Amber Archive Oct 2016: by thread

[AMBER] SHAKE problem ABHIJEET CHOWDHURY (Sat Oct 01 2016 - 04:40:07 PDT)
- Re: [AMBER] SHAKE problem Carlos Simmerling (Sat Oct 01 2016 - 05:29:31 PDT)
- Re: [AMBER] SHAKE problem Bill Ross (Sat Oct 01 2016 - 05:32:45 PDT)
  - Re: [AMBER] SHAKE problem ABHIJEET CHOWDHURY (Sat Oct 01 2016 - 07:41:21 PDT)
Re: [AMBER] on periodic conditions and unspecified launch failure Elisa Pieri (Sun Oct 02 2016 - 11:02:25 PDT)
- Re: [AMBER] on periodic conditions and unspecified launch failure Jason Swails (Mon Oct 03 2016 - 06:24:04 PDT)
Re: [AMBER] MMPBSA.py error Your ligand residues must be sequential in your complex maryam azimzadehirani (Sun Oct 02 2016 - 17:53:23 PDT)
- Re: [AMBER] MMPBSA.py error Your ligand residues must be sequential in your complex Jason Swails (Mon Oct 03 2016 - 08:00:04 PDT)
  - Re: [AMBER] MMPBSA.py error Your ligand residues must be sequential in your complex maryam azimzadehirani (Mon Oct 03 2016 - 20:11:51 PDT)
[AMBER] MMPBSA.py TrajError: Could not find number of frames in MMPBSA.mdcrd maryam azimzadehirani (Sun Oct 02 2016 - 18:01:24 PDT)
- Re: [AMBER] MMPBSA.py TrajError: Could not find number of frames in MMPBSA.mdcrd Hai Nguyen (Sun Oct 02 2016 - 18:21:30 PDT)
[AMBER] Got an error on tleap Elka Firmanda (Sun Oct 02 2016 - 22:31:34 PDT)
- Re: [AMBER] Got an error on tleap Bill Ross (Sun Oct 02 2016 - 22:46:15 PDT)
- Re: [AMBER] Got an error on tleap David A Case (Mon Oct 03 2016 - 04:36:49 PDT)
[AMBER] MM-PBSA result for small molecule-receptor complex Maryam Hamzehee (Sun Oct 02 2016 - 23:49:20 PDT)
- Re: [AMBER] MM-PBSA result for small molecule-receptor complex David A Case (Mon Oct 03 2016 - 04:44:02 PDT)
  - Re: [AMBER] MM-PBSA result for small molecule-receptor complex Bruno Falcone (Mon Oct 03 2016 - 10:07:14 PDT)
    - Re: [AMBER] MM-PBSA result for small molecule-receptor complex Maryam Hamzehee (Tue Oct 04 2016 - 01:25:47 PDT)
    - Re: [AMBER] MM-PBSA result for small molecule-receptor complex David A Case (Tue Oct 04 2016 - 05:17:07 PDT)
    - Re: [AMBER] MM-PBSA result for small molecule-receptor complex Bruno Falcone (Tue Oct 04 2016 - 06:58:31 PDT)
Re: [AMBER] setup time with pmemd.cuda Hannes Loeffler (Mon Oct 03 2016 - 01:07:02 PDT)
[AMBER] Increase titratable groups Orion Shih (Mon Oct 03 2016 - 02:54:20 PDT)
- Re: [AMBER] Increase titratable groups Jason Swails (Mon Oct 03 2016 - 06:24:35 PDT)
[AMBER] WHAM_ANALYSIS Thakur, Abhishek (Mon Oct 03 2016 - 12:49:46 PDT)
[AMBER] missing windows qm/mm Thakur, Abhishek (Mon Oct 03 2016 - 13:50:22 PDT)
[AMBER] Failing to compile AmberTools16 on Mac Sierra with Fink Alan (Mon Oct 03 2016 - 14:26:26 PDT)
- Re: [AMBER] Failing to compile AmberTools16 on Mac Sierra with Fink Jason Swails (Mon Oct 03 2016 - 16:32:12 PDT)
[AMBER] did not find amber.python xwnail2003.163.com (Tue Oct 04 2016 - 04:38:12 PDT)
- Re: [AMBER] did not find amber.python Bill Ross (Tue Oct 04 2016 - 04:54:19 PDT)
- Re: [AMBER] did not find amber.python David A Case (Tue Oct 04 2016 - 18:00:13 PDT)
[AMBER] time step changes during long simulation run Hirdesh Kumar (Tue Oct 04 2016 - 05:48:27 PDT)
- Re: [AMBER] time step changes during long simulation run Jason Swails (Tue Oct 04 2016 - 06:21:55 PDT)
  - Re: [AMBER] time step changes during long simulation run Hirdesh Kumar (Tue Oct 04 2016 - 06:26:40 PDT)
[AMBER] MD simulation by amber Atila Petrosian (Tue Oct 04 2016 - 09:52:25 PDT)
[AMBER] drmsd to reference with different mask Vlad Cojocaru (Tue Oct 04 2016 - 14:14:28 PDT)
- Re: [AMBER] drmsd to reference with different mask Daniel Roe (Wed Oct 05 2016 - 05:56:06 PDT)
  - Re: [AMBER] drmsd to reference with different mask Vlad Cojocaru (Wed Oct 05 2016 - 06:13:24 PDT)
    - Re: [AMBER] drmsd to reference with different mask Daniel Roe (Wed Oct 05 2016 - 06:48:38 PDT)
Re: [AMBER] AMBER Digest, Vol 1717, Issue 1 xwnail2003.163.com (Tue Oct 04 2016 - 15:50:45 PDT)
[AMBER] Amber14 using triple GTX 1080 Yohanes Gultom (Wed Oct 05 2016 - 04:59:09 PDT)
- Re: [AMBER] Amber14 using triple GTX 1080 Elka Firmanda (Wed Oct 05 2016 - 06:04:25 PDT)
- Re: [AMBER] Amber14 using triple GTX 1080 David A Case (Wed Oct 05 2016 - 07:18:24 PDT)
  - Re: [AMBER] Amber14 using triple GTX 1080 Yohanes Gultom (Wed Oct 05 2016 - 07:50:04 PDT)
[AMBER] hbond cutoff for %occupancy in series data (.gnu file) Hirdesh Kumar (Wed Oct 05 2016 - 05:10:45 PDT)
- Re: [AMBER] hbond cutoff for %occupancy in series data (.gnu file) Daniel Roe (Thu Oct 13 2016 - 06:26:32 PDT)
[AMBER] QM/MM calculation on protein+ligand (covalently bond) Corum, Katharine W (Wed Oct 05 2016 - 08:05:19 PDT)
[AMBER] update the reference structure along trajectory kurisaki (Wed Oct 05 2016 - 23:12:55 PDT)
- Re: [AMBER] update the reference structure along trajectory Daniel Roe (Thu Oct 13 2016 - 06:30:31 PDT)
[AMBER] issue regarding GLYCAM and amber FF Mahrukh Imtiaz (Wed Oct 05 2016 - 23:46:10 PDT)
- Re: [AMBER] issue regarding GLYCAM and amber FF David A Case (Thu Oct 06 2016 - 05:11:03 PDT)
  - Re: [AMBER] issue regarding GLYCAM and amber FF Mahrukh Imtiaz (Thu Oct 06 2016 - 05:19:11 PDT)
  - Re: [AMBER] issue regarding GLYCAM and amber FF Lachele Foley (Thu Oct 06 2016 - 08:45:07 PDT)
[AMBER] zn parameters Stefania Mirabella (Thu Oct 06 2016 - 06:34:06 PDT)
- Re: [AMBER] zn parameters Jacopo Sgrignani (Thu Oct 06 2016 - 06:53:10 PDT)
  - Re: [AMBER] zn parameters Stefania Mirabella (Thu Oct 13 2016 - 05:37:51 PDT)
[AMBER] Creating an AMBER input to Gaussian Aseel Bala (Thu Oct 06 2016 - 09:27:00 PDT)
- Re: [AMBER] Creating an AMBER input to Gaussian Daniel Roe (Thu Oct 06 2016 - 17:45:46 PDT)
[AMBER] Best practice for charmm to AMBER conversion with HEME group Korey M Reid (Thu Oct 06 2016 - 11:08:08 PDT)
- Re: [AMBER] Best practice for charmm to AMBER conversion with HEME group David A Case (Fri Oct 07 2016 - 08:55:27 PDT)
  - Re: [AMBER] Best practice for charmm to AMBER conversion with HEME group Korey M Reid (Fri Oct 07 2016 - 16:09:42 PDT)
    - Re: [AMBER] Best practice for charmm to AMBER conversion with HEME group David A Case (Sat Oct 08 2016 - 17:45:46 PDT)
[AMBER] Amber compilation problems Fabrício Bracht (Thu Oct 06 2016 - 13:01:34 PDT)
- Re: [AMBER] Amber compilation problems David A Case (Fri Oct 07 2016 - 08:48:43 PDT)
[AMBER] AF-NMR (Shifts5.1) for Nonstandard Residue Eleftherios A P Lambros (Thu Oct 06 2016 - 18:42:06 PDT)
[AMBER] GIST hydration analysis of big interface Sergey Samsonov (Fri Oct 07 2016 - 07:22:53 PDT)
- Re: [AMBER] GIST hydration analysis of big interface Steven Ramsey (Fri Oct 07 2016 - 07:56:43 PDT)
  - Re: [AMBER] GIST hydration analysis of big interface Steven Ramsey (Fri Oct 07 2016 - 08:31:39 PDT)
    - Re: [AMBER] GIST hydration analysis of big interface Sergey Samsonov (Sun Oct 09 2016 - 22:57:44 PDT)
[AMBER] Compiling Amber16 Daniel G. Oblinsky (Fri Oct 07 2016 - 08:21:06 PDT)
- Re: [AMBER] Compiling Amber16 Hai Nguyen (Fri Oct 07 2016 - 08:31:23 PDT)
[AMBER] Bug report for pdb4amber code (amber16) Yusuf Simsek (Fri Oct 07 2016 - 14:37:17 PDT)
- Re: [AMBER] Bug report for pdb4amber code (amber16) Hai Nguyen (Sat Oct 08 2016 - 10:11:53 PDT)
[AMBER] AmberTools16 Installation with openMPI fails? Ucisik, Melek Nihan (Fri Oct 07 2016 - 15:23:44 PDT)
- Re: [AMBER] AmberTools16 Installation with openMPI fails? Hai Nguyen (Fri Oct 07 2016 - 15:26:54 PDT)
- Re: [AMBER] AmberTools16 Installation with openMPI fails? Charles Lin (Fri Oct 07 2016 - 15:30:32 PDT)
  - Re: [AMBER] AmberTools16 Installation with openMPI fails? Ucisik, Melek Nihan (Sat Oct 08 2016 - 09:56:31 PDT)
    - Re: [AMBER] AmberTools16 Installation with openMPI fails? Ucisik, Melek Nihan (Mon Oct 10 2016 - 10:39:55 PDT)
    - Re: [AMBER] AmberTools16 Installation with openMPI fails? Marcelo Andrade Chagas (Mon Oct 10 2016 - 10:53:42 PDT)
    - Re: [AMBER] AmberTools16 Installation with openMPI fails? Gulsevin,Alican (Mon Oct 10 2016 - 11:02:44 PDT)
    - Re: [AMBER] AmberTools16 Installation with openMPI fails? Hai Nguyen (Mon Oct 10 2016 - 11:09:21 PDT)
    - Re: [AMBER] AmberTools16 Installation with openMPI fails? Daniel Roe (Wed Oct 12 2016 - 06:30:32 PDT)
[AMBER] Problem with aMD on membrane protein and/or the amd.log file filip fratev (Fri Oct 07 2016 - 20:02:36 PDT)
- Re: [AMBER] Problem with aMD on membrane protein and/or the amd.log file Samuel Bowerman (Sat Oct 08 2016 - 05:39:51 PDT)
  - Re: [AMBER] Problem with aMD on membrane protein and/or the amd.log file Filip Fratev (Sat Oct 08 2016 - 13:31:46 PDT)
[AMBER] mm_pbsa.pl error: Found unknown atflg DC 康宁 (Sat Oct 08 2016 - 02:04:06 PDT)
[AMBER] cpptraj and selection Dhiraj Srivastava (Sun Oct 09 2016 - 18:56:08 PDT)
- Re: [AMBER] cpptraj and selection Daniel Roe (Thu Oct 13 2016 - 05:50:40 PDT)
[AMBER] Steered MD collective variables abdennour braka (Mon Oct 10 2016 - 00:46:39 PDT)
- Re: [AMBER] Steered MD collective variables Feng Pan (Mon Oct 10 2016 - 13:51:52 PDT)
[AMBER] mmpbsa with atomic radii for ff14SB and parmbsc1 atom types Vlad Cojocaru (Tue Oct 11 2016 - 05:36:50 PDT)
- Re: [AMBER] mmpbsa with atomic radii for ff14SB and parmbsc1 atom types Vlad Cojocaru (Tue Oct 11 2016 - 05:42:25 PDT)
- Re: [AMBER] mmpbsa with atomic radii for ff14SB and parmbsc1 atom types Carlos Simmerling (Tue Oct 11 2016 - 05:57:04 PDT)
  - Re: [AMBER] mmpbsa with atomic radii for ff14SB and parmbsc1 atom types Vlad Cojocaru (Tue Oct 11 2016 - 06:12:19 PDT)
    - Re: [AMBER] mmpbsa with atomic radii for ff14SB and parmbsc1 atom types Niel Henriksen (Tue Oct 11 2016 - 07:10:54 PDT)
[AMBER] amb2gmx.pl (sh: rdparm: command not found) shahab shariati (Tue Oct 11 2016 - 09:32:40 PDT)
- Re: [AMBER] amb2gmx.pl (sh: rdparm: command not found) David A Case (Tue Oct 11 2016 - 10:52:22 PDT)
  - Re: [AMBER] amb2gmx.pl (sh: rdparm: command not found) Lorenzo Gontrani (Tue Oct 11 2016 - 11:17:52 PDT)
  - Re: [AMBER] amb2gmx.pl (sh: rdparm: command not found) shahab shariati (Tue Oct 11 2016 - 11:50:17 PDT)
    - Re: [AMBER] amb2gmx.pl (sh: rdparm: command not found) Alan (Tue Oct 11 2016 - 14:48:22 PDT)
    - Re: [AMBER] amb2gmx.pl (sh: rdparm: command not found) David A Case (Tue Oct 11 2016 - 17:59:33 PDT)
    - Re: [AMBER] amb2gmx.pl (sh: rdparm: command not found) shahab shariati (Wed Oct 12 2016 - 05:18:15 PDT)
    - Re: [AMBER] amb2gmx.pl (sh: rdparm: command not found) Daniel Roe (Wed Oct 12 2016 - 06:32:06 PDT)
    - Re: [AMBER] amb2gmx.pl (sh: rdparm: command not found) shahab shariati (Wed Oct 12 2016 - 12:19:51 PDT)
- Re: [AMBER] amb2gmx.pl (sh: rdparm: command not found) Hai Nguyen (Tue Oct 11 2016 - 10:59:39 PDT)
[AMBER] tleap loadamberparams failing on OSX Stefan Doerr (Tue Oct 11 2016 - 09:48:13 PDT)
- Re: [AMBER] tleap loadamberparams failing on OSX Gulsevin,Alican (Tue Oct 11 2016 - 09:58:01 PDT)
  - Re: [AMBER] tleap loadamberparams failing on OSX Stefan Doerr (Tue Oct 11 2016 - 14:43:23 PDT)
    - Re: [AMBER] tleap loadamberparams failing on OSX Bill Ross (Tue Oct 11 2016 - 15:03:34 PDT)
    - Re: [AMBER] tleap loadamberparams failing on OSX Hai Nguyen (Tue Oct 11 2016 - 15:08:49 PDT)
    - Re: [AMBER] tleap loadamberparams failing on OSX Jason Swails (Wed Oct 12 2016 - 05:09:04 PDT)
    - Re: [AMBER] tleap loadamberparams failing on OSX Stefan Doerr (Wed Oct 12 2016 - 06:13:00 PDT)
[AMBER] Ligand across membrane Fabrício Bracht (Tue Oct 11 2016 - 14:06:40 PDT)
- Re: [AMBER] Ligand across membrane Charles Lin (Tue Oct 11 2016 - 14:14:24 PDT)
  - Re: [AMBER] Ligand across membrane Fabrício Bracht (Tue Oct 11 2016 - 17:26:15 PDT)
    - Re: [AMBER] Ligand across membrane Dickson, Callum J (Wed Oct 12 2016 - 06:52:03 PDT)
    - Re: [AMBER] Ligand across membrane Fabrício Bracht (Thu Oct 13 2016 - 07:40:18 PDT)
[AMBER] MMPBSA results with Amber 12 versus Amber 16 Vlad Cojocaru (Wed Oct 12 2016 - 01:31:57 PDT)
- Re: [AMBER] MMPBSA results with Amber 12 versus Amber 16 Ray Luo (Wed Oct 12 2016 - 01:44:09 PDT)
  - Re: [AMBER] MMPBSA results with Amber 12 versus Amber 16 Vlad Cojocaru (Thu Oct 13 2016 - 01:47:29 PDT)
    - Re: [AMBER] MMPBSA results with Amber 12 versus Amber 16 Vlad Cojocaru (Thu Oct 13 2016 - 08:43:47 PDT)
    - Re: [AMBER] MMPBSA results with Amber 12 versus Amber 16 Ray Luo (Thu Oct 13 2016 - 15:23:27 PDT)
    - Re: [AMBER] MMPBSA results with Amber 12 versus Amber 16 Vlad Cojocaru (Fri Oct 14 2016 - 01:42:44 PDT)
    - Re: [AMBER] MMPBSA results with Amber 12 versus Amber 16 Ray Luo (Fri Oct 14 2016 - 08:44:17 PDT)
    - Re: [AMBER] MMPBSA results with Amber 12 versus Amber 16 Ray Luo (Fri Oct 14 2016 - 09:34:23 PDT)
    - Re: [AMBER] MMPBSA results with Amber 12 versus Amber 16 Vlad Cojocaru (Fri Oct 14 2016 - 10:35:02 PDT)
    - Re: [AMBER] MMPBSA results with Amber 12 versus Amber 16 Ray Luo (Fri Oct 14 2016 - 11:29:14 PDT)
    - Re: [AMBER] MMPBSA results with Amber 12 versus Amber 16 Vlad Cojocaru (Fri Oct 14 2016 - 11:38:49 PDT)
    - Re: [AMBER] MMPBSA results with Amber 12 versus Amber 16 Ray Luo (Tue Oct 18 2016 - 10:47:30 PDT)
    - Re: [AMBER] MMPBSA results with Amber 12 versus Amber 16 Vlad Cojocaru (Tue Oct 18 2016 - 14:21:51 PDT)
    - Re: [AMBER] MMPBSA results with Amber 12 versus Amber 16 Ray Luo (Tue Oct 18 2016 - 16:26:43 PDT)
    - Re: [AMBER] MMPBSA results with Amber 12 versus Amber 16 Vlad Cojocaru (Wed Oct 19 2016 - 02:19:57 PDT)
    - Re: [AMBER] MMPBSA results with Amber 12 versus Amber 16 Vlad Cojocaru (Wed Oct 19 2016 - 02:28:33 PDT)
    - Re: [AMBER] MMPBSA results with Amber 12 versus Amber 16 Vlad Cojocaru (Fri Oct 14 2016 - 10:40:23 PDT)
Re: [AMBER] Disparities in H-bond lifetimes calculated through different approaches Daniel Roe (Wed Oct 12 2016 - 07:07:25 PDT)
[AMBER] pbsa eneopt = 4 option Vlad Cojocaru (Wed Oct 12 2016 - 07:44:58 PDT)
- Re: [AMBER] pbsa eneopt = 4 option Ray Luo (Wed Oct 12 2016 - 08:32:36 PDT)
  - Re: [AMBER] pbsa eneopt = 4 option Vlad Cojocaru (Wed Oct 12 2016 - 10:03:51 PDT)
    - Re: [AMBER] pbsa eneopt = 4 option Ray Luo (Wed Oct 12 2016 - 11:41:18 PDT)
[AMBER] cpptraj grid output George Tzotzos (Wed Oct 12 2016 - 08:39:01 PDT)
- Re: [AMBER] cpptraj grid output Daniel Roe (Thu Oct 13 2016 - 05:45:04 PDT)
[AMBER] Correctly defining keywords in cpptraj - radial Stregone (Wed Oct 12 2016 - 15:45:36 PDT)
- Re: [AMBER] Correctly defining keywords in cpptraj - radial Daniel Roe (Thu Oct 13 2016 - 05:41:15 PDT)
  - Re: [AMBER] Correctly defining keywords in cpptraj - radial Stregone (Fri Oct 14 2016 - 05:19:36 PDT)
    - Re: [AMBER] Correctly defining keywords in cpptraj - radial Daniel Roe (Fri Oct 14 2016 - 06:41:08 PDT)
    - Re: [AMBER] Correctly defining keywords in cpptraj - radial Stregone (Fri Oct 14 2016 - 07:24:51 PDT)
[AMBER] cpptraj rmsd unit nm. Saman Yousuf ali (Thu Oct 13 2016 - 04:27:47 PDT)
- Re: [AMBER] cpptraj rmsd unit nm. Daniel Roe (Thu Oct 13 2016 - 05:32:53 PDT)
- Re: [AMBER] cpptraj rmsd unit nm. Daniel Roe (Fri Oct 14 2016 - 06:53:40 PDT)
Re: [AMBER] Cpptraj-PCA Warning Daniel Roe (Thu Oct 13 2016 - 06:14:51 PDT)
[AMBER] cpptraj nativecontacts George Tzotzos (Thu Oct 13 2016 - 06:57:29 PDT)
- Re: [AMBER] cpptraj nativecontacts Daniel Roe (Thu Oct 13 2016 - 07:17:11 PDT)
[AMBER] How to get average from 3 repeated tracjectory Setyanto Md (Thu Oct 13 2016 - 07:50:09 PDT)
- Re: [AMBER] How to get average from 3 repeated tracjectory Nhai (Thu Oct 13 2016 - 08:00:22 PDT)
  - Re: [AMBER] How to get average from 3 repeated tracjectory Setyanto Md (Thu Oct 13 2016 - 08:08:45 PDT)
    - Re: [AMBER] How to get average from 3 repeated tracjectory Carlos Simmerling (Thu Oct 13 2016 - 08:16:00 PDT)
    - Re: [AMBER] How to get average from 3 repeated tracjectory Setyanto Md (Thu Oct 13 2016 - 16:25:41 PDT)
[AMBER] Parmchk2 - Atom type of CX does not shown up in PARMCHK.DAT Miha Purg (Thu Oct 13 2016 - 08:42:00 PDT)
- Re: [AMBER] Parmchk2 - Atom type of CX does not shown up in PARMCHK.DAT David A Case (Thu Oct 13 2016 - 09:11:12 PDT)
  - Re: [AMBER] Parmchk2 - Atom type of CX does not shown up in PARMCHK.DAT Carlos Simmerling (Thu Oct 13 2016 - 09:27:49 PDT)
[AMBER] QM/MM MD with Amber-Gaussian interface Monsurat Lawal (Thu Oct 13 2016 - 12:41:49 PDT)
- Re: [AMBER] QM/MM MD with Amber-Gaussian interface Dr. Andreas W. Goetz (Thu Oct 13 2016 - 12:55:59 PDT)
[AMBER] Pure POPC Membrane Expands and Crashes Rodriguez, Yoel (Thu Oct 13 2016 - 13:33:07 PDT)
- Re: [AMBER] Pure POPC Membrane Expands and Crashes Dickson, Callum J (Thu Oct 13 2016 - 14:11:13 PDT)
  - Re: [AMBER] Pure POPC Membrane Expands and Crashes Rodriguez, Yoel (Thu Oct 13 2016 - 15:34:43 PDT)
[AMBER] Amber and gaff atom types Aditya G Rao (Thu Oct 13 2016 - 14:12:18 PDT)
- Re: [AMBER] Amber and gaff atom types David A Case (Sun Oct 16 2016 - 05:35:06 PDT)
[AMBER] extract frame from mdcrd file. Saman Yousuf ali (Fri Oct 14 2016 - 02:59:18 PDT)
- Re: [AMBER] extract frame from mdcrd file. Daniel Roe (Fri Oct 14 2016 - 05:00:57 PDT)
[AMBER] ACE and NME terminal add Mijiddorj Batsaikhan (Sat Oct 15 2016 - 09:45:57 PDT)
- Re: [AMBER] ACE and NME terminal add David A Case (Sat Oct 15 2016 - 17:50:04 PDT)
[AMBER] Error in equilibration steps after minimization Prayagraj Fandilolu (Sun Oct 16 2016 - 02:10:01 PDT)
- Re: [AMBER] Error in equilibration steps after minimization Bill Ross (Sun Oct 16 2016 - 03:08:33 PDT)
  - Re: [AMBER] Error in equilibration steps after minimization Prayagraj Fandilolu (Wed Oct 19 2016 - 03:06:47 PDT)
- Re: [AMBER] Error in equilibration steps after minimization Carlos Simmerling (Sun Oct 16 2016 - 05:01:45 PDT)
  - Re: [AMBER] Error in equilibration steps after minimization Prayagraj Fandilolu (Wed Oct 19 2016 - 03:08:33 PDT)
    - Re: [AMBER] Error in equilibration steps after minimization Carlos Simmerling (Wed Oct 19 2016 - 04:58:30 PDT)
    - Re: [AMBER] Error in equilibration steps after minimization David A Case (Wed Oct 19 2016 - 05:03:16 PDT)
[AMBER] LEaP error Paul Meister (Sun Oct 16 2016 - 13:09:29 PDT)
- Re: [AMBER] LEaP error Bill Ross (Sun Oct 16 2016 - 13:42:01 PDT)
  - Re: [AMBER] LEaP error Bill Ross (Sun Oct 16 2016 - 16:09:04 PDT)
[AMBER] Analysis of results Stacyann Nelson (Sun Oct 16 2016 - 20:14:49 PDT)
- Re: [AMBER] Analysis of results Hai Nguyen (Sun Oct 16 2016 - 20:36:12 PDT)
  - Re: [AMBER] Analysis of results Stacyann Nelson (Sun Oct 16 2016 - 20:49:32 PDT)
    - Re: [AMBER] Analysis of results Gulsevin,Alican (Sun Oct 16 2016 - 20:54:29 PDT)
    - Re: [AMBER] Analysis of results Hai Nguyen (Sun Oct 16 2016 - 20:58:25 PDT)
    - Re: [AMBER] Analysis of results Stacyann Nelson (Sun Oct 16 2016 - 21:04:01 PDT)
    - Re: [AMBER] Analysis of results Hai Nguyen (Sun Oct 16 2016 - 21:07:36 PDT)
    - Re: [AMBER] Analysis of results David A Case (Mon Oct 17 2016 - 04:36:45 PDT)
    - Re: [AMBER] Analysis of results Stacyann Nelson (Mon Oct 17 2016 - 05:06:48 PDT)
    - Re: [AMBER] Analysis of results David A Case (Mon Oct 17 2016 - 09:00:55 PDT)
    - Re: [AMBER] Analysis of results Stacyann Nelson (Mon Oct 17 2016 - 09:17:39 PDT)
[AMBER] compile Amber16 with the intel compiler Vlad Cojocaru (Mon Oct 17 2016 - 04:56:43 PDT)
- Re: [AMBER] compile Amber16 with the intel compiler David A Case (Mon Oct 17 2016 - 09:12:59 PDT)
  - Re: [AMBER] compile Amber16 with the intel compiler Vlad Cojocaru (Mon Oct 17 2016 - 09:22:14 PDT)
    - Re: [AMBER] compile Amber16 with the intel compiler David A Case (Mon Oct 17 2016 - 10:56:25 PDT)
    - Re: [AMBER] compile Amber16 with the intel compiler Vlad Cojocaru (Mon Oct 17 2016 - 11:20:39 PDT)
    - Re: [AMBER] compile Amber16 with the intel compiler David A Case (Tue Oct 18 2016 - 05:49:50 PDT)
    - Re: [AMBER] compile Amber16 with the intel compiler Vlad Cojocaru (Tue Oct 18 2016 - 06:01:58 PDT)
    - Re: [AMBER] compile Amber16 with the intel compiler David A Case (Tue Oct 18 2016 - 08:25:59 PDT)
- Re: [AMBER] compile Amber16 with the intel compiler Vlad Cojocaru (Tue Oct 18 2016 - 05:31:23 PDT)
  - Re: [AMBER] compile Amber16 with the intel compiler Vlad Cojocaru (Tue Oct 18 2016 - 07:57:18 PDT)
[AMBER] An issue with conformational changes during MD. Abhilash J (Mon Oct 17 2016 - 06:24:21 PDT)
- Re: [AMBER] An issue with conformational changes during MD. Hai Nguyen (Sun Oct 23 2016 - 10:22:30 PDT)
[AMBER] Small bug in MMPBSA/input_parser.py William Lees (Mon Oct 17 2016 - 07:17:34 PDT)
- Re: [AMBER] Small bug in MMPBSA/input_parser.py Hai Nguyen (Mon Oct 17 2016 - 13:06:16 PDT)
[AMBER] The value of NONBONDED_PARM_INDEX pointer Meiting Wang (Mon Oct 17 2016 - 07:57:17 PDT)
- Re: [AMBER] The value of NONBONDED_PARM_INDEX pointer David A Case (Mon Oct 17 2016 - 09:45:33 PDT)
[AMBER] UnitCell problem:Anisotropy records cannot be placed Zhou, Weijiang (Mon Oct 17 2016 - 08:03:56 PDT)
- Re: [AMBER] UnitCell problem:Anisotropy records cannot be placed David A Case (Mon Oct 17 2016 - 09:37:36 PDT)
[AMBER] native contacts Parviz Seifpanahi Shabane (Mon Oct 17 2016 - 09:25:33 PDT)
- Re: [AMBER] native contacts Daniel Roe (Mon Oct 17 2016 - 10:02:57 PDT)
  - Re: [AMBER] native contacts Parviz Seifpanahi Shabane (Mon Oct 17 2016 - 11:27:09 PDT)
    - Re: [AMBER] native contacts Parviz Seifpanahi Shabane (Mon Oct 17 2016 - 11:37:45 PDT)
    - Re: [AMBER] native contacts Daniel Roe (Mon Oct 17 2016 - 11:55:27 PDT)
    - Re: [AMBER] native contacts Parviz Seifpanahi Shabane (Mon Oct 17 2016 - 12:09:02 PDT)
    - Re: [AMBER] native contacts Daniel Roe (Mon Oct 17 2016 - 12:16:22 PDT)
[AMBER] Autoimage Error Life Sciences Inc (Mon Oct 17 2016 - 09:26:04 PDT)
- Re: [AMBER] Autoimage Error Daniel Roe (Mon Oct 17 2016 - 10:32:14 PDT)
[AMBER] WHAM analysis Thakur, Abhishek (Mon Oct 17 2016 - 14:20:58 PDT)
- Re: [AMBER] WHAM analysis Marc van der Kamp (Mon Oct 17 2016 - 14:34:26 PDT)
- Re: [AMBER] WHAM analysis Hai Nguyen (Mon Oct 17 2016 - 14:45:31 PDT)
  - Re: [AMBER] WHAM analysis Thakur, Abhishek (Mon Oct 17 2016 - 15:22:37 PDT)
    - Re: [AMBER] WHAM analysis Hai Nguyen (Mon Oct 17 2016 - 15:26:03 PDT)
[AMBER] update.4 of Amber16 and update.9 of AmberTools are not available jacky zhao (Mon Oct 17 2016 - 18:03:39 PDT)
- Re: [AMBER] update.4 of Amber16 and update.9 of AmberTools are not available Hai Nguyen (Mon Oct 17 2016 - 18:10:24 PDT)
  - Re: [AMBER] update.4 of Amber16 and update.9 of AmberTools are not available Hai Nguyen (Mon Oct 17 2016 - 18:17:33 PDT)
    - Re: [AMBER] update.4 of Amber16 and update.9 of AmberTools are not available jacky zhao (Mon Oct 17 2016 - 18:49:53 PDT)
[AMBER] update error of Amber16 and Tools jacky zhao (Mon Oct 17 2016 - 18:44:44 PDT)
- Re: [AMBER] update error of Amber16 and Tools Hai Nguyen (Mon Oct 17 2016 - 19:42:14 PDT)
  - Re: [AMBER] update error of Amber16 and Tools jacky zhao (Tue Oct 18 2016 - 03:01:40 PDT)
[AMBER] Scaling of Non-Bonding Potential for Specific Atom Pairs Samuel Walpole (PHA) (Tue Oct 18 2016 - 00:52:27 PDT)
- Re: [AMBER] Scaling of Non-Bonding Potential for Specific Atom Pairs David A Case (Tue Oct 18 2016 - 06:02:06 PDT)
[AMBER] configuration file for amber16 on IBM power Ye Mei (Tue Oct 18 2016 - 01:19:16 PDT)
- Re: [AMBER] configuration file for amber16 on IBM power jacky zhao (Tue Oct 18 2016 - 04:20:40 PDT)
[AMBER] Charmm to amber conversion of lipid Mahrukh Imtiaz (Tue Oct 18 2016 - 02:08:57 PDT)
[AMBER] cpptraj reimaging: frame reading issue. Saman Yousuf ali (Tue Oct 18 2016 - 02:44:58 PDT)
- Re: [AMBER] cpptraj reimaging: frame reading issue. Daniel Roe (Tue Oct 18 2016 - 05:49:31 PDT)
[AMBER] A question about PCA analysis Markowska (Tue Oct 18 2016 - 03:06:27 PDT)
- Re: [AMBER] A question about PCA analysis Hai Nguyen (Mon Oct 24 2016 - 14:48:59 PDT)
- Re: [AMBER] A question about PCA analysis Daniel Roe (Tue Oct 25 2016 - 05:28:16 PDT)
[AMBER] PBSA: sasopt=0 incompatible with eneopt=4, frcopt=5 Vlad Cojocaru (Tue Oct 18 2016 - 03:23:42 PDT)
- Re: [AMBER] PBSA: sasopt=0 incompatible with eneopt=4, frcopt=5 Ray Luo (Tue Oct 18 2016 - 08:39:31 PDT)
  - Re: [AMBER] PBSA: sasopt=0 incompatible with eneopt=4, frcopt=5 Vlad Cojocaru (Tue Oct 18 2016 - 14:23:43 PDT)
    - Re: [AMBER] PBSA: sasopt=0 incompatible with eneopt=4, frcopt=5 Ray Luo (Thu Oct 20 2016 - 09:22:40 PDT)
[AMBER] error of amber16 mpi version using open-mpi jacky zhao (Tue Oct 18 2016 - 03:41:32 PDT)
- Re: [AMBER] error of amber16 mpi version using open-mpi David A Case (Tue Oct 18 2016 - 06:08:14 PDT)
  - Re: [AMBER] error of amber16 mpi version using open-mpi Daniel Roe (Tue Oct 18 2016 - 06:22:06 PDT)
    - Re: [AMBER] error of amber16 mpi version using open-mpi jacky zhao (Tue Oct 18 2016 - 07:01:21 PDT)
    - Re: [AMBER] error of amber16 mpi version using open-mpi jacky zhao (Tue Oct 18 2016 - 07:02:50 PDT)
    - Re: [AMBER] error of amber16 mpi version using open-mpi jacky zhao (Tue Oct 18 2016 - 07:24:08 PDT)
    - Re: [AMBER] error of amber16 mpi version using open-mpi Daniel Roe (Tue Oct 18 2016 - 07:47:04 PDT)
    - Re: [AMBER] error of amber16 mpi version using open-mpi jacky zhao (Tue Oct 18 2016 - 08:27:30 PDT)
    - Re: [AMBER] error of amber16 mpi version using open-mpi jacky zhao (Tue Oct 18 2016 - 09:03:17 PDT)
    - Re: [AMBER] error of amber16 mpi version using open-mpi Ross Walker (Tue Oct 18 2016 - 09:34:53 PDT)
    - Re: [AMBER] error of amber16 mpi version using open-mpi jacky zhao (Tue Oct 18 2016 - 20:35:10 PDT)
[AMBER] Request for help for installing Amber Tools 16 Yogendra Ramtirtha (Tue Oct 18 2016 - 04:48:35 PDT)
- Re: [AMBER] Request for help for installing Amber Tools 16 Vlad Cojocaru (Tue Oct 18 2016 - 05:02:34 PDT)
  - Re: [AMBER] Request for help for installing Amber Tools 16 Yogendra Ramtirtha (Thu Oct 20 2016 - 09:30:38 PDT)
[AMBER] Bugs in CPPTRAJ V16.14 MOHD HOMAIDUR RAHMAN (Tue Oct 18 2016 - 04:56:47 PDT)
- Re: [AMBER] Bugs in CPPTRAJ V16.14 Daniel Roe (Tue Oct 18 2016 - 05:44:31 PDT)
Re: [AMBER] protein drift during NPT equilibrium David A Case (Tue Oct 18 2016 - 05:57:32 PDT)
[AMBER] FEW TI and calulation absolute free energy using soft core Cockroft, Nicholas T. (Tue Oct 18 2016 - 11:20:34 PDT)
- Re: [AMBER] FEW TI and calulation absolute free energy using soft core Hannes Loeffler (Tue Oct 18 2016 - 11:58:13 PDT)
  - Re: [AMBER] FEW TI and calulation absolute free energy using soft core Cockroft, Nicholas T. (Tue Oct 18 2016 - 12:50:37 PDT)
    - Re: [AMBER] FEW TI and calulation absolute free energy using soft core Hannes Loeffler (Tue Oct 18 2016 - 23:22:19 PDT)
[AMBER] how to make peptide Thakur, Abhishek (Tue Oct 18 2016 - 14:51:59 PDT)
- Re: [AMBER] how to make peptide Carlos Simmerling (Tue Oct 18 2016 - 14:54:03 PDT)
  - Re: [AMBER] how to make peptide Thakur, Abhishek (Tue Oct 18 2016 - 15:19:33 PDT)
    - Re: [AMBER] how to make peptide Carlos Simmerling (Tue Oct 18 2016 - 15:21:08 PDT)
    - Re: [AMBER] how to make peptide Thakur, Abhishek (Tue Oct 18 2016 - 15:26:39 PDT)
    - Re: [AMBER] how to make peptide Hai Nguyen (Tue Oct 18 2016 - 15:37:46 PDT)
    - Re: [AMBER] how to make peptide Thakur, Abhishek (Tue Oct 18 2016 - 16:24:18 PDT)
    - Re: [AMBER] how to make peptide Nhai (Tue Oct 18 2016 - 16:28:39 PDT)
    - Re: [AMBER] how to make peptide Carlos Simmerling (Tue Oct 18 2016 - 16:43:47 PDT)
    - Re: [AMBER] how to make peptide Thakur, Abhishek (Tue Oct 18 2016 - 16:55:51 PDT)
    - Re: [AMBER] how to make peptide Carlos Simmerling (Tue Oct 18 2016 - 18:05:40 PDT)
    - Re: [AMBER] how to make peptide Thakur, Abhishek (Wed Oct 19 2016 - 06:09:41 PDT)
    - Re: [AMBER] how to make peptide Carlos Simmerling (Wed Oct 19 2016 - 06:23:42 PDT)
    - Re: [AMBER] how to make peptide Thakur, Abhishek (Wed Oct 19 2016 - 06:54:47 PDT)
[AMBER] heating step: volume, density and pressure plots. Saman Yousuf ali (Wed Oct 19 2016 - 00:54:45 PDT)
- Re: [AMBER] heating step: volume, density and pressure plots. David A Case (Wed Oct 19 2016 - 04:54:17 PDT)
  - Re: [AMBER] heating step: volume, density and pressure plots. Ruth Helena Tichauer (Fri Oct 21 2016 - 02:52:04 PDT)
    - Re: [AMBER] heating step: volume, density and pressure plots. Daniel Roe (Fri Oct 21 2016 - 07:56:26 PDT)
- Re: [AMBER] heating step: volume, density and pressure plots. ruqaiya khalil (Wed Oct 19 2016 - 10:30:19 PDT)
[AMBER] How to make replicas using leap Stacyann Nelson (Wed Oct 19 2016 - 06:38:24 PDT)
[AMBER] Update 16 for AmberTools 16 CPPTRAJ Daniel Roe (Wed Oct 19 2016 - 06:55:42 PDT)
- Re: [AMBER] Update 16 for AmberTools 16 CPPTRAJ jacky zhao (Thu Oct 20 2016 - 04:11:56 PDT)
[AMBER] Help with GIST analysis Sérgio Marques (Wed Oct 19 2016 - 08:31:59 PDT)
- Re: [AMBER] Help with GIST analysis Steven Ramsey (Wed Oct 19 2016 - 13:56:41 PDT)
  - Re: [AMBER] Help with GIST analysis Sérgio Marques (Thu Oct 20 2016 - 02:18:02 PDT)
  - Re: [AMBER] Help with GIST analysis Daniel Roe (Thu Oct 20 2016 - 06:33:10 PDT)
    - Re: [AMBER] Help with GIST analysis Sérgio Marques (Thu Oct 20 2016 - 08:38:47 PDT)
    - Re: [AMBER] Help with GIST analysis Jonathan Gough (Thu Oct 20 2016 - 08:51:35 PDT)
    - Re: [AMBER] Help with GIST analysis Sérgio Marques (Fri Oct 21 2016 - 04:13:16 PDT)
    - Re: [AMBER] Help with GIST analysis Jonathan Gough (Fri Oct 21 2016 - 11:17:19 PDT)
    - Re: [AMBER] Help with GIST analysis Sérgio Marques (Mon Oct 24 2016 - 00:22:30 PDT)
    - Re: [AMBER] Help with GIST analysis Steven Ramsey (Mon Oct 24 2016 - 10:13:26 PDT)
    - Re: [AMBER] Help with GIST analysis Sérgio Marques (Mon Oct 24 2016 - 11:44:03 PDT)
[AMBER] frcmod file error Thakur, Abhishek (Wed Oct 19 2016 - 09:06:22 PDT)
- Re: [AMBER] frcmod file error Bill Ross (Wed Oct 19 2016 - 09:16:42 PDT)
  - Re: [AMBER] frcmod file error Bill Ross (Wed Oct 19 2016 - 09:18:29 PDT)
- Re: [AMBER] frcmod file error Bill Ross (Wed Oct 19 2016 - 09:35:57 PDT)
- Re: [AMBER] frcmod file error David A Case (Wed Oct 19 2016 - 12:27:20 PDT)
  - Re: [AMBER] frcmod file error Thakur, Abhishek (Wed Oct 19 2016 - 14:28:50 PDT)
    - Re: [AMBER] frcmod file error David A Case (Wed Oct 19 2016 - 17:06:36 PDT)
    - Re: [AMBER] frcmod file error Thakur, Abhishek (Thu Oct 20 2016 - 07:37:37 PDT)
    - Re: [AMBER] frcmod file error Carlos Simmerling (Thu Oct 20 2016 - 07:40:39 PDT)
    - Re: [AMBER] frcmod file error Thakur, Abhishek (Thu Oct 20 2016 - 07:46:03 PDT)
    - Re: [AMBER] frcmod file error Carlos Simmerling (Thu Oct 20 2016 - 07:54:36 PDT)
    - Re: [AMBER] frcmod file error Thakur, Abhishek (Thu Oct 20 2016 - 08:04:09 PDT)
    - Re: [AMBER] frcmod file error Carlos Simmerling (Thu Oct 20 2016 - 08:11:05 PDT)
    - Re: [AMBER] frcmod file error Thakur, Abhishek (Thu Oct 20 2016 - 08:17:58 PDT)
    - Re: [AMBER] frcmod file error Carlos Simmerling (Thu Oct 20 2016 - 08:26:51 PDT)
    - Re: [AMBER] frcmod file error Thakur, Abhishek (Thu Oct 20 2016 - 08:35:08 PDT)
    - Re: [AMBER] frcmod file error Carlos Simmerling (Thu Oct 20 2016 - 08:39:43 PDT)
    - Re: [AMBER] frcmod file error Thakur, Abhishek (Thu Oct 20 2016 - 08:59:19 PDT)
    - Re: [AMBER] frcmod file error Carlos Simmerling (Thu Oct 20 2016 - 09:14:53 PDT)
    - Re: [AMBER] frcmod file error Thakur, Abhishek (Thu Oct 20 2016 - 09:29:19 PDT)
    - Re: [AMBER] frcmod file error Carlos Simmerling (Thu Oct 20 2016 - 09:33:09 PDT)
    - Re: [AMBER] frcmod file error Thakur, Abhishek (Thu Oct 20 2016 - 09:40:21 PDT)
    - Re: [AMBER] frcmod file error David A Case (Thu Oct 20 2016 - 09:35:44 PDT)
    - Re: [AMBER] frcmod file error Thakur, Abhishek (Thu Oct 20 2016 - 09:57:17 PDT)
    - Re: [AMBER] frcmod file error Thakur, Abhishek (Thu Oct 20 2016 - 11:28:33 PDT)
    - Re: [AMBER] frcmod file error David A Case (Fri Oct 21 2016 - 05:14:41 PDT)
    - Re: [AMBER] frcmod file error Bill Ross (Fri Oct 21 2016 - 05:43:38 PDT)
    - Re: [AMBER] frcmod file error Thakur, Abhishek (Fri Oct 21 2016 - 07:02:57 PDT)
    - Re: [AMBER] frcmod file error Carlos Simmerling (Fri Oct 21 2016 - 07:23:25 PDT)
    - Re: [AMBER] frcmod file error David A Case (Fri Oct 21 2016 - 11:21:33 PDT)
    - Re: [AMBER] frcmod file error Bill Ross (Fri Oct 21 2016 - 12:09:07 PDT)
    - Re: [AMBER] frcmod file error Thakur, Abhishek (Sat Oct 22 2016 - 11:17:38 PDT)
    - Re: [AMBER] frcmod file error Carlos Simmerling (Fri Oct 21 2016 - 07:19:48 PDT)
    - Re: [AMBER] frcmod file error Thakur, Abhishek (Fri Oct 21 2016 - 07:25:16 PDT)
- Re: [AMBER] frcmod file error Hector A. Baldoni (Fri Oct 21 2016 - 08:42:29 PDT)
[AMBER] Difference between POPI and DOPI membranes? and about lipid headgroups Mijiddorj Batsaikhan (Wed Oct 19 2016 - 09:25:21 PDT)
[AMBER] help in solvent box Robin Jain (Wed Oct 19 2016 - 23:37:21 PDT)
[AMBER] cpptraj: format of diagmatrix output Marc van der Kamp (Thu Oct 20 2016 - 04:20:04 PDT)
- Re: [AMBER] cpptraj: format of diagmatrix output Daniel Roe (Thu Oct 20 2016 - 05:06:56 PDT)
  - Re: [AMBER] cpptraj: format of diagmatrix output Marc van der Kamp (Thu Oct 20 2016 - 09:19:31 PDT)
[AMBER] Adding a Dummy Atom to Benzene Samuel Walpole (PHA) (Thu Oct 20 2016 - 07:59:17 PDT)
- Re: [AMBER] Adding a Dummy Atom to Benzene Carlos Simmerling (Thu Oct 20 2016 - 08:03:13 PDT)
  - Re: [AMBER] Adding a Dummy Atom to Benzene Samuel Walpole (PHA) (Thu Oct 20 2016 - 10:02:57 PDT)
    - Re: [AMBER] Adding a Dummy Atom to Benzene Carlos Simmerling (Fri Oct 21 2016 - 05:13:38 PDT)
    - Re: [AMBER] Adding a Dummy Atom to Benzene David A Case (Fri Oct 21 2016 - 05:19:06 PDT)
    - Re: [AMBER] Adding a Dummy Atom to Benzene Samuel Walpole (PHA) (Fri Oct 21 2016 - 05:36:16 PDT)
[AMBER] ambmask and periodic boundaries Aseel Bala (Thu Oct 20 2016 - 11:41:12 PDT)
- Re: [AMBER] ambmask and periodic boundaries Daniel Roe (Thu Oct 20 2016 - 11:45:20 PDT)
  - Re: [AMBER] ambmask and periodic boundaries Aseel Bala (Thu Oct 20 2016 - 12:53:02 PDT)
[AMBER] uneven bond formed after cyclization of peptide Thakur, Abhishek (Thu Oct 20 2016 - 16:32:57 PDT)
- Re: [AMBER] uneven bond formed after cyclization of peptide Andy Watkins (Thu Oct 20 2016 - 17:38:00 PDT)
  - Re: [AMBER] uneven bond formed after cyclization of peptide Xu Dong (Mon Oct 24 2016 - 06:51:56 PDT)
[AMBER] cpptraj Saman Yousuf ali (Thu Oct 20 2016 - 21:12:47 PDT)
[AMBER] Methyl groups Imma Speciale (Fri Oct 21 2016 - 07:26:42 PDT)
- Re: [AMBER] Methyl groups Elvis Martis (Fri Oct 21 2016 - 07:42:12 PDT)
  - Re: [AMBER] Methyl groups Imma Speciale (Fri Oct 21 2016 - 07:57:04 PDT)
- Re: [AMBER] Methyl groups Elvis Martis (Fri Oct 21 2016 - 08:07:20 PDT)
[AMBER] problem with STRIP command. Parviz Seifpanahi Shabane (Fri Oct 21 2016 - 08:23:58 PDT)
- Re: [AMBER] problem with STRIP command. Daniel Roe (Fri Oct 21 2016 - 09:06:41 PDT)
[AMBER] Regarding Hydroxyproline parameter Saikat Dutta chowdhury (Fri Oct 21 2016 - 21:42:23 PDT)
- Re: [AMBER] Regarding Hydroxyproline parameter David A Case (Sat Oct 22 2016 - 17:14:27 PDT)
  - Re: [AMBER] Regarding Hydroxyproline parameter Saikat Dutta chowdhury (Sat Oct 22 2016 - 19:47:36 PDT)
    - Re: [AMBER] Regarding Hydroxyproline parameter Hai Nguyen (Sat Oct 22 2016 - 21:30:44 PDT)
[AMBER] The error of 'RESTARTED DUE to LINMIN FAILURE' and the 'cudaFree GpuBuffer::Deallocate failed unspecified launch failure' windy (Fri Oct 21 2016 - 23:09:26 PDT)
- Re: [AMBER] The error of 'RESTARTED DUE to LINMIN FAILURE' and the 'cudaFree GpuBuffer::Deallocate failed unspecified launch failure' Bill Ross (Fri Oct 21 2016 - 23:26:07 PDT)
  - Re: [AMBER] The error of 'RESTARTED DUE to LINMIN FAILURE' and the 'cudaFree GpuBuffer::Deallocate failed unspecified launch failure' windy (Sat Oct 22 2016 - 00:21:15 PDT)
    - Re: [AMBER] The error of 'RESTARTED DUE to LINMIN FAILURE' and the 'cudaFree GpuBuffer::Deallocate failed unspecified launch failure' Bill Ross (Sat Oct 22 2016 - 00:42:08 PDT)
    - Re: [AMBER] The error of 'RESTARTED DUE to LINMIN FAILURE' and the 'cudaFree GpuBuffer::Deallocate failed unspecified launch failure' windy (Sat Oct 22 2016 - 02:03:01 PDT)
    - Re: [AMBER] The error of 'RESTARTED DUE to LINMIN FAILURE' and the 'cudaFree GpuBuffer::Deallocate failed unspecified launch failure' Bill Ross (Sat Oct 22 2016 - 16:14:38 PDT)
    - Re: [AMBER] The error of 'RESTARTED DUE to LINMIN FAILURE' and the 'cudaFree GpuBuffer::Deallocate failed unspecified launch failure' windy (Sun Oct 23 2016 - 02:03:14 PDT)
    - Re: [AMBER] The error of 'RESTARTED DUE to LINMIN FAILURE' and the 'cudaFree GpuBuffer::Deallocate failed unspecified launch failure' Bill Ross (Sun Oct 23 2016 - 10:06:18 PDT)
- Re: [AMBER] The error of 'RESTARTED DUE to LINMIN FAILURE' and the 'cudaFree GpuBuffer::Deallocate failed unspecified launch failure' David A Case (Sun Oct 23 2016 - 18:12:23 PDT)
  - Re: [AMBER] The error of 'RESTARTED DUE to LINMIN FAILURE' and the 'cudaFree GpuBuffer::Deallocate failed unspecified launch failure' XP Chen (Mon Oct 24 2016 - 23:28:22 PDT)
[AMBER] cpptraj: ligand and active site rmsd Saman Yousuf ali (Sat Oct 22 2016 - 01:42:01 PDT)
- Re: [AMBER] cpptraj: ligand and active site rmsd Hai Nguyen (Sun Oct 23 2016 - 10:17:08 PDT)
[AMBER] VMD hydrogen bonds calculation Pooja Kesari (Sat Oct 22 2016 - 23:21:45 PDT)
- Re: [AMBER] VMD hydrogen bonds calculation Bill Ross (Sat Oct 22 2016 - 23:27:20 PDT)
  - Re: [AMBER] VMD hydrogen bonds calculation Pooja Kesari (Sun Oct 23 2016 - 21:06:29 PDT)
[AMBER] cpptraj readdata bad_alloc Niel Henriksen (Sun Oct 23 2016 - 12:01:42 PDT)
- Re: [AMBER] cpptraj readdata bad_alloc Daniel Roe (Mon Oct 24 2016 - 08:10:08 PDT)
  - Re: [AMBER] cpptraj readdata bad_alloc Daniel Roe (Mon Oct 24 2016 - 08:22:50 PDT)
    - Re: [AMBER] cpptraj readdata bad_alloc Daniel Roe (Mon Oct 24 2016 - 09:45:12 PDT)
    - Re: [AMBER] cpptraj readdata bad_alloc Niel Henriksen (Mon Oct 24 2016 - 10:02:47 PDT)
[AMBER] problem equilibrating the structure giulia palermo (Sun Oct 23 2016 - 13:43:25 PDT)
- Re: [AMBER] problem equilibrating the structure Carlos Simmerling (Sun Oct 23 2016 - 15:30:22 PDT)
- Re: [AMBER] problem equilibrating the structure David A Case (Sun Oct 23 2016 - 18:17:22 PDT)
  - Re: [AMBER] problem equilibrating the structure giulia palermo (Tue Oct 25 2016 - 08:21:39 PDT)
[AMBER] centering a molecule in a frame with command line cpptraj Aseel Bala Ahmed (Sun Oct 23 2016 - 15:25:15 PDT)
- Re: [AMBER] centering a molecule in a frame with command line cpptraj Nhai (Sun Oct 23 2016 - 15:33:15 PDT)
  - Re: [AMBER] centering a molecule in a frame with command line cpptraj Aseel Bala Ahmed (Sun Oct 23 2016 - 18:27:14 PDT)
[AMBER] time of MD Stefania Mirabella (Mon Oct 24 2016 - 01:33:42 PDT)
- Re: [AMBER] time of MD Jacopo Sgrignani (Mon Oct 24 2016 - 01:47:21 PDT)
- Re: [AMBER] time of MD David A Case (Mon Oct 24 2016 - 04:58:53 PDT)
  - Re: [AMBER] time of MD Stefania Mirabella (Mon Oct 24 2016 - 05:58:26 PDT)
[AMBER] Setting MM-PBSA script Jag Silwal (Mon Oct 24 2016 - 11:03:57 PDT)
- Re: [AMBER] Setting MM-PBSA script Hai Nguyen (Mon Oct 24 2016 - 11:15:46 PDT)
  - Re: [AMBER] Setting MM-PBSA script Jag Silwal (Mon Oct 24 2016 - 16:14:40 PDT)
- Re: [AMBER] Setting MM-PBSA script William Lees (Tue Oct 25 2016 - 03:12:14 PDT)
  - Re: [AMBER] Setting MM-PBSA script Jag Silwal (Tue Oct 25 2016 - 06:56:16 PDT)
    - Re: [AMBER] Setting MM-PBSA script William Lees (Wed Oct 26 2016 - 07:14:01 PDT)
[AMBER] aMD used for simulated small peptide with non-standard residues Gabriel Jara (Mon Oct 24 2016 - 11:38:42 PDT)
- Re: [AMBER] aMD used for simulated small peptide with non-standard residues David A Case (Tue Oct 25 2016 - 05:21:22 PDT)
- Re: [AMBER] aMD used for simulated small peptide with non-standard residues Gabriel Jara (Fri Oct 28 2016 - 10:16:31 PDT)
[AMBER] Gaussian through sander-cutoffs Aseel Bala (Mon Oct 24 2016 - 12:11:44 PDT)
[AMBER] cpptraj: rms around 5 angstrom of ligand issue. Saman Yousuf ali (Mon Oct 24 2016 - 22:01:07 PDT)
- Re: [AMBER] cpptraj: rms around 5 angstrom of ligand issue. Nhai (Mon Oct 24 2016 - 22:07:41 PDT)
- Re: [AMBER] cpptraj: rms around 5 angstrom of ligand issue. Saman Yousuf ali (Mon Oct 24 2016 - 22:23:37 PDT)
  - Re: [AMBER] cpptraj: rms around 5 angstrom of ligand issue. Daniel Roe (Tue Oct 25 2016 - 05:14:31 PDT)
[AMBER] Deprotonated serine residue. Dd H (Tue Oct 25 2016 - 01:06:55 PDT)
- Re: [AMBER] Deprotonated serine residue. David A Case (Tue Oct 25 2016 - 05:17:42 PDT)
- Re: [AMBER] Deprotonated serine residue. FyD (Wed Oct 26 2016 - 01:27:42 PDT)
  - Re: [AMBER] Deprotonated serine residue. Dd H (Thu Oct 27 2016 - 05:06:40 PDT)
Re: [AMBER] MM-PBSA calculation in different temprature shahab shariati (Tue Oct 25 2016 - 03:29:30 PDT)
- Re: [AMBER] MM-PBSA calculation in different temprature shahab shariati (Wed Oct 26 2016 - 11:18:15 PDT)
  - Re: [AMBER] MM-PBSA calculation in different temprature Hai Nguyen (Wed Oct 26 2016 - 11:24:55 PDT)
    - Re: [AMBER] MM-PBSA calculation in different temprature shahab shariati (Thu Oct 27 2016 - 09:13:50 PDT)
    - Re: [AMBER] MM-PBSA calculation in different temprature Hai Nguyen (Thu Oct 27 2016 - 10:06:56 PDT)
[AMBER] replicating a box in all direction Aseel Bala (Tue Oct 25 2016 - 11:47:48 PDT)
[AMBER] Zinc ion visualization from Amber trajectory Aditya Padhi (Tue Oct 25 2016 - 17:45:38 PDT)
- Re: [AMBER] Zinc ion visualization from Amber trajectory Eiros Zamora, Juan (Wed Oct 26 2016 - 04:37:34 PDT)
  - Re: [AMBER] Zinc ion visualization from Amber trajectory Aditya Padhi (Wed Oct 26 2016 - 19:11:31 PDT)
[AMBER] Van der waals and electrostatic energy calculations using cpptraj? Aishani Prem (Wed Oct 26 2016 - 11:27:41 PDT)
- Re: [AMBER] Van der waals and electrostatic energy calculations using cpptraj? Daniel Roe (Wed Oct 26 2016 - 11:33:32 PDT)
- Re: [AMBER] Van der waals and electrostatic energy calculations using cpptraj? Hai Nguyen (Wed Oct 26 2016 - 17:13:50 PDT)
  - Re: [AMBER] Van der waals and electrostatic energy calculations using cpptraj? Aishani Prem (Wed Oct 26 2016 - 17:31:09 PDT)
[AMBER] Issue with parametrization of lipid using lipid14 forcefield Mahrukh Imtiaz (Wed Oct 26 2016 - 23:33:05 PDT)
- Re: [AMBER] Issue with parametrization of lipid using lipid14 forcefield Bill Ross (Thu Oct 27 2016 - 01:55:32 PDT)
[AMBER] Explicit solvent CpHMD - Are protonation state evaluations done on the GPU in Amber 16? Eric Lang (Thu Oct 27 2016 - 01:13:17 PDT)
- Re: [AMBER] Explicit solvent CpHMD - Are protonation state evaluations done on the GPU in Amber 16? Adrian Roitberg (Thu Oct 27 2016 - 07:36:13 PDT)
- Re: [AMBER] Explicit solvent CpHMD - Are protonation state evaluations done on the GPU in Amber 16? Jason Swails (Thu Oct 27 2016 - 12:58:59 PDT)
[AMBER] cannot find Chamber in Amber16 Abhishek TYAGI (Thu Oct 27 2016 - 04:25:41 PDT)
- Re: [AMBER] cannot find Chamber in Amber16 Daniel Roe (Thu Oct 27 2016 - 04:56:38 PDT)
- Re: [AMBER] cannot find Chamber in Amber16 David A Case (Thu Oct 27 2016 - 05:18:52 PDT)
[AMBER] editing checkpoint name Aseel Bala (Thu Oct 27 2016 - 09:11:50 PDT)
[AMBER] Can we combine amber and gaff atom types? Aditya G Rao (Thu Oct 27 2016 - 09:20:48 PDT)
- Re: [AMBER] Can we combine amber and gaff atom types? Carlos Simmerling (Thu Oct 27 2016 - 09:38:30 PDT)
  - Re: [AMBER] Can we combine amber and gaff atom types? Aditya G Rao (Thu Oct 27 2016 - 10:31:52 PDT)
    - Re: [AMBER] Can we combine amber and gaff atom types? David Cerutti (Thu Oct 27 2016 - 11:45:15 PDT)
[AMBER] number of bins used in wham analysis Thakur, Abhishek (Thu Oct 27 2016 - 13:11:54 PDT)
[AMBER] Separate forcefield for oligosaccharide residues? Nikolay N. Kuzmich (Fri Oct 28 2016 - 03:21:05 PDT)
- Re: [AMBER] Separate forcefield for oligosaccharide residues? David A Case (Fri Oct 28 2016 - 06:44:30 PDT)
- Re: [AMBER] Separate forcefield for oligosaccharide residues? FyD (Sat Oct 29 2016 - 03:27:47 PDT)
  - Re: [AMBER] Separate forcefield for oligosaccharide residues? Lachele Foley (Sat Oct 29 2016 - 13:14:02 PDT)
    - Re: [AMBER] Separate forcefield for oligosaccharide residues? FyD (Mon Oct 31 2016 - 09:22:48 PDT)
[AMBER] pH calculation of site in md simulation Shilpa Gupta (Fri Oct 28 2016 - 03:51:41 PDT)
- Re: [AMBER] pH calculation of site in md simulation Bill Ross (Fri Oct 28 2016 - 04:27:31 PDT)
[AMBER] dysprosium vdw parameters Florent Barbault (Fri Oct 28 2016 - 05:12:13 PDT)
- Re: [AMBER] dysprosium vdw parameters Pengfei Li (Fri Oct 28 2016 - 11:18:02 PDT)
  - Re: [AMBER] dysprosium vdw parameters Barbault Florent (Sat Oct 29 2016 - 09:43:41 PDT)
[AMBER] MCPB.py Mahmood Jasim (Fri Oct 28 2016 - 11:21:36 PDT)
- Re: [AMBER] MCPB.py Pengfei Li (Fri Oct 28 2016 - 13:25:40 PDT)
  - Re: [AMBER] MCPB.py Pengfei Li (Sat Oct 29 2016 - 20:33:03 PDT)
    - Re: [AMBER] MCPB.py Mahmood Jasim (Mon Oct 31 2016 - 09:21:46 PDT)
    - Re: [AMBER] MCPB.py Pengfei Li (Mon Oct 31 2016 - 17:46:43 PDT)
[AMBER] 126_parmed.in in tutorial A20. Jun Doo (Sun Oct 30 2016 - 03:26:22 PDT)
- Re: [AMBER] 126_parmed.in in tutorial A20. Pengfei Li (Mon Oct 31 2016 - 18:10:44 PDT)
[AMBER] REMD hang without error 宁璐璐 (Sun Oct 30 2016 - 19:37:06 PDT)
[AMBER] amber 杨满意 (Sun Oct 30 2016 - 20:23:05 PDT)
[AMBER] semiempirical MD simulation for systems contain metal atoms 杨满意 (Sun Oct 30 2016 - 20:45:52 PDT)
- Re: [AMBER] semiempirical MD simulation for systems contain metal atoms Elvis Martis (Sun Oct 30 2016 - 20:59:40 PDT)
  - Re: [AMBER] semiempirical MD simulation for systems contain metal atoms 杨满意 (Mon Oct 31 2016 - 00:41:37 PDT)
[AMBER] Regarding multipl cutoffs Sudhanshu Shanker (Sun Oct 30 2016 - 22:13:32 PDT)
- Re: [AMBER] Regarding multipl cutoffs Jason Swails (Mon Oct 31 2016 - 03:53:18 PDT)
[AMBER] deal with organometaliic with MCPB.py 杨满意 (Mon Oct 31 2016 - 03:24:44 PDT)
[AMBER] Change in dihedral angle Sudip Das (Mon Oct 31 2016 - 04:07:57 PDT)
- Re: [AMBER] Change in dihedral angle Carlos Simmerling (Mon Oct 31 2016 - 04:53:30 PDT)
  - Re: [AMBER] Change in dihedral angle Sudip Das (Mon Oct 31 2016 - 05:20:13 PDT)
[AMBER] [mdout_analyzer.py] Problem with OS X El Capitan Eiros Zamora, Juan (Mon Oct 31 2016 - 05:09:27 PDT)
- Re: [AMBER] [mdout_analyzer.py] Problem with OS X El Capitan Jason Swails (Mon Oct 31 2016 - 11:48:49 PDT)
[AMBER] Problem reading coordinates or velocities from *.rst, GB solvation model Nikolay N. Kuzmich (Mon Oct 31 2016 - 11:34:35 PDT)
- Re: [AMBER] Problem reading coordinates or velocities from *.rst, GB solvation model Carlos Simmerling (Mon Oct 31 2016 - 11:43:15 PDT)

Amber Archive Oct 2016 by thread