Amber Archive Oct 2015: by date

Thursday, 1 October 2015
- [AMBER] /share/apps/amber/amber14/bin/sander.MPI: error while loading shared libraries: libmpi_cxx.so.1: cannot open shared object file: No such file or directory Atila Petrosian
- Re: [AMBER] /share/apps/amber/amber14/bin/sander.MPI: error while loading shared libraries: libmpi_cxx.so.1: cannot open shared object file: No such file or directory Repic Matej
- [AMBER] QMMM SCC-DFTB: ERROR ON EWEVGE in AMBER 12 using the new set 3ob-3-1 Emilio Lence
- Re: [AMBER] QMMM SCC-DFTB: ERROR ON EWEVGE in AMBER 12 using the new set 3ob-3-1 Gustavo Seabra
- Re: [AMBER] QMMM SCC-DFTB: ERROR ON EWEVGE in AMBER 12 using the new set 3ob-3-1 Emilio Lence
- [AMBER] Parameters for trigonal bi-pyramid and square bi-pyramid Fe(II) Francesco Pietra
- [AMBER] Units of the dipole moment? Ucisik, Melek Nihan
- Re: [AMBER] Units of the dipole moment? Daniel Roe
- Re: [AMBER] Updates for PBSA energy calculations Christina Berti
- Re: [AMBER] Updates for PBSA energy calculations Jason Swails
- [AMBER] Building a structure of levansucrase (1PT2) with a fructosyl residue attached to Asp86 Surasak Chunsrivirot
Friday, 2 October 2015
- [AMBER] Problem with VDW energy Brent Krueger
- Re: [AMBER] Problem with VDW energy Ross Walker
- [AMBER] ^.^. as a new atom type when running DFTB with sander from Ambertools 15 Emilio Lence
- Re: [AMBER] Problem with VDW energy David A Case
- Re: [AMBER] Problem with VDW energy Brent Krueger
- Re: [AMBER] ^.^. as a new atom type when running DFTB with sander from Ambertools 15 Gustavo Seabra
- [AMBER] problem with randomizing velocities Kalenkiewicz, Andrew (NIH/NICHD) [F]
- Re: [AMBER] problem with randomizing velocities Bill Ross
- Re: [AMBER] problem with randomizing velocities Bill Ross
- [AMBER] TIP3 water not recognized Chitrak Gupta
- Re: [AMBER] TIP3 water not recognized Bill Ross
- Re: [AMBER] problem with randomizing velocities Hector A. Baldoni
Saturday, 3 October 2015
- [AMBER] mixing rules for various water models in AMBER conor parks
- Re: [AMBER] Building a structure of levansucrase (1PT2) with a fructosyl residue attached to Asp86 Lachele Foley
- Re: [AMBER] mixing rules for various water models in AMBER Jason Swails
- Re: [AMBER] mixing rules for various water models in AMBER conor parks
Sunday, 4 October 2015
- [AMBER] QM/MM performance Sofia Vasilakaki
- Re: [AMBER] mixing rules for various water models in AMBER Jason Swails
- Re: [AMBER] mixing rules for various water models in AMBER Conor Parks
- Re: [AMBER] mixing rules for various water models in AMBER Jason Swails
- Re: [AMBER] AMBER Digest, Vol 1361, Issue 1 Chitrak Gupta
- Re: [AMBER] QM/MM performance David A Case
- Re: [AMBER] AMBER Digest, Vol 1361, Issue 1 Jason Swails
- [AMBER] CpHMD for non protein residues Rahul Ramesh
- Re: [AMBER] CpHMD for non protein residues Adrian Roitberg
- Re: [AMBER] CpHMD for non protein residues Rahul Ramesh
- Re: [AMBER] CpHMD for non protein residues Jason Swails
- [AMBER] Question about mask in cpptraj Mohd Farid Ismail
- Re: [AMBER] Question about mask in cpptraj Daniel Roe
- Re: [AMBER] Question about mask in cpptraj Mohd Farid Ismail
- Re: [AMBER-Developers] [AMBER] problem with randomizing velocities David A Case
Monday, 5 October 2015
- Re: [AMBER] Building a structure of levansucrase (1PT2) with a fructosyl residue attached to Asp86 Surasak Chunsrivirot
- Re: [AMBER] ^.^. as a new atom type when running DFTB with sander from Ambertools 15 Emilio Lence
- Re: [AMBER] Leap : problem with copying and combining DNA items Jérémie Knoops
- Re: [AMBER] Question about mask in cpptraj Daniel Roe
- Re: [AMBER] ^.^. as a new atom type when running DFTB with sander from Ambertools 15 Gustavo Seabra
- Re: [AMBER] CpHMD for non protein residues Brian Radak
- [AMBER] SC15 Call for abstracts - "Producing High-Performance and Sustainable Software for Molecular Simulation" Ross Walker
- Re: [AMBER] ^.^. as a new atom type when running DFTB with sander from Ambertools 15 Jonathan Sheehan
- [AMBER] Atom 1512 was assigned a lower molecule # than previous atom Osman, Roman
- Re: [AMBER] ^.^. as a new atom type when running DFTB with sander from Ambertools 15 Jonathan Sheehan
- Re: [AMBER] Atom 1512 was assigned a lower molecule # than previous atom Daniel Roe
- Re: [AMBER] Atom 1512 was assigned a lower molecule # than previous atom Osman, Roman
- Re: [AMBER] Atom 1512 was assigned a lower molecule # than previous atom Daniel Roe
- Re: [AMBER] ^.^. as a new atom type when running DFTB with sander from Ambertools 15 Gustavo Seabra
- [AMBER] Info: Bond types are assigned for valence state 5 with penalty of 1 Atila Petrosian
- Re: [AMBER] Leap : problem with copying and combining DNA items David A Case
- Re: [AMBER] Info: Bond types are assigned for valence state 5 with penalty of 1 David A Case
- Re: [AMBER] Question about mask in cpptraj Mohd Farid Ismail
- [AMBER] Pairwise energy decomposition Sara Omar
Tuesday, 6 October 2015
- Re: [AMBER] Pairwise energy decomposition Carlos Simmerling
- Re: [AMBER] ^.^. as a new atom type when running DFTB with sander from Ambertools 15 Emilio Lence
- [AMBER] cpin file Arjun Sharma
- Re: [AMBER] cpin file Jason Swails
Wednesday, 7 October 2015
- [AMBER] How to do a QMMM calculation with a dynamic QM region 崔克新
- Re: [AMBER] How to do a QMMM calculation with a dynamic QM region Emilio Lence
- Re: [AMBER] How to do a QMMM calculation with a dynamic QM region Hector A. Baldoni
- Re: [AMBER] ^.^. as a new atom type when running DFTB with sander from Ambertools 15 Jonathan Sheehan
- [AMBER] SIGSEGV: Segmentation Fault Steven Cole Mercer
- Re: [AMBER] SIGSEGV: Segmentation Fault Scott Brozell
- [AMBER] hydrogen bond cpptraj Lara rajam
- Re: [AMBER] ^.^. as a new atom type when running DFTB with sander from Ambertools 15 Gustavo Seabra
- Re: [AMBER] ^.^. as a new atom type when running DFTB with sander from Ambertools 15 David A Case
- Re: [AMBER] ^.^. as a new atom type when running DFTB with sander from Ambertools 15 Daniel Roe
- [AMBER] Dihedral/improper coefficient in AMBER + rmin vs sigma for lennard jones conor parks
- Re: [AMBER] ^.^. as a new atom type when running DFTB with sander from Ambertools 15 Jonathan Sheehan
Thursday, 8 October 2015
- Re: [AMBER] ^.^. as a new atom type when running DFTB with sander from Ambertools 15 Emilio Lence
- Re: [AMBER] ^.^. as a new atom type when running DFTB with sander from Ambertools 15 Jason Swails
- Re: [AMBER] Dihedral/improper coefficient in AMBER + rmin vs sigma for lennard jones Jason Swails
- [AMBER] Controlling size of the box Nicholus Bhattacharjee
- Re: [AMBER] Controlling size of the box Jason Swails
- Re: [AMBER] Controlling size of the box David A Case
- Re: [AMBER] Controlling size of the box Jason Swails
- [AMBER] "Vlimit exceeded for step..." error Vu Truong
- Re: [AMBER] "Vlimit exceeded for step..." error David A Case
Friday, 9 October 2015
- Re: [AMBER] Controlling size of the box Nicholus Bhattacharjee
- Re: [AMBER] Controlling size of the box Daniel Roe
- [AMBER] Cytochrome P450 with heme simulation Abelak, Kavin
- [AMBER] AIB parameter Elisa Frezza
- [AMBER] http://q4md-forcefieldtools.org/ unavailable Jérémie Knoops
- [AMBER] Restraints Wong Li Zhe
- Re: [AMBER] Restraints Emilio Lence
- Re: [AMBER] Restraints Wong Li Zhe
- Re: [AMBER] Restraints David A Case
- Re: [AMBER] Cytochrome P450 with heme simulation Jason Swails
- [AMBER] Restraints Wong Li Zhe
- Re: [AMBER] Restraints Jason Swails
- Re: [AMBER] Restraints Jason Swails
- [AMBER] Restraints Wong Li Zhe
- [AMBER] Restraints Wong Li Zhe
- Re: [AMBER] Restraints Jason Swails
- [AMBER] Restraints Wong Li Zhe
- Re: [AMBER] AMBER Digest, Vol 1364, Issue 1 Arjun Sharma
- [AMBER] resp input format 16I5 stecue.gmail.com
- Re: [AMBER] AMBER Digest, Vol 1364, Issue 1 Jason Swails
- [AMBER] h-bond calculation - tokenise error Sidhu, Khushwant (Dr.)
- Re: [AMBER] h-bond calculation - tokenise error Daniel Roe
- Re: [AMBER] resp input format 16I5 Jason Swails
- Re: [AMBER] resp input format 16I5 stecue.gmail.com
- [AMBER] non-standard residue (DNA-protein crosslink) Jackle, Chasen
- Re: [AMBER] non-standard residue (DNA-protein crosslink) Carlos Simmerling
- Re: [AMBER] "Vlimit exceeded for step..." error Vu Truong
- [AMBER] Making Parameter and Topology Files for Protein-Ligand Complex Jim Wu
Saturday, 10 October 2015
- Re: [AMBER] Making Parameter and Topology Files for Protein-Ligand Complex Emilio Lence
- Re: [AMBER] "Vlimit exceeded for step..." error David A Case
- Re: [AMBER] Making Parameter and Topology Files for Protein-Ligand Complex David A Case
Sunday, 11 October 2015
- Re: [AMBER] Error: ptraj is needed for MMPBSA Ayesha Kanwal
- Re: [AMBER] Error: ptraj is needed for MMPBSA Ayesha Kanwal
- Re: [AMBER] Error: ptraj is needed for MMPBSA Jason Swails
- Re: [AMBER] Error: ptraj is needed for MMPBSA Jason Swails
- [AMBER] Prepgen difficulty Robert Molt
Monday, 12 October 2015
- Re: [AMBER] http://q4md-forcefieldtools.org/ unavailable Emilio Lence
- [AMBER] query about Bromide ion forcefield parameter jagannath mondal
- Re: [AMBER] Prepgen difficulty David A Case
- Re: [AMBER] query about Bromide ion forcefield parameter David A Case
- Re: [AMBER] Error: ptraj is needed for MMPBSA Ayesha Kanwal
- Re: [AMBER] Prepgen difficulty Marion, Antoine
- Re: [AMBER] Error: ptraj is needed for MMPBSA Daniel Roe
- Re: [AMBER] Error: ptraj is needed for MMPBSA Ayesha Kanwal
- Re: [AMBER] Error: ptraj is needed for MMPBSA Kenneth Huang
- Re: [AMBER] Error: ptraj is needed for MMPBSA Jason Swails
- [AMBER] A question about MMPBSA calculation anu chandra
- Re: [AMBER] A question about MMPBSA calculation Jason Swails
- [AMBER] How do you place two molecules in one water box? David Eugene Jones
- Re: [AMBER] How do you place two molecules in one water box? Ben Roberts
- Re: [AMBER] How do you place two molecules in one water box? Lachele Foley
- Re: [AMBER] How do you place two molecules in one water box? David Eugene Jones
- Re: [AMBER] How do you place two molecules in one water box? Ben Roberts
- Re: [AMBER] How do you place two molecules in one water box? David Eugene Jones
- Re: [AMBER] Error: ptraj is needed for MMPBSA Ayesha Kanwal
- [AMBER] Temperature fluctuations in stage heating Anitha Jagadesh
Tuesday, 13 October 2015
- Re: [AMBER] Temperature fluctuations in stage heating Repic Matej
- Re: [AMBER] Error: ptraj is needed for MMPBSA Jason Swails
- [AMBER] many atoms, same name Hadeer ELHabashy
- [AMBER] cpptraj density Björn Karlsson
- Re: [AMBER] many atoms, same name Jason Swails
- Re: [AMBER] Error: ptraj is needed for MMPBSA Ayesha Kanwal
- Re: [AMBER] Error: ptraj is needed for MMPBSA Jason Swails
- [AMBER] AmberTools14 configuration problem Ivanov, Maxim
- Re: [AMBER] many atoms, same name case
- [AMBER] Real-time hydrogen bond formation using VMD Abhipriya K
Wednesday, 14 October 2015
- Re: [AMBER] Real-time hydrogen bond formation using VMD Repic Matej
- Re: [AMBER] Real-time hydrogen bond formation using VMD Abhipriya K
- Re: [AMBER] Real-time hydrogen bond formation using VMD amin.imtech.res.in
- [AMBER] EVB related query bijyalaxmi athokpam
- Re: [AMBER] [SPAM] AMBER Digest, Vol 1365, Issue 1 崔克新
- Re: [AMBER] Error: ptraj is needed for MMPBSA Ayesha Kanwal
- [AMBER] Minimization Wong Li Zhe
- [AMBER] difficulties in generate .prmtop and .inpcrd file for complex using Guassian calculated ligand charges Jin Zhang
- Re: [AMBER] difficulties in generate .prmtop and .inpcrd file for complex using Guassian calculated ligand charges Emilio Lence
- [AMBER] error with line 165 of cpinutil.py Hadeer ELHabashy
- Re: [AMBER] Minimization Emilio Lence
- Re: [AMBER] Error: ptraj is needed for MMPBSA Jason Swails
- Re: [AMBER] error with line 165 of cpinutil.py Jason Swails
- Re: [AMBER] error with line 165 of cpinutil.py Hadeer ELHabashy
- [AMBER] Is it possible to simulate a periodic crystal ? Hadeer ELHabashy
- Re: [AMBER] error with line 165 of cpinutil.py Juan Eiros Zamora
- Re: [AMBER] error with line 165 of cpinutil.py Jason Swails
- Re: [AMBER] Is it possible to simulate a periodic crystal ? Jason Swails
- Re: [AMBER] error with line 165 of cpinutil.py Hadeer ELHabashy
- Re: [AMBER] RESP charge fitting Xing
- Re: [AMBER] RESP charge fitting li he
- [AMBER] RESP charge calculation li he
- Re: [AMBER] RESP charge calculation li he
- Re: [AMBER] Is it possible to simulate a periodic crystal ? Hadeer ELHabashy
- [AMBER] Ho Atom Inclusion in PDB from Leap Robert Molt
- Re: [AMBER] Error: ptraj is needed for MMPBSA Ayesha Kanwal
- Re: [AMBER] Is it possible to simulate a periodic crystal ? Hadeer ELHabashy
- Re: [AMBER] Ho Atom Inclusion in PDB from Leap David A Case
- [AMBER] tinker_to_amber does not work Sun
- Re: [AMBER] Ho Atom Inclusion in PDB from Leap Robert Molt
- Re: [AMBER] tinker_to_amber does not work Jason Swails
Thursday, 15 October 2015
- [AMBER] cutoff problem with a periodic crystal box Hadeer ELHabashy
- [AMBER] difficulties in generate .prmtop and .inpcrd file for complex using Guassian calculated ligand charges MarcZhang
- [AMBER] No Internet Access Shahryar Alavi
- Re: [AMBER] difficulties in generate .prmtop and .inpcrd file for complex using Guassian calculated ligand charges Emilio Lence
- [AMBER] What is the formula for calculating EPtot? Yip Yew Mun
- [AMBER] Fwd: EVB related query bijyalaxmi athokpam
- Re: [AMBER] What is the formula for calculating EPtot? Jason Swails
- Re: [AMBER] cutoff problem with a periodic crystal box Jason Swails
- [AMBER] Correctly deriving force constants for Amber Nash, Anthony
- Re: [AMBER] cutoff problem with a periodic crystal box Hadeer ELHabashy
- Re: [AMBER] EVB related query David A Case
- Re: [AMBER] cutoff problem with a periodic crystal box David A Case
- Re: [AMBER] difficulties in generate .prmtop and .inpcrd file for complex using Guassian calculated ligand charges David A Case
- Re: [AMBER] What is the formula for calculating EPtot? David A Case
- [AMBER] System gets unwrap while iwrap=1 in ti Khabiri, Morteza
- Re: [AMBER] System gets unwrap while iwrap=1 in ti Jason Swails
- Re: [AMBER] System gets unwrap while iwrap=1 in ti Khabiri, Morteza
- Re: [AMBER] System gets unwrap while iwrap=1 in ti Jason Swails
- Re: [AMBER] What is the formula for calculating EPtot? Conor Parks
- Re: [AMBER] tinker_to_amber does not work Sun
- Re: [AMBER] What is the formula for calculating EPtot? Daniel Roe
- Re: [AMBER] tinker_to_amber does not work Jason Swails
- Re: [AMBER] What is the formula for calculating EPtot? Jason Swails
- Re: [AMBER] No Internet Access Ross Walker
- Re: [AMBER] What is the formula for calculating EPtot? conor parks
- Re: [AMBER] problem with randomizing velocities Kalenkiewicz, Andrew (NIH/NICHD) [F]
- Re: [AMBER] What is the formula for calculating EPtot? Jason Swails
- Re: [AMBER] RESP charge calculation li he
- Re: [AMBER] problem with randomizing velocities David A Case
- Re: [AMBER] Correctly deriving force constants for Amber David A Case
- [AMBER] Not atom type for Bromine atom in amber GAFF force field? MarcZhang
- Re: [AMBER-Developers] [AMBER] problem with randomizing velocities Ross Walker
- Re: [AMBER] What is the formula for calculating EPtot? conor parks
- Re: [AMBER] Not atom type for Bromine atom in amber GAFF force field? Jason Swails
- Re: [AMBER] Is it possible to simulate a periodic crystal ? David A Case
- [AMBER] FW: System gets unwrap while iwrap=1 in ti Khabiri, Morteza
- Re: [AMBER] Correctly deriving force constants for Amber Nash, Anthony
- Re: [AMBER] Correctly deriving force constants for Amber Adrian Roitberg
- Re: [AMBER] Correctly deriving force constants for Amber Nash, Anthony
- Re: [AMBER] RESP charge calculation David A Case
- Re: [AMBER] difficulties in generate .prmtop and .inpcrd file MarcZhang
- Re: [AMBER] Not atom type for Bromine atom in amber GAFF MarcZhang
- Re: [AMBER] RESP charge calculation li he
- Re: [AMBER] FW: System gets unwrap while iwrap=1 in ti case
- Re: [AMBER] compare two trajectories Xing
- [AMBER] CpHMD for non protein residues Rahul Ramesh
- Re: [AMBER] query about Bromide ion forcefield parameter jagannath mondal
Friday, 16 October 2015
- Re: [AMBER] FW: System gets unwrap while iwrap=1 in ti Jason Swails
- Re: [AMBER] CpHMD for non protein residues Jason Swails
- [AMBER] Documentation on Prepin File Format Robert Molt
- [AMBER] CPPTRAJ : different RMSD calculation in a single run anu chandra
- Re: [AMBER] query about Bromide ion forcefield parameter Jason Swails
- Re: [AMBER] Documentation on Prepin File Format Jason Swails
- Re: [AMBER] CPPTRAJ : different RMSD calculation in a single run Jason Swails
- Re: [AMBER] Documentation on Prepin File Format Robert Molt
- Re: [AMBER] query about Bromide ion forcefield parameter Brent Krueger
- Re: [AMBER] CPPTRAJ : different RMSD calculation in a single run anu chandra
- Re: [AMBER] System gets unwrap while iwrap=1 in ti Khabiri, Morteza
- Re: [AMBER] CPPTRAJ : different RMSD calculation in a single run Jason Swails
- Re: [AMBER] tinker_to_amber does not work David A Case
- [AMBER] Random Number Generator Flag Ig Guqin Shi
- [AMBER] Random Number Generator Flag Ig Guqin Shi
- Re: [AMBER] Random Number Generator Flag Ig Ross Walker
- Re: [AMBER] Random Number Generator Flag Ig Guqin Shi
- Re: [AMBER] Random Number Generator Flag Ig Jason Swails
- Re: [AMBER] Random Number Generator Flag Ig Jason Swails
- Re: [AMBER] Documentation on Prepin File Format David A Case
- Re: [AMBER] CpHMD for non protein residues Rahul Ramesh
- Re: [AMBER] AmberTools14 configuration problem David A Case
- Re: [AMBER] Random Number Generator Flag Ig Guqin Shi
- [AMBER] sander missing from AmberTools15? Novosielski, Ryan
- Re: [AMBER] sander missing from AmberTools15? David A Case
- [AMBER] Help Balajee Ramachandran
- Re: [AMBER] sander missing from AmberTools15? Jason Swails
- Re: [AMBER] CpHMD for non protein residues Jason Swails
- Re: [AMBER] sander missing from AmberTools15? Novosielski, Ryan
- Re: [AMBER] Help Jason Swails
- Re: [AMBER] Help Carlos Simmerling
- Re: [AMBER] sander missing from AmberTools15? Jason Swails
- Re: [AMBER] sander missing from AmberTools15? Novosielski, Ryan
- Re: [AMBER] sander missing from AmberTools15? Daniel Roe
- Re: [AMBER] sander missing from AmberTools15? Novosielski, Ryan
- Re: [AMBER] sander missing from AmberTools15? Daniel Roe
- Re: [AMBER] sander missing from AmberTools15? Jason Swails
- Re: [AMBER] sander missing from AmberTools15? Novosielski, Ryan
- [AMBER] Leap PDB Input Error Robert Molt
- Re: [AMBER] Leap PDB Input Error case
- Re: [AMBER] RESP charge calculation Luciano Costa
Saturday, 17 October 2015
- [AMBER] donor and acceptor masks Hadeer ELHabashy
- Re: [AMBER] donor and acceptor masks Emilio Lence
- Re: [AMBER] difficulties in generate .prmtop and .inpcrd file Emilio Lence
- Re: [AMBER] donor and acceptor masks Daniel Roe
- Re: [AMBER] donor and acceptor masks Emilio Lence
- [AMBER] Fwd: donor and acceptor masks Emilio Lence
- Re: [AMBER] donor and acceptor masks Hadeer ELHabashy
- Re: [AMBER] donor and acceptor masks Jason Swails
- Re: [AMBER] donor and acceptor masks Hadeer ELHabashy
- Re: [AMBER] donor and acceptor masks Jason Swails
- Re: [AMBER] donor and acceptor masks Hadeer ELHabashy
- Re: [AMBER] donor and acceptor masks Hadeer ELHabashy
- Re: [AMBER] donor and acceptor masks Daniel Roe
- Re: [AMBER] AmberTools14 configuration problem Jason Swails
- Re: [AMBER] donor and acceptor masks Hadeer ELHabashy
- Re: [AMBER] donor and acceptor masks Hadeer ELHabashy
- Re: [AMBER] donor and acceptor masks Thomas Cheatham
- Re: [AMBER] donor and acceptor masks Hadeer ELHabashy
- Re: [AMBER] donor and acceptor masks Daniel Roe
- Re: [AMBER] donor and acceptor masks Hadeer ELHabashy
- Re: [AMBER] donor and acceptor masks Daniel Roe
Sunday, 18 October 2015
- Re: [AMBER] CpHMD for non protein residues Rahul Ramesh
- [AMBER] Membrane protein imagining problems Romero, Raquel
- [AMBER] R.E.D. server down or out? Tan Yaw Sing
- [AMBER] CPPTRAJ Wong Li Zhe
- Re: [AMBER] CPPTRAJ Nhai
- Re: [AMBER] CPPTRAJ Thomas Cheatham
Monday, 19 October 2015
- [AMBER] RED-tools Repic Matej
- [AMBER] Why is water box getting bigger? Karolina Markowska
- Re: [AMBER] Why is water box getting bigger? David A Case
- [AMBER] MMPBSA tutorial A3.2 Fabian gmail
- Re: [AMBER] MMPBSA tutorial A3.2 Fabian gmail
- [AMBER] Differences on MMPBSA calculation results MarcZhang
- [AMBER] Differences on MMPBSA calculation results MarcZhang
- Re: [AMBER] MMPBSA tutorial A3.2 Jason Swails
- Re: [AMBER] Differences on MMPBSA calculation results Jason Swails
- Re: [AMBER] MMPBSA tutorial A3.2 Fabian gmail
- [AMBER] [cpptraj] Changes in RMSF functionality? Juan Eiros Zamora
- Re: [AMBER] [cpptraj] Changes in RMSF functionality? Daniel Roe
- Re: [AMBER] Membrane protein imagining problems Daniel Roe
- Re: [AMBER] Membrane protein imagining problems Hai Nguyen
- [AMBER] 1-4 nonbonded interactions does not cancel in MMPBSA calculation Renato Freitas
- [AMBER] Lennard-Jones parameter for Sp, Sp2 and Sp3 Nitrogen Ebert Maximilian
- [AMBER] Problems with the installation of ambertools15. Jinfeng Huang
- [AMBER] The formulas of per-residue and pairwise-residue free energy decomposition in mm_pbsa wliu
Tuesday, 20 October 2015
- Re: [AMBER] 1-4 nonbonded interactions does not cancel in MMPBSA calculation Jérémie Knoops
- Re: [AMBER] Differences on MMPBSA calculation results MarcZhang
- Re: [AMBER] MMPBSA tutorial A3.2 Fabian gmail
- Re: [AMBER] MMPBSA tutorial A3.2 Vlad Cojocaru
- Re: [AMBER] Membrane protein imagining problems Romero, Raquel
- Re: [AMBER] Problems with the installation of ambertools15. David A Case
- [AMBER] Tutorial 3 section 1 Abelak, Kavin
- Re: [AMBER] Tutorial 3 section 1 Vlad Cojocaru
- [AMBER] gromacs to amber file format neha chaudhary
- Re: [AMBER] MMPBSA tutorial A3.2 Fabian gmail
- Re: [AMBER] MMPBSA tutorial A3.2 Fabian gmail
- Re: [AMBER] gromacs to amber file format Hai Nguyen
- Re: [AMBER] The formulas of per-residue and pairwise-residue free energy decomposition in mm_pbsa Jason Swails
- Re: [AMBER] 1-4 nonbonded interactions does not cancel in MMPBSA calculation Jason Swails
- Re: [AMBER] Differences on MMPBSA calculation results Jason Swails
- Re: [AMBER] gromacs to amber file format Jason Swails
- Re: [AMBER] MMPBSA tutorial A3.2 Jason Swails
- Re: [AMBER] MMPBSA tutorial A3.2 Fabian gmail
- Re: [AMBER] MMPBSA tutorial A3.2 Jason Swails
- [AMBER] Measuring distance between protein and graphene surface Krantzman, Kristin D
- Re: [AMBER] Measuring distance between protein and graphene surface Hai Nguyen
- Re: [AMBER] Measuring minimum distance between protein and graphene surface Krantzman, Kristin D
- Re: [AMBER] Differences on MMPBSA calculation results Ray Luo, Ph.D.
- Re: [AMBER] Measuring minimum distance between protein and graphene surface Christina Bergonzo
- Re: [AMBER] Measuring minimum distance between protein and graphene surface Krantzman, Kristin D
- [AMBER] SGLDg Jérémie Knoops
Wednesday, 21 October 2015
- Re: [AMBER] Why is water box getting bigger? Karolina Markowska
- Re: [AMBER] Why is water box getting bigger? Jason Swails
- [AMBER] The magnitude and the direction of the electric field Hadeer ELHabashy
- [AMBER] MMPBSA: multiple trajectory approach usage George Tzotzos
- Re: [AMBER] MMPBSA: multiple trajectory approach usage Dwight McGee
- Re: [AMBER] SGLDg Wu, Xiongwu (NIH/NHLBI) [E]
- Re: [AMBER] MMPBSA: multiple trajectory approach usage George Tzotzos
- [AMBER] pmemd.cuda.MPI on Comet- MPI dying Kenneth Huang
- Re: [AMBER] MMPBSA: multiple trajectory approach usage Dwight McGee
- Re: [AMBER] MMPBSA: multiple trajectory approach usage George Tzotzos
- [AMBER] Problem configuring amber14 Mochena, Mogus D.
- Re: [AMBER] Problem configuring amber14 Jason Swails
- Re: [AMBER] Problem configuring amber14 David A Case
- Re: [AMBER] pmemd.cuda.MPI on Comet- MPI dying Ross Walker
- [AMBER] ff12SB vs ff14SB for protein-ligand MD simulations? yunshi11 .
- Re: [AMBER] ff12SB vs ff14SB for protein-ligand MD simulations? Carlos Simmerling
- Re: [AMBER] ff12SB vs ff14SB for protein-ligand MD simulations? yunshi11 .
- [AMBER] ff12SB vs ff14SB for protein-ligand MD simulations? koushik kasavajhala
Thursday, 22 October 2015
- Re: [AMBER] MMPBSA tutorial A3.2 Fabian gmail
- Re: [AMBER] Problem configuring amber14 Fabian gmail
- Re: [AMBER] MMPBSA tutorial A3.2 Fabian gmail
- Re: [AMBER] MMPBSA tutorial A3.2 Fabian gmail
- Re: [AMBER] MMPBSA tutorial A3.2 Jason Swails
- [AMBER] MMPBSA for peptides interaction Fabian gmail
- Re: [AMBER] MMPBSA tutorial A3.2 Fabian gmail
- Re: [AMBER] Why is water box getting bigger? Karolina Markowska
- [AMBER] How can amber differentiate between terminal Oxygens Hadeer ELHabashy
- Re: [AMBER] Why is water box getting bigger? Jason Swails
- Re: [AMBER] pmemd.cuda.MPI on Comet- MPI dying Kenneth Huang
- [AMBER] 12-6-4 LJ-type nonbonded model Fe(III)-M(II) Marcelo Andrade Chagas
- Re: [AMBER] 12-6-4 LJ-type nonbonded model Fe(III)-M(II) Pengfei Li
- [AMBER] Steps after: AMBER annealing with restriaints in vocuum.? towards improving the quality of structure with out RDC, Dihedrals Kumar cerm
- Re: [AMBER] 12-6-4 LJ-type nonbonded model Fe(III)-M(II) Marcelo Andrade Chagas
- [AMBER] Time correlation function of an atom Hadeer ELHabashy
- Re: [AMBER] Time correlation function of an atom Adrian Roitberg
- Re: [AMBER] Time correlation function of an atom Hadeer ELHabashy
- Re: [AMBER] pmemd.cuda.MPI on Comet- MPI dying Ross Walker
- Re: [AMBER] 12-6-4 LJ-type nonbonded model Fe(III)-M(II) Marcelo Andrade Chagas
- Re: [AMBER] 12-6-4 LJ-type nonbonded model Fe(III)-M(II) Marcelo Andrade Chagas
- Re: [AMBER] 12-6-4 LJ-type nonbonded model Fe(III)-M(II) Marcelo Andrade Chagas
- [AMBER] Polardecomp in 3D-RISM fails Josep Maria Campanera Alsina
- Re: [AMBER] RED-tools Nash, Anthony
- Re: [AMBER] Polardecomp in 3D-RISM fails Tyler Luchko (Lists)
- Re: [AMBER] RED-tools Jason Swails
- Re: [AMBER] Polardecomp in 3D-RISM fails Jason Swails
- Re: [AMBER] RED-tools Nash, Anthony
- Re: [AMBER] 12-6-4 LJ-type nonbonded model Fe(III)-M(II) Pengfei Li
- [AMBER] Atom match error in MMPBSA calculation Progress Zhang
- Re: [AMBER] How can amber differentiate between terminal Oxygens David A Case
- Re: [AMBER] RED-tools Hector A. Baldoni
- Re: [AMBER] Time correlation function of an atom David A Case
- [AMBER] Metal Ion Model Carlos Modenutti
- Re: [AMBER] pmemd.cuda.MPI on Comet- MPI dying Kenneth Huang
- Re: [AMBER] pmemd.cuda.MPI on Comet- MPI dying Ross Walker
Friday, 23 October 2015
- [AMBER] If it's possible to add restraint on the steered MD ? 崔克新
- [AMBER] Steps after: AMBER annealing with restraints in vacuum.? towards improving the quality of structure with out RDC, Dihedrals V. Kumar
- [AMBER] Steps after: AMBER annealing with restraints in vacuum.? towards improving the quality of structure with out RDC, Dihedrals V. Kumar
- [AMBER] QM/MM Umbrella Mahmood Jasim
- Re: [AMBER] QM/MM Umbrella Adrian Roitberg
- [AMBER] Stopping sander in production phase. Why? Atila Petrosian
- Re: [AMBER] Problem configuring amber14 Mochena, Mogus D.
- [AMBER] Best suitable 'igb' value for MMPBSA.py calculation anu chandra
- Re: [AMBER] Problem configuring amber14 Jason Swails
- Re: [AMBER] Stopping sander in production phase. Why? Atila Petrosian
- Re: [AMBER] Stopping sander in production phase. Why? Adrian Roitberg
- Re: [AMBER] Best suitable 'igb' value for MMPBSA.py calculation Jason Swails
- Re: [AMBER] Why is water box getting bigger? Karolina Markowska
- Re: [AMBER] Stopping sander in production phase. Why? Atila Petrosian
- Re: [AMBER] Best suitable 'igb' value for MMPBSA.py calculation Hai Nguyen
- Re: [AMBER] Stopping sander in production phase. Why? Jason Swails
- Re: [AMBER] Stopping sander in production phase. Why? Atila Petrosian
- Re: [AMBER] Stopping sander in production phase. Why? Jason Swails
- [AMBER] aMD: Bad data for namelist object ethreshp Claire Coderch Boué
- Re: [AMBER] RED-tools Hector A. Baldoni
- Re: [AMBER] Best suitable 'igb' value for MMPBSA.py calculation Ray Luo, Ph.D.
- Re: [AMBER] Best suitable 'igb' value for MMPBSA.py calculation Carlos Simmerling
- Re: [AMBER] Metal Ion Model Pengfei Li
- [AMBER] compatibility of targeted MD with GPU amber vs. sander Naomi Rose Latorraca
- Re: [AMBER] compatibility of targeted MD with GPU amber vs. sander Charles Lin
- Re: [AMBER] 12-6-4 LJ-type nonbonded model Fe(III)-M(II) Marcelo Andrade Chagas
- Re: [AMBER] 12-6-4 LJ-type nonbonded model Fe(III)-M(II) Ross Walker
Saturday, 24 October 2015
- Re: [AMBER] aMD: Bad data for namelist object ethreshp David A Case
- Re: [AMBER] Steps after: AMBER annealing with restriaints in vocuum.? towards improving the quality of structure with out RDC, Dihedrals David A Case
- Re: [AMBER] 12-6-4 LJ-type nonbonded model Fe(III)-M(II) Pengfei Li
- Re: [AMBER] Query about adding hydrogens David Case
- Re: [AMBER] Best suitable 'igb' value for MMPBSA.py calculation psu4.uic.edu
- Re: [AMBER] Steps after: AMBER annealing with restriaints in vocuum.? towards improving the quality of structure with out RDC, Dihedrals V. Kumar
Sunday, 25 October 2015
- [AMBER] ALA but must be GLY MM-PBSA bharat lakhani
- [AMBER] how to convert mdcrd to NetCDF trajectory file? shahab shariati
- Re: [AMBER] how to convert mdcrd to NetCDF trajectory file? shahab shariati
- Re: [AMBER] how to convert mdcrd to NetCDF trajectory file? shahab shariati
- Re: [AMBER] ALA but must be GLY MM-PBSA Aleksandra Skoric
- Re: [AMBER] how to convert mdcrd to NetCDF trajectory file? Nhai
- Re: [AMBER] how to convert mdcrd to NetCDF trajectory file? Soumendranath Bhakat
- Re: [AMBER] RED-tools Steven M. Graham
- Re: [AMBER] RED-tools Hector A. Baldoni
Monday, 26 October 2015
- [AMBER] Constant pH MD Hadeer ELHabashy
- Re: [AMBER] Constant pH MD Hadeer ELHabashy
- Re: [AMBER] how to convert mdcrd to NetCDF trajectory file? V. Kumar
- Re: [AMBER] How can amber differentiate between terminal Oxygens Hadeer ELHabashy
- [AMBER] atomiccorr Hadeer ELHabashy
- Re: [AMBER] Why is water box getting bigger? Karolina Markowska
- Re: [AMBER] How can amber differentiate between terminal Oxygens Jason Swails
- Re: [AMBER] Why is water box getting bigger? Jason Swails
- Re: [AMBER] Why is water box getting bigger? Karolina Markowska
- Re: [AMBER] How can amber differentiate between terminal Oxygens Hadeer ELHabashy
- Re: [AMBER] How can amber differentiate between terminal Oxygens Jason Swails
- Re: [AMBER] How can amber differentiate between terminal Oxygens Hadeer ELHabashy
- Re: [AMBER] How can amber differentiate between terminal Oxygens Jason Swails
- Re: [AMBER] How can amber differentiate between terminal Oxygens Hadeer ELHabashy
- Re: [AMBER] Oxygen parameters for AMBER99SB-ILDN Ebert Maximilian
- Re: [AMBER] How can amber differentiate between terminal Oxygens Jason Swails
- Re: [AMBER] How can amber differentiate between terminal Oxygens Hadeer ELHabashy
- Re: [AMBER] How can amber differentiate between terminal Oxygens Jason Swails
- [AMBER] paramfit multiple dihedrals combination CHAMI F.
- [AMBER] paramfit multiple dihedral commbination CHAMI F.
- Re: [AMBER] paramfit multiple dihedral commbination Adrian Roitberg
- [AMBER] cpptraj - bridging water Lara rajam
- Re: [AMBER] paramfit multiple dihedral commbination Carlos Simmerling
- [AMBER] ante-MMPBSA question Mohammad Salem
- Re: [AMBER] ante-MMPBSA question Mohammad Salem
- [AMBER] AmberTools 15, Mac El Captain and Fink Alan
- Re: [AMBER] AmberTools 15, Mac El Captain and Fink Ross Walker
- Re: [AMBER] AmberTools 15, Mac El Captain and Fink Alan
- Re: [AMBER] AmberTools 15, Mac El Captain and Fink Jason Swails
- Re: [AMBER] AmberTools 15, Mac El Captain and Fink Jason Swails
Tuesday, 27 October 2015
- [AMBER] parameters for Boron jixiaofeng
- [AMBER] (too) high absolute values for charges using resp and gaussian Jérémie Knoops
- Re: [AMBER] (too) high absolute values for charges using resp and gaussian Karl Kirschner
- Re: [AMBER] (too) high absolute values for charges using resp and gaussian Ye Mei
- Re: [AMBER] AmberTools 15, Mac El Captain and Fink Alan
- [AMBER] coordination number Hadeer ELHabashy
- Re: [AMBER] How can amber differentiate between terminal Oxygens Hadeer ELHabashy
- [AMBER] Help - buy the Amber software Adam Winiarski
- Re: [AMBER] QM/MM Umbrella Mahmood Jasim
- Re: [AMBER] Polardecomp in 3D-RISM fails Josep Maria Campanera Alsina
- Re: [AMBER] QM/MM Umbrella Adrian Roitberg
- [AMBER] unusual structure_after equilibration Andrew Bostick
- [AMBER] Resulting cutoff is too small for your lower limit jfliu
- Re: [AMBER] Resulting cutoff is too small for your lower limit Carlos Simmerling
- Re: [AMBER] unusual structure_after equilibration Carlos Simmerling
- [AMBER] N- and C- terminals constant PH simulation Hadeer ELHabashy
- [AMBER] small energy jump when restoring a simulation production Fabian gmail
- Re: [AMBER] small energy jump when restoring a simulation production Carlos Simmerling
- Re: [AMBER] QM/MM Umbrella Brian Radak
- Re: [AMBER] small energy jump when restoring a simulation production Fabian gmail
- Re: [AMBER] ante-MMPBSA question Daniel Roe
- Re: [AMBER] cpptraj - bridging water Daniel Roe
- Re: [AMBER] N- and C- terminals constant PH simulation Jason Swails
- Re: [AMBER] ante-MMPBSA question Jason Swails
- Re: [AMBER] small energy jump when restoring a simulation production Jason Swails
- Re: [AMBER] cpptraj - bridging water Lara rajam
- Re: [AMBER] small energy jump when restoring a simulation production Adrian Roitberg
- Re: [AMBER] small energy jump when restoring a simulation production Fabian gmail
- Re: [AMBER] QM/MM Umbrella Emilio Lence
- Re: [AMBER] small energy jump when restoring a simulation production Jason Swails
- Re: [AMBER] small energy jump when restoring a simulation production Fabian gmail
- Re: [AMBER] pmemd.cuda.MPI on Comet- MPI dying Kenneth Huang
- Re: [AMBER] pmemd.cuda.MPI on Comet- MPI dying Ross Walker
- Re: [AMBER] small energy jump when restoring a simulation production Fabian gmail
- Re: [AMBER] small energy jump when restoring a simulation production Carlos Simmerling
- [AMBER] QMMM with inorganic molecules Robert Arbon
- Re: [AMBER] small energy jump when restoring a simulation production Jason Swails
- Re: [AMBER] small energy jump when restoring a simulation production Jason Swails
- Re: [AMBER] Resulting cutoff is too small for your lower limit case
- Re: [AMBER] QMMM with inorganic molecules Brian Radak
- Re: [AMBER] small energy jump when restoring a simulation production Fabian Glaser
- [AMBER] missingdisulfide Abelak, Kavin
- Re: [AMBER] small energy jump when restoring a simulation production Jason Swails
- Re: [AMBER] missingdisulfide Jason Swails
- [AMBER] Replica exchange temperature distribution maryam azimzadehirani
- Re: [AMBER] Replica exchange temperature distribution Jason Swails
- Re: [AMBER] The formulas of per-residue and pairwise-residue free energy decomposition in mm_pbsa wliu
- Re: [AMBER] Replica exchange temperature distribution maryam azimzadehirani
Wednesday, 28 October 2015
- [AMBER] Charmm to Amber (where’s chamber?) Alan
- Re: [AMBER] Charmm to Amber (where’s chamber?) Alan
- Re: [AMBER] Charmm to Amber (where’s chamber?) David A Case
- [AMBER] cpptraj uses huge memory space while doing molsurf calculation anu chandra
- Re: [AMBER] Charmm to Amber (where’s chamber?) Jason Swails
- [AMBER] Different Parameters for Nonbonded Interactions Batuhan Kav
- [AMBER] Guanine base pair planarity in G-guadruplex V. Kumar
- [AMBER] how to generate a model beta-sheet structure Jagannath Mondal
- Re: [AMBER] how to generate a model beta-sheet structure Hai Nguyen
- [AMBER] applying restraints using tinker Christina Berti
- Re: [AMBER] applying restraints using tinker Jason Swails
- Re: [AMBER] Different Parameters for Nonbonded Interactions Jason Swails
- Re: [AMBER] pmemd.cuda.MPI on Comet- MPI dying Kenneth Huang
- Re: [AMBER] Halogen bond force field in AMBER psu4.uic.edu
Thursday, 29 October 2015
- Re: [AMBER] QMMM with inorganic molecules Robert Arbon
- [AMBER] Tutorial 22 - aMD - how long should it last on Titan Black? Karolina Markowska
- [AMBER] Guanine base pair planarity in G-guadruplex V. Kumar
- Re: [AMBER] Tutorial 22 - aMD - how long should it last on Titan Black? case
- [AMBER] [AMEBR] Amino acid side-chain carbonyl C=O(ASP, GLU) and side-cahin -HN (LYS, ARG) close proximity V. Kumar
- Re: [AMBER] how to generate a model beta-sheet structure Daniel Roe
- Re: [AMBER] atomiccorr Daniel Roe
- Re: [AMBER] how to convert mdcrd to NetCDF trajectory file? Daniel Roe
- Re: [AMBER] Tutorial 22 - aMD - how long should it last on Titan Black? Ross Walker
- [AMBER] MMPBSA for multiple mutants Fabian gmail
- Re: [AMBER] Tutorial 22 - aMD - how long should it last on Titan Black? Karolina Markowska
- Re: [AMBER] MMPBSA for multiple mutants Jason Swails
- Re: [AMBER] MMPBSA for multiple mutants Fabian gmail
- Re: [AMBER] cpptraj uses huge memory space while doing molsurf calculation Daniel Roe
- Re: [AMBER] Charmm to Amber (where’s chamber?) Alan
- Re: [AMBER] Charmm to Amber (where’s chamber?) Jason Swails
- [AMBER] Glycam force field parameters for derivatives? yunshi11 .
- [AMBER] How to prevent the water molecules entering into the binding pocket during the MD simulation ? fjliu
Friday, 30 October 2015
- Re: [AMBER] How to prevent the water molecules entering into the binding pocket during the MD simulation ? Vitaly V. Chaban
- [AMBER] Why PBSA decomposition takes so long time? MarcZhang
- Re: [AMBER] [AMEBR] Amino acid side-chain carbonyl C=O(ASP, GLU) and side-cahin -HN (LYS, ARG) close proximity Carlos Simmerling
- Re: [AMBER] N- and C- terminals constant PH simulation Hadeer ELHabashy
- Re: [AMBER] N- and C- terminals constant PH simulation Dr. Anselm Horn
- Re: [AMBER] Why PBSA decomposition takes so long time? Jason Swails
- [AMBER] ions cannot be viewed in gaussview Martina Devi
- Re: [AMBER] Charmm to Amber (where’s chamber?) Alan
- Re: [AMBER] Charmm to Amber (where’s chamber?) Jason Swails
- Re: [AMBER] ions cannot be viewed in gaussview Jason Swails
- [AMBER] AMBER14 testing error Mahmoud A. A. Ibrahim
- Re: [AMBER] AMBER14 testing error Hai Nguyen
- Re: [AMBER] AMBER14 testing error Marcelo Andrade Chagas
- Re: [AMBER] Metal Ion Model Carlos Modenutti
- Re: [AMBER] Metal Ion Model Pengfei Li
- [AMBER] Elementary VMD Problem with Amber Trajectory Robert Molt
- Re: [AMBER] Elementary VMD Problem with Amber Trajectory Jason Swails
- Re: [AMBER] Elementary VMD Problem with Amber Trajectory Robert Molt
- [AMBER] mmpbsa.py error Mohammad Salem
- Re: [AMBER] mmpbsa.py error Jason Swails
- Re: [AMBER] Glycam force field parameters for derivatives? Lachele Foley
Saturday, 31 October 2015
- Re: [AMBER] AMBER14 testing error Mahmoud A. A. Ibrahim
- Re: [AMBER] AMBER14 testing error Jason Swails
- Re: [AMBER] ions cannot be viewed in gaussview Martina Devi
- Re: [AMBER] ions cannot be viewed in gaussview Jason Swails
- [AMBER] &rst + distance + coordinate restraint Gerald Monard
- Re: [AMBER] &rst + distance + coordinate restraint Gerald Monard
- Re: [AMBER] mmpbsa.py error Mohammad Salem
- Re: [AMBER] ions cannot be viewed in gaussview Gustavo Seabra
- Re: [AMBER] mmpbsa.py error Jason Swails
- [AMBER] Can't install AMBER14: MissingProgram...Install patch from your package manager Jose Borreguero
- Re: [AMBER] Can't install AMBER14: MissingProgram...Install patch from your package manager Daniel Roe

Last message date: Sat Oct 31 2015 - 17:00:02 PDT
Archived on: Fri Apr 19 2024 - 05:55:00 PDT

Amber Archive Oct 2015 by date