Amber Archive Apr 2019: by thread

[AMBER] How the instantaneous temperature is calculated in Amber ? Marek Maly (Sun Mar 31 2019 - 17:35:05 PDT)
- Re: [AMBER] How the instantaneous temperature is calculated in Amber ? Marek Maly (Sun Mar 31 2019 - 20:02:36 PDT)
- Re: [AMBER] How the instantaneous temperature is calculated in Amber ? Marek Maly (Sun Mar 31 2019 - 20:20:18 PDT)
  - Re: [AMBER] How the instantaneous temperature is calculated in Amber ? Carlos Simmerling (Mon Apr 01 2019 - 04:16:16 PDT)
    - Re: [AMBER] How the instantaneous temperature is calculated in Amber ? Marek Maly (Mon Apr 01 2019 - 10:37:31 PDT)
[AMBER] How to build the central fragment of a modified nucleotide in the AMBER force fields 21818674.zju.edu.cn (Sun Mar 31 2019 - 19:28:55 PDT)
Re: [AMBER] huge reference.frc in MMPBSA Antoine Marion (Sun Mar 31 2019 - 21:20:27 PDT)
[AMBER] Fwd: AMBER Digest, Vol 2600, Issue 1 SATYAJIT KHATUA (Mon Apr 01 2019 - 00:45:18 PDT)
Re: [AMBER] NFE error: Cannot read &abmd namelist Jason Imamoto (Mon Apr 01 2019 - 00:54:59 PDT)
- Re: [AMBER] NFE error: Cannot read &abmd namelist Feng Pan (Tue Apr 02 2019 - 16:56:47 PDT)
[AMBER] Equilibration in multiple steps with decrement in force constants Priyabrata Das (Mon Apr 01 2019 - 03:19:34 PDT)
- Re: [AMBER] Equilibration in multiple steps with decrement in force constants Carlos Simmerling (Mon Apr 01 2019 - 04:11:30 PDT)
  - Re: [AMBER] Equilibration in multiple steps with decrement in force constants Priyabrata Das (Mon Apr 01 2019 - 04:30:14 PDT)
    - Re: [AMBER] Equilibration in multiple steps with decrement in force constants Carlos Simmerling (Mon Apr 01 2019 - 06:29:41 PDT)
    - Re: [AMBER] Equilibration in multiple steps with decrement in force constants Priyabrata Das (Mon Apr 01 2019 - 10:04:08 PDT)
    - Re: [AMBER] Equilibration in multiple steps with decrement in force constants Carlos Simmerling (Mon Apr 01 2019 - 11:38:16 PDT)
[AMBER] New compile-issue macOS, CPPTRAJ Gustaf Olsson (Mon Apr 01 2019 - 05:04:14 PDT)
- Re: [AMBER] New compile-issue macOS, CPPTRAJ David A Case (Mon Apr 01 2019 - 07:45:28 PDT)
- Re: [AMBER] New compile-issue macOS, CPPTRAJ Daniel Roe (Mon Apr 01 2019 - 08:18:46 PDT)
  - Re: [AMBER] New compile-issue macOS, CPPTRAJ Gustaf Olsson (Tue Apr 02 2019 - 00:27:58 PDT)
    - Re: [AMBER] New compile-issue macOS, CPPTRAJ Gustaf Olsson (Tue Apr 02 2019 - 06:23:48 PDT)
    - Re: [AMBER] New compile-issue macOS, CPPTRAJ Hai Nguyen (Tue Apr 02 2019 - 06:26:56 PDT)
    - Re: [AMBER] New compile-issue macOS, CPPTRAJ Gustaf Olsson (Tue Apr 02 2019 - 06:40:03 PDT)
    - Re: [AMBER] New compile-issue macOS, CPPTRAJ Hai Nguyen (Tue Apr 02 2019 - 07:20:23 PDT)
    - Re: [AMBER] New compile-issue macOS, CPPTRAJ Gustaf Olsson (Tue Apr 02 2019 - 23:36:19 PDT)
    - Re: [AMBER] New compile-issue macOS, CPPTRAJ David A Case (Wed Apr 03 2019 - 07:36:59 PDT)
    - Re: [AMBER] New compile-issue macOS, CPPTRAJ Gustaf Olsson (Thu Apr 04 2019 - 06:16:01 PDT)
    - Re: [AMBER] New compile-issue macOS, CPPTRAJ Daniel Roe (Thu Apr 04 2019 - 06:30:51 PDT)
    - Re: [AMBER] New compile-issue macOS, CPPTRAJ Gustaf Olsson (Thu Apr 04 2019 - 06:54:53 PDT)
    - Re: [AMBER] New compile-issue macOS, CPPTRAJ David A Case (Fri Apr 05 2019 - 06:01:56 PDT)
    - Re: [AMBER] New compile-issue macOS, CPPTRAJ David A Case (Mon Apr 08 2019 - 04:57:11 PDT)
    - Re: [AMBER] New compile-issue macOS, CPPTRAJ Gustaf Olsson (Mon Apr 08 2019 - 06:48:20 PDT)
    - Re: [AMBER] New compile-issue macOS, CPPTRAJ David A Case (Wed Apr 03 2019 - 05:24:27 PDT)
    - Re: [AMBER] New compile-issue macOS, CPPTRAJ Hai Nguyen (Wed Apr 03 2019 - 05:54:30 PDT)
    - Re: [AMBER] New compile-issue macOS, CPPTRAJ Hai Nguyen (Wed Apr 03 2019 - 05:59:45 PDT)
Re: [AMBER] varying pressure conditions? Shayna Hilburg (Mon Apr 01 2019 - 08:21:07 PDT)
- Re: [AMBER] varying pressure conditions? Carlos Simmerling (Mon Apr 01 2019 - 08:23:06 PDT)
Re: [AMBER] Problems calculating density over distance Lucas Bandeira (Mon Apr 01 2019 - 09:13:25 PDT)
[AMBER] regarding simulation Charu Sharma (JRF) (Tue Apr 02 2019 - 00:55:53 PDT)
- Re: [AMBER] regarding simulation David A Case (Tue Apr 02 2019 - 05:20:38 PDT)
[AMBER] Box with a “separator” Alessandro Mariani (Tue Apr 02 2019 - 02:59:01 PDT)
[AMBER] Negative dihedral angle n glycan simulation Rajarshi Roy (Tue Apr 02 2019 - 04:04:58 PDT)
- Re: [AMBER] Negative dihedral angle n glycan simulation Lachele Foley (Mon Apr 08 2019 - 08:24:16 PDT)
  - Re: [AMBER] Negative dihedral angle n glycan simulation Lachele Foley (Mon Apr 08 2019 - 08:49:58 PDT)
- Re: [AMBER] Negative dihedral angle n glycan simulation Rajarshi Roy (Tue Apr 09 2019 - 00:55:44 PDT)
  - Re: [AMBER] Negative dihedral angle n glycan simulation Lachele Foley (Tue Apr 09 2019 - 10:32:58 PDT)
    - Re: [AMBER] Negative dihedral angle n glycan simulation Lachele Foley (Wed Apr 10 2019 - 12:13:57 PDT)
    - Re: [AMBER] Negative dihedral angle n glycan simulation Irfan Alibay (Thu Apr 11 2019 - 04:43:51 PDT)
    - Re: [AMBER] Negative dihedral angle n glycan simulation Rajarshi Roy (Thu Apr 11 2019 - 09:45:11 PDT)
    - Re: [AMBER] Negative dihedral angle n glycan simulation Rajarshi Roy (Thu Apr 11 2019 - 10:01:20 PDT)
    - Re: [AMBER] Negative dihedral angle n glycan simulation Lachele Foley (Fri Apr 26 2019 - 18:10:18 PDT)
    - Re: [AMBER] Negative dihedral angle n glycan simulation Rajarshi Roy (Fri Apr 26 2019 - 19:20:08 PDT)
[AMBER] leap duplicates bond ('triangular' bond) warning Fabian Glaser (Tue Apr 02 2019 - 05:16:39 PDT)
- Re: [AMBER] leap duplicates bond ('triangular' bond) warning Pietro Aronica (Tue Apr 02 2019 - 05:45:04 PDT)
[AMBER] rms2d analysis Debarati DasGupta (Tue Apr 02 2019 - 11:38:26 PDT)
- Re: [AMBER] rms2d analysis Daniel Roe (Tue Apr 02 2019 - 12:43:54 PDT)
  - Re: [AMBER] rms2d analysis Debarati DasGupta (Wed Apr 03 2019 - 06:20:20 PDT)
[AMBER] KeyError: 4018 for iron containing enzyme (prolyl hydroxylase) Mahesh kumar Teli (Tue Apr 02 2019 - 22:06:32 PDT)
- Re: [AMBER] KeyError: 4018 for iron containing enzyme (prolyl hydroxylase) Aashish Bhatt (Wed Apr 03 2019 - 05:48:11 PDT)
  - Re: [AMBER] KeyError: 4018 for iron containing enzyme (prolyl hydroxylase) Mahesh kumar Teli (Wed Apr 03 2019 - 19:14:48 PDT)
[AMBER] tests with different # of threads Vaibhav Dixit (Wed Apr 03 2019 - 03:26:04 PDT)
- Re: [AMBER] tests with different # of threads David A Case (Wed Apr 03 2019 - 05:30:44 PDT)
  - Re: [AMBER] tests with different # of threads Vaibhav Dixit (Thu Apr 04 2019 - 08:11:38 PDT)
[AMBER] cudaMemcpyToSymbol: SetSim copy to cSim failed invalid device symbol ( GeForce RTX 2080) bjyx20090941 (Wed Apr 03 2019 - 07:24:23 PDT)
- Re: [AMBER] cudaMemcpyToSymbol: SetSim copy to cSim failed invalid device symbol ( GeForce RTX 2080) accuratefreeenergy.gmail.com (Wed Apr 03 2019 - 07:36:36 PDT)
Re: [AMBER] cudaMemcpyToSymbol: SetSim copy to cSim failed bjyx20090941 (Wed Apr 03 2019 - 20:21:49 PDT)
- Re: [AMBER] cudaMemcpyToSymbol: SetSim copy to cSim failed Ross Walker (Thu Apr 04 2019 - 07:36:32 PDT)
[AMBER] mmpbsa error MYRIAN TORRES RICO (Thu Apr 04 2019 - 01:08:44 PDT)
[AMBER] mmpbsa error MYRIAN TORRES RICO (Thu Apr 04 2019 - 02:07:07 PDT)
- Re: [AMBER] mmpbsa error Daniel Roe (Fri Apr 05 2019 - 08:06:08 PDT)
[AMBER] Problem calculating water density over distance Lucas Bandeira (Thu Apr 04 2019 - 13:35:38 PDT)
Re: [AMBER] metal-oxide-metal interactions Pengfei Li (Thu Apr 04 2019 - 17:44:44 PDT)
[AMBER] location related redox-potential? Feng, Zimin (Fri Apr 05 2019 - 09:15:00 PDT)
- Re: [AMBER] location related redox-potential? Cruzeiro,Vinicius Wilian D (Fri Apr 05 2019 - 16:31:36 PDT)
  - Re: [AMBER] location related redox-potential? Feng, Zimin (Sun Apr 07 2019 - 14:34:05 PDT)
[AMBER] Can Amber constant pH run with CHARMM force field? Chen Yifan (Fri Apr 05 2019 - 11:51:35 PDT)
- Re: [AMBER] Can Amber constant pH run with CHARMM force field? Feng, Zimin (Fri Apr 05 2019 - 13:56:57 PDT)
- Re: [AMBER] Can Amber constant pH run with CHARMM force field? Cruzeiro,Vinicius Wilian D (Fri Apr 05 2019 - 16:15:16 PDT)
  - Re: [AMBER] Can Amber constant pH run with CHARMM force field? Chen Yifan (Fri Apr 05 2019 - 19:12:56 PDT)
- Re: [AMBER] Can Amber constant pH run with CHARMM force field? Jason Swails (Sun Apr 07 2019 - 17:19:37 PDT)
[AMBER] 2 job positions InterX Inc. Molecular Simulation and Molecular ForceField Scientists Ganesh Kamath (Fri Apr 05 2019 - 12:58:51 PDT)
[AMBER] outtraj question Xiaoyu Wang (Fri Apr 05 2019 - 15:35:10 PDT)
- Re: [AMBER] outtraj question Daniel Roe (Tue Apr 30 2019 - 07:23:30 PDT)
Re: [AMBER] metal parameters Fabian Glaser (Fri Apr 05 2019 - 21:56:51 PDT)
- Re: [AMBER] metal parameters Pengfei Li (Sat Apr 06 2019 - 14:39:29 PDT)
[AMBER] pmemd.CUDA vs pmemd.MPI for equilibration of protein-ligand and trajectory identification for mmpbsa Prasanth G, Research Scholar (Fri Apr 05 2019 - 23:47:01 PDT)
[AMBER] 2 job positions InterX Inc. Molecular Simulation and Molecular ForceField Scientists Ganesh Kamath (Sat Apr 06 2019 - 08:00:24 PDT)
Re: [AMBER] preparing a new pdb Boutheïna KERKENI (Sun Apr 07 2019 - 03:56:11 PDT)
[AMBER] Ligand Splitting Issue Tamsila Parveen (Sun Apr 07 2019 - 04:21:59 PDT)
- Re: [AMBER] Ligand Splitting Issue David Case (Sun Apr 07 2019 - 18:22:03 PDT)
[AMBER] Error working with pytleap ARITRA MITRA (Mon Apr 08 2019 - 03:58:33 PDT)
- Re: [AMBER] Error working with pytleap David A Case (Mon Apr 08 2019 - 04:44:42 PDT)
[AMBER] Problem in setting parameters for the modified nucleotide Xiaoting Mao (Mon Apr 08 2019 - 06:10:58 PDT)
[AMBER] Creating a water model from scratch Gustavo Seabra (Mon Apr 08 2019 - 11:55:39 PDT)
- Re: [AMBER] Creating a water model from scratch David Cerutti (Mon Apr 08 2019 - 12:36:46 PDT)
[AMBER] secstruct issue in CPPTRAJ SARAH JEANNE LEFAVE (Mon Apr 08 2019 - 13:22:18 PDT)
- Re: [AMBER] secstruct issue in CPPTRAJ Daniel Roe (Wed Apr 10 2019 - 11:28:42 PDT)
  - Re: [AMBER] secstruct issue in CPPTRAJ Daniel Roe (Wed Apr 10 2019 - 12:16:06 PDT)
    - Re: [AMBER] secstruct issue in CPPTRAJ Daniel Roe (Tue Apr 16 2019 - 05:26:58 PDT)
    - Re: [AMBER] [UCE] Re: secstruct issue in CPPTRAJ SARAH JEANNE LEFAVE (Tue Apr 16 2019 - 05:44:35 PDT)
[AMBER] Question about QM/MM simulation in vacuum connecting Amber and Gaussian 09 package 王婷婷 (Mon Apr 08 2019 - 17:36:31 PDT)
- Re: [AMBER] Question about QM/MM simulation in vacuum connecting Amber and Gaussian 09 package Roitberg,Adrian E (Mon Apr 08 2019 - 17:41:56 PDT)
[AMBER] mmpbsa MYRIAN TORRES RICO (Tue Apr 09 2019 - 01:22:16 PDT)
- Re: [AMBER] mmpbsa Chris Moth (Tue Apr 09 2019 - 19:30:18 PDT)
[AMBER] Calculate zero point energy for a protein (no ligand) system Akshay Prabhakant (Tue Apr 09 2019 - 04:42:58 PDT)
- Re: [AMBER] Calculate zero point energy for a protein (no ligand) system Carlos Simmerling (Tue Apr 09 2019 - 04:47:57 PDT)
  - Re: [AMBER] Calculate zero point energy for a protein (no ligand) system Robert Molt (Tue Apr 09 2019 - 05:26:43 PDT)
  - Re: [AMBER] Calculate zero point energy for a protein (no ligand) system Akshay Prabhakant (Tue Apr 09 2019 - 05:32:19 PDT)
    - Re: [AMBER] Calculate zero point energy for a protein (no ligand) system Carlos Simmerling (Tue Apr 09 2019 - 05:36:05 PDT)
    - Re: [AMBER] Calculate zero point energy for a protein (no ligand) system Akshay Prabhakant (Tue Apr 09 2019 - 05:46:42 PDT)
    - Re: [AMBER] Calculate zero point energy for a protein (no ligand) system MOHD HOMAIDUR RAHMAN (Tue Apr 09 2019 - 11:49:17 PDT)
[AMBER] Force field parameters for modified amino acid residues (carboxy glutamates) Tanusree S (Tue Apr 09 2019 - 21:42:30 PDT)
[AMBER] Patches for AmberTools18 viktor drobot (Wed Apr 10 2019 - 04:26:12 PDT)
- Re: [AMBER] Patches for AmberTools18 Stephan Schott (Wed Apr 10 2019 - 05:38:58 PDT)
  - Re: [AMBER] Patches for AmberTools18 Hai Nguyen (Wed Apr 10 2019 - 13:19:11 PDT)
[AMBER] REGARDING MPI Charu Sharma (JRF) (Wed Apr 10 2019 - 11:06:10 PDT)
[AMBER] Question about chemical reaction in vacuum with adding an extra reaction field (Specify dielectric constant in vacuum) 王婷婷 (Wed Apr 10 2019 - 18:03:59 PDT)
- Re: [AMBER] Question about chemical reaction in vacuum with adding an extra reaction field (Specify dielectric constant in vacuum) David A Case (Thu Apr 11 2019 - 06:57:52 PDT)
  - Re: [AMBER] Question about chemical reaction in vacuum with adding an extra reaction field (Specify dielectric constant in vacuum) 王婷婷 (Thu Apr 11 2019 - 18:40:46 PDT)
[AMBER] parameters for isolated zwitter ion tyrosine angad sharma (Wed Apr 10 2019 - 23:15:25 PDT)
- Re: [AMBER] parameters for isolated zwitter ion tyrosine Elvis Martis (Wed Apr 10 2019 - 23:50:29 PDT)
[AMBER] Capping RNA Mihaljevic-Juric Paula (Mme) (Thu Apr 11 2019 - 02:56:08 PDT)
- [AMBER] cReAtInG PDB Boutheïna KERKENI (Thu Apr 11 2019 - 03:13:20 PDT)
  - Re: [AMBER] cReAtInG PDB David A Case (Thu Apr 11 2019 - 07:06:11 PDT)
- Re: [AMBER] Capping RNA David A Case (Thu Apr 11 2019 - 07:03:46 PDT)
[AMBER] T4 vs RTX2080Ti Giovanni Grazioso (Thu Apr 11 2019 - 08:00:42 PDT)
- Re: [AMBER] T4 vs RTX2080Ti Shenglong Wang (Thu Apr 11 2019 - 08:03:00 PDT)
  - Re: [AMBER] T4 vs RTX2080Ti David Cerutti (Fri Apr 12 2019 - 08:21:38 PDT)
[AMBER] COM Dihedral Restraint Kung, Ryan (Thu Apr 11 2019 - 08:23:17 PDT)
- Re: [AMBER] COM Dihedral Restraint Kellon Belfon (Thu Apr 11 2019 - 09:34:45 PDT)
[AMBER] Problem calculating water mass density over distance Lucas Bandeira (Thu Apr 11 2019 - 09:00:23 PDT)
- Re: [AMBER] Problem calculating water mass density over distance Gerardo Zerbetto De Palma (Thu Apr 11 2019 - 09:05:18 PDT)
  - Re: [AMBER] Problem calculating water mass density over distance Lucas Bandeira (Thu Apr 11 2019 - 09:08:47 PDT)
    - Re: [AMBER] Problem calculating water mass density over distance Gerardo Zerbetto De Palma (Thu Apr 11 2019 - 09:37:30 PDT)
    - Re: [AMBER] Problem calculating water mass density over distance Lucas Bandeira (Thu Apr 11 2019 - 09:48:23 PDT)
    - Re: [AMBER] Problem calculating water mass density over distance Gerardo Zerbetto De Palma (Thu Apr 11 2019 - 07:54:08 PDT)
[AMBER] Electrostatic interactions in LIE method Debarati DasGupta (Thu Apr 11 2019 - 10:57:19 PDT)
[AMBER] namd and amber md energies do not match Akshay Prabhakant (Thu Apr 11 2019 - 11:33:01 PDT)
- Re: [AMBER] namd and amber md energies do not match David A Case (Fri Apr 12 2019 - 05:37:56 PDT)
  - Re: [AMBER] namd and amber md energies do not match Akshay Prabhakant (Mon Apr 15 2019 - 23:00:28 PDT)
Re: [AMBER] charged residue mutation free energy Hosein Geraili Daronkola (Fri Apr 12 2019 - 00:04:12 PDT)
[AMBER] Confusion regarding ff14SB and ff99SBildn forcefields RITUPARNA ROY (Fri Apr 12 2019 - 00:09:12 PDT)
- Re: [AMBER] Confusion regarding ff14SB and ff99SBildn forcefields David Cerutti (Fri Apr 12 2019 - 00:36:01 PDT)
[AMBER] How to source oldff in tleap Saikat Pal (Fri Apr 12 2019 - 04:32:54 PDT)
- Re: [AMBER] How to source oldff in tleap Saikat Pal (Fri Apr 12 2019 - 04:43:24 PDT)
- Re: [AMBER] How to source oldff in tleap Carlos Simmerling (Fri Apr 12 2019 - 05:00:25 PDT)
- Re: [AMBER] How to source oldff in tleap David A Case (Fri Apr 12 2019 - 05:47:29 PDT)
[AMBER] Question about NEB Lillian Chong (Fri Apr 12 2019 - 06:02:57 PDT)
[AMBER] Problems in setting parameters for the modified nucleotide Xiaoting Mao (Fri Apr 12 2019 - 06:08:43 PDT)
[AMBER] silver parameters Uroš Javornik (Fri Apr 12 2019 - 06:29:12 PDT)
- Re: [AMBER] silver parameters Christina Bergonzo (Fri Apr 12 2019 - 06:48:50 PDT)
[AMBER] pdb4amber install w/ conda Paul, Austin (Fri Apr 12 2019 - 09:16:21 PDT)
- Re: [AMBER] pdb4amber install w/ conda Hai Nguyen (Fri Apr 12 2019 - 09:49:23 PDT)
  - Re: [AMBER] pdb4amber install w/ conda Hai Nguyen (Fri Apr 12 2019 - 23:14:10 PDT)
[AMBER] Save RST from mdcrd containing velocities Yuliana Bosken (Sat Apr 13 2019 - 02:40:05 PDT)
- Re: [AMBER] Save RST from mdcrd containing velocities Daniel Roe (Thu Apr 18 2019 - 10:59:21 PDT)
Re: [AMBER] Problem in setting parameters for non standard DG residue:O6-Methylguanine Xiaoting Mao (Sat Apr 13 2019 - 02:48:14 PDT)
[AMBER] Guidance on WHAM Daniel Fernández Remacha (Sat Apr 13 2019 - 06:19:01 PDT)
- Re: [AMBER] Guidance on WHAM Zachary Fallon (Tue Apr 16 2019 - 12:23:01 PDT)
  - Re: [AMBER] Guidance on WHAM Carlos Simmerling (Tue Apr 16 2019 - 12:43:34 PDT)
  - Re: [AMBER] Guidance on WHAM Daniel Fernández Remacha (Wed Apr 17 2019 - 03:59:17 PDT)
    - Re: [AMBER] Guidance on WHAM Zachary Fallon (Wed Apr 17 2019 - 10:21:56 PDT)
    - Re: [AMBER] Guidance on WHAM Daniel Fernández Remacha (Thu Apr 18 2019 - 11:28:40 PDT)
    - Re: [AMBER] Guidance on WHAM Zachary Fallon (Thu Apr 18 2019 - 12:35:43 PDT)
[AMBER] RTX 2070 GPU Card Ajeet Kumar Yadav (Mon Apr 15 2019 - 03:02:01 PDT)
[AMBER] Atoms per processor Charo del Genio (Mon Apr 15 2019 - 04:36:10 PDT)
- Re: [AMBER] Atoms per processor David A Case (Mon Apr 15 2019 - 07:37:15 PDT)
[AMBER] mdgx CreateBellyMask error Anthony Bogetti (Mon Apr 15 2019 - 07:50:02 PDT)
- Re: [AMBER] mdgx CreateBellyMask error David Cerutti (Mon Apr 15 2019 - 08:02:08 PDT)
[AMBER] Fixing few box dimensions in semiisotropic/anisotropic pressure scaling Kyeong-jun Jeong (Mon Apr 15 2019 - 13:56:54 PDT)
- Re: [AMBER] Fixing few box dimensions in semiisotropic/anisotropic pressure scaling David A Case (Tue Apr 16 2019 - 06:12:08 PDT)
[AMBER] How to use GaMD in amber16 ATUL KUMAR (Tue Apr 16 2019 - 01:35:25 PDT)
[AMBER] Problems in forcefield parameterization of Mercury Muthukumaran Rajagopalan (Tue Apr 16 2019 - 10:24:35 PDT)
- Re: [AMBER] Problems in forcefield parameterization of Mercury Pengfei Li (Tue Apr 16 2019 - 18:31:35 PDT)
  - Re: [AMBER] Problems in forcefield parameterization of Mercury Muthukumaran Rajagopalan (Tue Apr 16 2019 - 22:36:14 PDT)
    - Re: [AMBER] Problems in forcefield parameterization of Mercury Pengfei Li (Fri Apr 19 2019 - 08:42:20 PDT)
[AMBER] How to select dihedral angles to reweight accelerated molecular dynamics simulation of protein Mayank Dixit (Tue Apr 16 2019 - 17:48:47 PDT)
- Re: [AMBER] How to select dihedral angles to reweight accelerated molecular dynamics simulation of protein Chetna Tyagi (Wed Apr 17 2019 - 00:57:18 PDT)
  - Re: [AMBER] How to select dihedral angles to reweight accelerated molecular dynamics simulation of protein Mayank Dixit (Thu Apr 18 2019 - 07:47:04 PDT)
[AMBER] pKa calculation Tanmoy Paul (Tue Apr 16 2019 - 23:18:58 PDT)
[AMBER] mol2 files for FEW Zhonghua Xia (Wed Apr 17 2019 - 01:33:24 PDT)
- Re: [AMBER] mol2 files for FEW David A Case (Wed Apr 17 2019 - 05:06:50 PDT)
  - Re: [AMBER] mol2 files for FEW Zhonghua Xia (Tue Apr 30 2019 - 07:48:28 PDT)
[AMBER] Mg2+_preparation_general_rule Antonio Amber Carlesso (Wed Apr 17 2019 - 08:27:11 PDT)
- Re: [AMBER] Mg2+_preparation_general_rule Antonio Amber Carlesso (Wed Apr 17 2019 - 09:53:47 PDT)
[AMBER] More macOS compilation issues.... Gustaf Olsson (Thu Apr 18 2019 - 01:20:39 PDT)
- Re: [AMBER] More macOS compilation issues.... Hai Nguyen (Thu Apr 18 2019 - 06:47:08 PDT)
  - Re: [AMBER] More macOS compilation issues.... Gustaf Olsson (Sun Apr 21 2019 - 03:31:39 PDT)
    - Re: [AMBER] More macOS compilation issues.... Gustaf Olsson (Sun Apr 21 2019 - 13:37:05 PDT)
    - Re: [AMBER] More macOS compilation issues.... David A Case (Mon Apr 22 2019 - 13:07:11 PDT)
    - Re: [AMBER] More macOS compilation issues.... Gustaf Olsson (Mon Apr 22 2019 - 22:20:11 PDT)
    - Re: [AMBER] More macOS compilation issues.... Gustaf Olsson (Thu Apr 25 2019 - 13:08:51 PDT)
    - Re: [AMBER] More macOS compilation issues.... Gustaf Olsson (Thu Apr 25 2019 - 23:49:37 PDT)
    - Re: [AMBER] More macOS compilation issues.... David A Case (Fri Apr 26 2019 - 06:48:32 PDT)
    - Re: [AMBER] More macOS compilation issues.... Gustaf Olsson (Fri Apr 26 2019 - 22:48:25 PDT)
- Re: [AMBER] More macOS compilation issues.... David A Case (Thu Apr 18 2019 - 10:33:25 PDT)
[AMBER] AMBER - Heating MD Systems An Ta (Thu Apr 18 2019 - 05:48:37 PDT)
- Re: [AMBER] AMBER - Heating MD Systems Carlos Simmerling (Thu Apr 18 2019 - 06:03:41 PDT)
  - Re: [AMBER] AMBER - Heating MD Systems An Ta (Thu Apr 18 2019 - 06:23:32 PDT)
    - Re: [AMBER] AMBER - Heating MD Systems Carlos Simmerling (Thu Apr 18 2019 - 08:43:54 PDT)
    - Re: [AMBER] AMBER - Heating MD Systems An Ta (Thu Apr 18 2019 - 10:58:58 PDT)
- Re: [AMBER] AMBER - Heating MD Systems Lin Song (Thu Apr 18 2019 - 08:38:30 PDT)
[AMBER] "Problem installing Miniconda" Seibold, Steve Allan (Thu Apr 18 2019 - 08:43:30 PDT)
- Re: [AMBER] "Problem installing Miniconda" Hai Nguyen (Thu Apr 18 2019 - 08:57:55 PDT)
  - Re: [AMBER] "Problem installing Miniconda" David A Case (Thu Apr 18 2019 - 10:55:27 PDT)
    - Re: [AMBER] "Problem installing Miniconda" Hai Nguyen (Thu Apr 18 2019 - 11:00:05 PDT)
    - Re: [AMBER] "Problem installing Miniconda" Seibold, Steve Allan (Thu Apr 18 2019 - 11:44:39 PDT)
[AMBER] Force field for C-C Di-Tyrosine Linkage Bharat Manna (Thu Apr 18 2019 - 03:45:55 PDT)
[AMBER] RTX-2070 supported(untested)? Yeyue Xiong (Thu Apr 18 2019 - 13:29:28 PDT)
- Re: [AMBER] RTX-2070 supported(untested)? David Cerutti (Thu Apr 18 2019 - 14:28:33 PDT)
  - Re: [AMBER] RTX-2070 supported(untested)? Carlos Simmerling (Fri Apr 19 2019 - 05:05:48 PDT)
    - Re: [AMBER] RTX-2070 supported(untested)? Bill Ross (Fri Apr 19 2019 - 05:11:25 PDT)
[AMBER] MM PBSA - clarification Prasanth G, Research Scholar (Fri Apr 19 2019 - 06:14:33 PDT)
- Re: [AMBER] MM PBSA - clarification Ray Luo (Fri Apr 19 2019 - 06:35:12 PDT)
- Re: [AMBER] MM PBSA - clarification Prasanth G, Research Scholar (Sun Apr 21 2019 - 23:17:41 PDT)
  - Re: [AMBER] MM PBSA - clarification Thomas Evangelidis (Mon Apr 22 2019 - 06:31:00 PDT)
[AMBER] smflags in configure script viktor drobot (Fri Apr 19 2019 - 07:19:24 PDT)
- Re: [AMBER] smflags in configure script Charles Lin (Mon Apr 22 2019 - 12:52:10 PDT)
- Re: [AMBER] smflags in configure script David A Case (Mon Apr 22 2019 - 13:03:56 PDT)
[AMBER] trouble in amberFATA: Atom doesn't have a type Maximilien BERNE (Fri Apr 19 2019 - 09:19:14 PDT)
- Re: [AMBER] trouble in amberFATA: Atom doesn't have a type Sally Pias (Fri Apr 19 2019 - 12:09:19 PDT)
[AMBER] Change the trajectory format. Parviz Seifpanahi Shabane (Fri Apr 19 2019 - 12:12:39 PDT)
- Re: [AMBER] Change the trajectory format. Thomas Cheatham (Wed Apr 24 2019 - 23:15:14 PDT)
  - Re: [AMBER] Change the trajectory format. Daniel Roe (Thu Apr 25 2019 - 04:54:18 PDT)
[AMBER] possible bug in charmmlipid2amber.py liu junjun (Mon Apr 22 2019 - 00:14:17 PDT)
[AMBER] Suggestions on running a qm-mm simulation for studying a group transfer reaction Prayagraj Fandilolu (Mon Apr 22 2019 - 05:43:24 PDT)
[AMBER] regarding radius of gyration angad sharma (Mon Apr 22 2019 - 06:03:04 PDT)
- Re: [AMBER] regarding radius of gyration Carlos Simmerling (Mon Apr 22 2019 - 07:02:36 PDT)
[AMBER] Computing forces by trajectory post-processing with sander Casalini Tommaso (Mon Apr 22 2019 - 12:54:10 PDT)
- Re: [AMBER] Computing forces by trajectory post-processing with sander Alen Ahmetovic (Mon Apr 22 2019 - 16:50:40 PDT)
  - Re: [AMBER] Computing forces by trajectory post-processing with sander Yuliana Bosken (Mon Apr 22 2019 - 20:44:34 PDT)
- Re: [AMBER] Computing forces by trajectory post-processing with sander Daniel Roe (Tue Apr 23 2019 - 06:56:30 PDT)
  - Re: [AMBER] Computing forces by trajectory post-processing with sander Casalini Tommaso (Wed Apr 24 2019 - 01:09:51 PDT)
[AMBER] problem in locating Aqvist Mg2+ parameter in amber ATUL KUMAR (Mon Apr 22 2019 - 21:52:18 PDT)
- Re: [AMBER] problem in locating Aqvist Mg2+ parameter in amber David Case (Tue Apr 23 2019 - 05:23:49 PDT)
[AMBER] A-DNA Charu Sharma (JRF) (Mon Apr 22 2019 - 22:17:26 PDT)
- Re: [AMBER] A-DNA David Case (Tue Apr 23 2019 - 05:13:52 PDT)
  - Re: [AMBER] A-DNA Charu Sharma (JRF) (Tue Apr 23 2019 - 11:51:09 PDT)
[AMBER] Issue with cpptraj.MPI Benard, Dany (Tue Apr 23 2019 - 05:44:23 PDT)
- Re: [AMBER] Issue with cpptraj.MPI Pratul Agarwal (Tue Apr 23 2019 - 05:52:05 PDT)
  - Re: [AMBER] Issue with cpptraj.MPI Pratul Agarwal (Tue Apr 23 2019 - 05:58:41 PDT)
  - Re: [AMBER] Issue with cpptraj.MPI Benard, Dany (Tue Apr 23 2019 - 06:01:36 PDT)
    - Re: [AMBER] Issue with cpptraj.MPI Daniel Roe (Tue Apr 23 2019 - 06:34:31 PDT)
- Re: [AMBER] Issue with cpptraj.MPI Daniel Roe (Tue Apr 23 2019 - 05:52:46 PDT)
[AMBER] saving output of Gaussian accelerated MD Qinghua Liao (Tue Apr 23 2019 - 07:41:28 PDT)
[AMBER] charge in constant redox cein file vs. prmtop file Feng, Zimin (Tue Apr 23 2019 - 15:03:24 PDT)
- Re: [AMBER] charge in constant redox cein file vs. prmtop file Cruzeiro,Vinicius Wilian D (Tue Apr 23 2019 - 15:51:31 PDT)
  - Re: [AMBER] charge in constant redox cein file vs. prmtop file Feng, Zimin (Wed Apr 24 2019 - 09:14:30 PDT)
    - Re: [AMBER] charge in constant redox cein file vs. prmtop file Cruzeiro,Vinicius Wilian D (Wed Apr 24 2019 - 09:51:12 PDT)
    - Re: [AMBER] charge in constant redox cein file vs. prmtop file Feng, Zimin (Wed Apr 24 2019 - 11:10:41 PDT)
[AMBER] styrene sulfonate molecule building using xleap Shilpa Gupta (Tue Apr 23 2019 - 23:32:36 PDT)
- Re: [AMBER] styrene sulfonate molecule building using xleap David A Case (Wed Apr 24 2019 - 04:45:08 PDT)
[AMBER] Problem with heating the system ATUL KUMAR (Wed Apr 24 2019 - 01:57:34 PDT)
- Re: [AMBER] Problem with heating the system Bill Ross (Wed Apr 24 2019 - 01:49:56 PDT)
  - Re: [AMBER] Problem with heating the system ATUL KUMAR (Wed Apr 24 2019 - 02:06:52 PDT)
- Re: [AMBER] Problem with heating the system David A Case (Wed Apr 24 2019 - 04:47:18 PDT)
  - Re: [AMBER] Problem with heating the system ATUL KUMAR (Wed Apr 24 2019 - 04:53:58 PDT)
    - Re: [AMBER] Problem with heating the system Pratul Agarwal (Wed Apr 24 2019 - 05:14:12 PDT)
[AMBER] secondary structure angad sharma (Wed Apr 24 2019 - 04:32:53 PDT)
- Re: [AMBER] secondary structure Carlos Simmerling (Wed Apr 24 2019 - 04:59:50 PDT)
[AMBER] Targeted MD Elena Gomez (Thu Apr 25 2019 - 01:08:18 PDT)
- Re: [AMBER] Targeted MD Carlos Simmerling (Thu Apr 25 2019 - 05:01:37 PDT)
[AMBER] issues with pmemd.cuda Veenis, Andrew Jay (Thu Apr 25 2019 - 08:11:46 PDT)
- Re: [AMBER] issues with pmemd.cuda David A Case (Thu Apr 25 2019 - 10:43:32 PDT)
  - Re: [AMBER] issues with pmemd.cuda Veenis, Andrew Jay (Fri Apr 26 2019 - 07:08:02 PDT)
[AMBER] processing trajectories subjected to GIST analysis Alfredo Quevedo (Tue Apr 23 2019 - 23:19:47 PDT)
- Re: [AMBER] processing trajectories subjected to GIST analysis Daniel Roe (Tue Apr 30 2019 - 06:58:42 PDT)
[AMBER] Simulation with Protein, cofactor and Ligand Prasanth G, Research Scholar (Thu Apr 25 2019 - 11:41:05 PDT)
[AMBER] Antechamber question David Poole (Thu Apr 25 2019 - 16:03:37 PDT)
[AMBER] setting up triplicate runs Yin, Guowei (Thu Apr 25 2019 - 18:08:00 PDT)
- Re: [AMBER] setting up triplicate runs David Cerutti (Thu Apr 25 2019 - 19:02:45 PDT)
[AMBER] dihedral scanning with GAFF and GAFF2 Qasim Pars (Fri Apr 26 2019 - 03:22:33 PDT)
[AMBER] Any help on how to implement it in cpptraj? Debarati DasGupta (Fri Apr 26 2019 - 09:25:11 PDT)
- Re: [AMBER] Any help on how to implement it in cpptraj? Daniel Roe (Tue Apr 30 2019 - 06:43:21 PDT)
[AMBER] Release of AmberTools19 David Case (Fri Apr 26 2019 - 17:59:43 PDT)
[AMBER] AmberTools19 - macOS 10.14.4 - Xcode 10.2.1 - clang Gustaf Olsson (Sat Apr 27 2019 - 05:58:27 PDT)
- Re: [AMBER] AmberTools19 - macOS 10.14.4 - Xcode 10.2.1 - clang Hai Nguyen (Sat Apr 27 2019 - 09:36:49 PDT)
  - Re: [AMBER] AmberTools19 - macOS 10.14.4 - Xcode 10.2.1 - clang Gustaf Olsson (Sat Apr 27 2019 - 11:25:03 PDT)
- Re: [AMBER] AmberTools19 - macOS 10.14.4 - Xcode 10.2.1 - clang David Case (Sun Apr 28 2019 - 09:49:13 PDT)
  - Re: [AMBER] AmberTools19 - macOS 10.14.4 - Xcode 10.2.1 - clang Gustaf Olsson (Sun Apr 28 2019 - 14:12:38 PDT)
[AMBER] NpT simulations in interfacial system Lucas Bandeira (Sat Apr 27 2019 - 07:38:33 PDT)
- Re: [AMBER] NpT simulations in interfacial system David Case (Sun Apr 28 2019 - 09:56:50 PDT)
[AMBER] AmberTools19 - macOS 10.14.4 - Xcode 10.2.1 - GCC8.3 Gustaf Olsson (Sat Apr 27 2019 - 11:44:00 PDT)
[AMBER] xleap display Yin, Guowei (Sat Apr 27 2019 - 14:49:20 PDT)
- Re: [AMBER] xleap display Bill Ross (Sat Apr 27 2019 - 15:49:56 PDT)
  - Re: [AMBER] xleap display Bill Ross (Sat Apr 27 2019 - 15:57:41 PDT)
  - Re: [AMBER] xleap display Yin, Guowei (Sat Apr 27 2019 - 19:54:15 PDT)
    - Re: [AMBER] xleap display Bill Ross (Sat Apr 27 2019 - 21:28:56 PDT)
- Re: [AMBER] xleap display Pratul Agarwal (Sat Apr 27 2019 - 16:02:31 PDT)
  - Re: [AMBER] xleap display Bill Ross (Sat Apr 27 2019 - 16:31:50 PDT)
- Re: [AMBER] xleap display Gustaf Olsson (Sun Apr 28 2019 - 05:58:47 PDT)
[AMBER] Novel Force Field Parameters for Aromatic Dihedrals Erdem Yeler (Sun Apr 28 2019 - 13:09:41 PDT)
[AMBER] WHAM umbrella PMF of ligand Z diffusion on lipid molecule zmatovic.kg.ac.rs (Mon Apr 29 2019 - 04:05:27 PDT)
[AMBER] constant-pressure equilibration with a water droplet Anthony Bogetti (Mon Apr 29 2019 - 08:37:40 PDT)
- Re: [AMBER] constant-pressure equilibration with a water droplet Carlos Simmerling (Mon Apr 29 2019 - 09:07:25 PDT)
- Re: [AMBER] constant-pressure equilibration with a water droplet David A Case (Mon Apr 29 2019 - 11:06:09 PDT)
[AMBER] Why is SPAM throwing errors when I see none in my input files or trajectories. Debarati DasGupta (Mon Apr 29 2019 - 13:25:58 PDT)
- Re: [AMBER] Why is SPAM throwing errors when I see none in my input files or trajectories. Daniel Roe (Tue Apr 30 2019 - 06:12:07 PDT)
[AMBER] Regarding cosine content calculation in AMBER Rajarshi Roy (Mon Apr 29 2019 - 22:22:40 PDT)
- Re: [AMBER] Regarding cosine content calculation in AMBER Daniel Roe (Tue Apr 30 2019 - 06:16:45 PDT)
  - Re: [AMBER] Regarding cosine content calculation in AMBER Rajarshi Roy (Tue Apr 30 2019 - 08:47:39 PDT)
    - Re: [AMBER] Regarding cosine content calculation in AMBER Pratul Agarwal (Tue Apr 30 2019 - 08:53:56 PDT)
    - Re: [AMBER] Regarding cosine content calculation in AMBER Rajarshi Roy (Tue Apr 30 2019 - 09:14:09 PDT)
    - Re: [AMBER] Regarding cosine content calculation in AMBER Pratul Agarwal (Tue Apr 30 2019 - 09:46:56 PDT)
    - Re: [AMBER] Regarding cosine content calculation in AMBER Rajarshi Roy (Tue Apr 30 2019 - 10:39:37 PDT)
[AMBER] mmpbsa error MYRIAN TORRES RICO (Tue Apr 30 2019 - 02:01:54 PDT)
- Re: [AMBER] mmpbsa error David A Case (Tue Apr 30 2019 - 04:28:17 PDT)
  - Re: [AMBER] mmpbsa error MYRIAN TORRES RICO (Tue Apr 30 2019 - 09:28:57 PDT)
[AMBER] CPPTRAJ gnu extension not working anu chandra (Tue Apr 30 2019 - 10:00:08 PDT)
[AMBER] [rok.ucsd.edu: AT19 cpptraj MPI build issue (Linux, x86_64, gnu)] David A Case (Tue Apr 30 2019 - 12:55:23 PDT)

Amber Archive Apr 2019 by thread