li
- Re: [AMBER] Antechamber RESP calculation error Rana Rehan Khalid
- Re: [AMBER] PMEMD TERMINATED ABNORMALLY (But simulation run with sander command) Rana Rehan Khalid
- Re: [AMBER] Question about MCPB.py Pengfei Li
- Re: [AMBER] MCPB.py AmberTools17 Pengfei Li
- Re: [AMBER] Antechamber RESP calculation error Pengfei Li
- Re: [AMBER] Amber16 electric field parameters Pengfei Li
- [AMBER] Different production speeds at different pHs when doing explicit constant pH simulations Andrew Schaub
Sunday, 24 September 2017
- Re: [AMBER] Different production speeds at different pHs when doing explicit constant pH simulations Adrian Roitberg
- [AMBER] CpHMD: seeking clarification George Tzotzos
Monday, 25 September 2017
- [AMBER] cluster analysis using cpptraj Sowmya Indrakumar
- Re: [AMBER] cluster analysis using cpptraj Bill Ross
- Re: [AMBER] cluster analysis using cpptraj Bill Ross
- Re: [AMBER] cluster analysis using cpptraj Bill Ross
- Re: [AMBER] cluster analysis using cpptraj Sowmya Indrakumar
- Re: [AMBER] cluster analysis using cpptraj Thomas Cheatham
- Re: [AMBER] cluster analysis using cpptraj Sowmya Indrakumar
- Re: [AMBER] cluster analysis using cpptraj Sowmya Indrakumar
- Re: [AMBER] cluster analysis using cpptraj Bill Ross
- Re: [AMBER] CpHMD: seeking clarification Eric Lang
- Re: [AMBER] How to calculate RDF with 'radial' 杨满意
- Re: [AMBER] cluster analysis using cpptraj Daniel Roe
- Re: [AMBER] cluster analysis using cpptraj Elvis Martis
- Re: [AMBER] cluster analysis using cpptraj Sowmya Indrakumar
- Re: [AMBER] CpHMD: seeking clarification George Tzotzos
- [AMBER] Using FEW with a transmembrane protein Tarsis
- Re: [AMBER] cpinutil.py Pacheco, Sayuri
- Re: [AMBER] cpinutil.py Hai Nguyen
- Re: [AMBER] Different production speeds at different pHs when doing explicit constant pH simulations Andrew Schaub
- [AMBER] water bridge analysis Thakur, Abhishek
- [AMBER] analysizing the trajectory for water interaction Thakur, Abhishek
- Re: [AMBER] water bridge analysis pancham lal Gupta
- [AMBER] PyRed Steven M. Graham
- [AMBER] How to save reimaged trajectory file during MD? Ravi Abrol
Tuesday, 26 September 2017
- [AMBER] Problem with MM-GBSA decomposition Sergey Samsonov
- [AMBER] A query about coordinate saving frequency for solvation entropy calculation using GIST SHAILESH KUMAR
- Re: [AMBER] How to save reimaged trajectory file during MD? Elvis Martis
- Re: [AMBER] SHAKE failure Lizelle Lubbe
- Re: [AMBER] SHAKE failure Lizelle Lubbe
- Re: [AMBER] SHAKE failure Lizelle Lubbe
- Re: [AMBER] How to save reimaged trajectory file during MD? Ravi Abrol
- [AMBER] Problem in analysing radius of gyration value in CPPTRAJ krishna.2015.iitg.ernet.in
- [AMBER] cpptraj distance: error George Tzotzos
- Re: [AMBER] cpptraj distance: error Daniel Roe
- Re: [AMBER] cpptraj distance: error George Tzotzos
- Re: [AMBER] cpptraj distance: error Daniel Roe
- Re: [AMBER] How to save reimaged trajectory file during MD? David A Case
- Re: [AMBER] Different production speeds at different pHs when doing explicit constant pH simulations Jason Swails
- [AMBER] Air-water interface jesus berlanga
- Re: [AMBER] Air-water interface Bill Ross
Wednesday, 27 September 2017
- Re: [AMBER] Problem in analysing radius of gyration value in CPPTRAJ Daniel Roe
- Re: [AMBER] Problem in analysing radius of gyration value in CPPTRAJ Hai Nguyen
- [AMBER] Error with MMGBSA/PBSA jacob wick
- Re: [AMBER] Error with MMGBSA/PBSA Elvis Martis
- Re: [AMBER] Error with MMGBSA/PBSA jacob wick
- Re: [AMBER] Air-water interface jesus berlanga
- Re: [AMBER] Error with MMGBSA/PBSA Elvis Martis
- Re: [AMBER] Air-water interface Bill Ross
- Re: [AMBER] Problem with MM-GBSA decomposition Daniel Roe
- Re: [AMBER] How to save reimaged trajectory file during MD? Ravi Abrol
- [AMBER] [Fwd: Re: Problem in analysing radius of gyration value in CPPTRAJ] krishna.2015.iitg.ernet.in
- [AMBER] Avoid pH Titration of LYS and TYR R zu
- [AMBER] Dr. Nick Riviera Eric Pettersen
- Re: [AMBER] Avoid pH Titration of LYS and TYR Adrian Roitberg
- Re: [AMBER] Dr. Nick Riviera Eric Pettersen
- Re: [AMBER] Dr. Nick Riviera Niel Henriksen
- Re: [AMBER] Dr. Nick Riviera Eric Pettersen
- Re: [AMBER] Dr. Nick Riviera Scott Brozell
Thursday, 28 September 2017
- Re: [AMBER] Problem with MM-GBSA decomposition Sergey Samsonov
- Re: [AMBER] Problem in analysing radius of gyration value in CPPTRAJ krishna.2015.iitg.ernet.in
- [AMBER] moveanchor waleed zalloum
- [AMBER] RAC_analysis jacky zhao
- Re: [AMBER] Error with MMGBSA/PBSA jacob wick
- [AMBER] leaprc.constph and ff14sb R zu
- [AMBER] Cpptraj Sayuri Pacheco
- Re: [AMBER] Cpptraj Daniel Roe
- Re: [AMBER] RAC_analysis Daniel Roe
- Re: [AMBER] Cpptraj Sayuri Pacheco
- Re: [AMBER] moveanchor Daniel Roe
- Re: [AMBER] leaprc.constph and ff14sb R zu
- [AMBER] trajout last x frames cpptraj Hughes, Travis
- Re: [AMBER] Avoid pH Titration of LYS and TYR R zu
- [AMBER] identiy the step of interaction from an entire trajectory Thakur, Abhishek
- Re: [AMBER] Error with MMGBSA/PBSA Elvis Martis
- Re: [AMBER] Cpptraj Pacheco, Sayuri
- Re: [AMBER] Cpptraj Pacheco, Sayuri
- [AMBER] barostat with large coupling constant R zu
- Re: [AMBER] trajout last x frames cpptraj R zu
- Re: [AMBER] trajout last x frames cpptraj R zu
- Re: [AMBER] leaprc.constph and ff14sb Carlos Simmerling
- Re: [AMBER] trajout last x frames cpptraj Hai Nguyen
- Re: [AMBER] trajout last x frames cpptraj Hai Nguyen
Friday, 29 September 2017
- Re: [AMBER] trajout last x frames cpptraj Hughes, Travis
- [AMBER] identifying the step of hbond interaction from trajectories Thakur, Abhishek
- [AMBER] Multiple Simulations on One GPU R zu
Saturday, 30 September 2017
- Re: [AMBER] Multiple Simulations on One GPU Ross Walker

Last message date: Sat Sep 30 2017 - 06:00:03 PDT
Archived on: Fri Nov 22 2024 - 05:55:31 PST

Amber Archive Sep 2017 by date