Amber Archive Jan 2022: by thread

Re: [AMBER] sqm performance: does it run in parallel? Alan (Sat Jan 01 2022 - 02:51:57 PST)
Re: [AMBER] Non-standard residue parameterization questions Matthew Guberman-Pfeffer (Sat Jan 01 2022 - 09:39:09 PST)
[AMBER] Why SANDER can't rotate the dihedral for some angles? [Metal Center] Erdem Yeler (Sat Jan 01 2022 - 14:38:15 PST)
- Re: [AMBER] Why SANDER can't rotate the dihedral for some angles? [Metal Center] David A Case (Mon Jan 03 2022 - 07:27:33 PST)
  - Re: [AMBER] Why SANDER can't rotate the dihedral for some angles? [Metal Center] Erdem Yeler (Fri Jan 07 2022 - 16:28:52 PST)
Re: [AMBER] DE Shaw RNA parameters error David A Case (Sun Jan 02 2022 - 10:03:30 PST)
Re: [AMBER] TIP4PD water box error David A Case (Sun Jan 02 2022 - 10:08:23 PST)
Re: [AMBER] Extending constant pH to additional titratable groups Jason Swails (Mon Jan 03 2022 - 09:12:30 PST)
Re: [AMBER] Li salt parameterisation issue Damiano Spadoni (Mon Jan 03 2022 - 08:05:31 PST)
Re: [AMBER] amber20 - test suite picks up the wrong libgfortran David A Case (Mon Jan 03 2022 - 13:08:23 PST)
- Re: [AMBER] amber20 - test suite picks up the wrong libgfortran tluchko (Tue Jan 04 2022 - 13:46:08 PST)
  - Re: [AMBER] amber20 - test suite picks up the wrong libgfortran Mark Dixon (Wed Jan 05 2022 - 07:02:02 PST)
[AMBER] Fw: regarding no tortion terms MIRA JHAWAR (Tue Jan 04 2022 - 03:17:26 PST)
[AMBER] regading no tortion terms MIRA JHAWAR (Tue Jan 04 2022 - 03:22:34 PST)
- Re: [AMBER] regading no tortion terms David A Case (Tue Jan 04 2022 - 06:04:37 PST)
  - Re: [AMBER] regading no tortion terms MIRA JHAWAR (Sun Jan 09 2022 - 22:08:55 PST)
    - Re: [AMBER] regading no tortion terms MIRA JHAWAR (Sun Jan 09 2022 - 22:12:35 PST)
    - Re: [AMBER] regading no tortion terms David A Case (Mon Jan 10 2022 - 06:14:12 PST)
    - Re: [AMBER] regading no tortion terms MIRA JHAWAR (Mon Jan 10 2022 - 06:29:42 PST)
    - Re: [AMBER] regading no tortion terms MIRA JHAWAR (Mon Jan 10 2022 - 08:03:14 PST)
    - Re: [AMBER] regading no tortion terms MIRA JHAWAR (Tue Jan 11 2022 - 04:03:43 PST)
    - Re: [AMBER] regading no tortion terms David A Case (Tue Jan 11 2022 - 06:15:37 PST)
    - Re: [AMBER] regading no tortion terms MIRA JHAWAR (Tue Jan 11 2022 - 06:20:52 PST)
    - Re: [AMBER] regading no tortion terms MIRA JHAWAR (Mon Jan 10 2022 - 04:08:02 PST)
    - Re: [AMBER] regading no tortion terms Dr. Anselm Horn (Mon Jan 10 2022 - 06:15:41 PST)
- Re: [AMBER] regading no tortion terms MIRA JHAWAR (Tue Jan 11 2022 - 07:30:52 PST)
  - Re: [AMBER] regading no tortion terms David A Case (Tue Jan 11 2022 - 18:07:56 PST)
    - Re: [AMBER] regading no tortion terms MIRA JHAWAR (Tue Jan 11 2022 - 20:12:23 PST)
[AMBER] 1D-RISM Convergence ABDUL BASIT (Tue Jan 04 2022 - 06:34:50 PST)
- Re: [AMBER] 1D-RISM Convergence tluchko (Tue Jan 04 2022 - 12:04:14 PST)
[AMBER] cudaMemcpy GpuBuffer::Download failed an illegal memory access was encountered Renato Araujo (Tue Jan 04 2022 - 09:42:54 PST)
- Re: [AMBER] cudaMemcpy GpuBuffer::Download failed an illegal memory access was encountered David A Case (Tue Jan 04 2022 - 13:10:10 PST)
[AMBER] lipid modification to a nucleic acid base Daniel Konstantinovsky (Tue Jan 04 2022 - 11:54:21 PST)
- Re: [AMBER] lipid modification to a nucleic acid base Carlos Simmerling (Wed Jan 05 2022 - 04:49:09 PST)
[AMBER] How to use MN2+ parameter (.dat and .prp) files downloaded form AMBER parameter database of Bryce group Pranabesh Mandal (PhD, Bioinformatics August-2019) (Wed Jan 05 2022 - 03:49:37 PST)
- Re: [AMBER] How to use MN2+ parameter (.dat and .prp) files downloaded form AMBER parameter database of Bryce group Dr. Anselm Horn (Wed Jan 05 2022 - 04:40:06 PST)
- Re: [AMBER] How to use MN2+ parameter (.dat and .prp) files downloaded form AMBER parameter database of Bryce group Pranabesh Mandal (PhD, Bioinformatics August-2019) (Thu Jan 06 2022 - 21:18:18 PST)
  - Re: [AMBER] How to use MN2+ parameter (.dat and .prp) files downloaded form AMBER parameter database of Bryce group Dr. Anselm Horn (Thu Jan 06 2022 - 23:14:43 PST)
- Re: [AMBER] How to use MN2+ parameter (.dat and .prp) files downloaded form AMBER parameter database of Bryce group Pranabesh Mandal (PhD, Bioinformatics August-2019) (Fri Jan 07 2022 - 21:04:28 PST)
Re: [AMBER] Hydrogen Bonding Analysis Daniel Roe (Wed Jan 05 2022 - 06:21:18 PST)
[AMBER] GCC and EuroSAMPL Satellite Workshop 2022 - Submission deadline extension Guessregen, Stefan /DE (Wed Jan 05 2022 - 09:50:50 PST)
[AMBER] Heating only a region of the system Liao (Wed Jan 05 2022 - 12:05:15 PST)
- Re: [AMBER] Heating only a region of the system David A Case (Fri Jan 07 2022 - 09:20:29 PST)
[AMBER] CV_type Ming Tang (Thu Jan 06 2022 - 18:40:55 PST)
- Re: [AMBER] CV_type Feng Pan (Fri Jan 07 2022 - 08:05:47 PST)
[AMBER] RESP doesn't incorporate charge constraint Daniel Konstantinovsky (Fri Jan 07 2022 - 09:54:42 PST)
- Re: [AMBER] RESP doesn't incorporate charge constraint Matthew Guberman-Pfeffer (Fri Jan 07 2022 - 10:42:28 PST)
  - Re: [AMBER] RESP doesn't incorporate charge constraint Daniel Konstantinovsky (Fri Jan 07 2022 - 11:12:25 PST)
    - Re: [AMBER] RESP doesn't incorporate charge constraint Matthew Guberman-Pfeffer (Fri Jan 07 2022 - 11:18:02 PST)
Re: [AMBER] tleap error: "expected 'default'" Matthew Guberman-Pfeffer (Fri Jan 07 2022 - 13:50:30 PST)
- Re: [AMBER] tleap error: "expected 'default'" Daniel Konstantinovsky (Fri Jan 07 2022 - 14:17:07 PST)
  - Re: [AMBER] tleap error: "expected 'default'" Matthew Guberman-Pfeffer (Fri Jan 07 2022 - 16:41:03 PST)
[AMBER] Problem with reading a mol2 file into tleap David A Case (Fri Jan 07 2022 - 18:04:45 PST)
[AMBER] Amber20 minimization, the rendered .rst file is corrupted and unreadable Yi Ren (Fri Jan 07 2022 - 19:01:01 PST)
- Re: [AMBER] Amber20 minimization, the rendered .rst file is corrupted and unreadable David A Case (Sat Jan 08 2022 - 05:43:00 PST)
  - Re: [AMBER] Amber20 minimization, the rendered .rst file is corrupted and unreadable Yi Ren (Sat Jan 08 2022 - 16:59:24 PST)
- Re: [AMBER] Amber20 minimization, the rendered .rst file is corrupted and unreadable Carlos Simmerling (Sat Jan 08 2022 - 06:07:27 PST)
- Re: [AMBER] Amber20 minimization, the rendered .rst file is corrupted and unreadable Daniel Roe (Sat Jan 08 2022 - 06:42:14 PST)
[AMBER] MCPB.py error in GAMESS-US calculations ABDUL BASIT (Sat Jan 08 2022 - 05:51:00 PST)
[AMBER] FEP calculation in tutorial 9 xiangyu (Sat Jan 08 2022 - 08:12:13 PST)
[AMBER] RESP VS ESP charge fitting Nagar, Hemant (Sat Jan 08 2022 - 17:39:22 PST)
[AMBER] attaching a residue to DNA Daniel Konstantinovsky (Sun Jan 09 2022 - 05:37:22 PST)
- Re: [AMBER] attaching a residue to DNA Christina Bergonzo (Mon Jan 10 2022 - 06:04:23 PST)
Re: [AMBER] CPPTRAJ Segmentation Fault with modified topology file Chris Lee (Sun Jan 09 2022 - 08:43:03 PST)
- Re: [AMBER] CPPTRAJ Segmentation Fault with modified topology file Daniel Roe (Sun Jan 09 2022 - 14:13:49 PST)
  - Re: [AMBER] CPPTRAJ Segmentation Fault with modified topology file Daniel Roe (Mon Jan 10 2022 - 07:42:17 PST)
[AMBER] Multi-GPU oddity James Kress (Sun Jan 09 2022 - 15:30:11 PST)
[AMBER] Problem in mmpbsa calculation Rakesh Roy (Sun Jan 09 2022 - 21:46:47 PST)
[AMBER] Problems with mdgx torsion parameters fitting - possible bug with polymers? Casalini Tommaso (Sun Jan 09 2022 - 23:51:49 PST)
- Re: [AMBER] Problems with mdgx torsion parameters fitting - possible bug with polymers? David Cerutti (Mon Jan 10 2022 - 09:43:51 PST)
[AMBER] SMD negative distance Jacopo Sgrignani (Mon Jan 10 2022 - 07:17:02 PST)
[AMBER] how to stop making terminal residue Daniel Konstantinovsky (Mon Jan 10 2022 - 08:34:03 PST)
- Re: [AMBER] how to stop making terminal residue David A Case (Tue Jan 11 2022 - 06:18:46 PST)
  - Re: [AMBER] how to stop making terminal residue Daniel Konstantinovsky (Tue Jan 11 2022 - 07:08:54 PST)
    - Re: [AMBER] how to stop making terminal residue David A Case (Tue Jan 11 2022 - 08:06:20 PST)
    - Re: [AMBER] how to stop making terminal residue Dr. Anselm Horn (Wed Jan 12 2022 - 01:01:00 PST)
[AMBER] Help in ligand preparation_antechamber Arooma Maryam (Mon Jan 10 2022 - 10:59:19 PST)
- Re: [AMBER] Help in ligand preparation_antechamber David A Case (Tue Jan 11 2022 - 07:20:00 PST)
[AMBER] Amber21/Orca5.0?==?utf-8?q? QM/MM simulations Antonio Frances Monerris (Mon Jan 10 2022 - 11:22:07 PST)
[AMBER] Reg: PLP - LYS parameters Lara rajam (Mon Jan 10 2022 - 11:47:14 PST)
- Re: [AMBER] Reg: PLP - LYS parameters Gerald Monard (Mon Jan 10 2022 - 16:42:43 PST)
[AMBER] MCPB, atom mismatch and naming problem Matthew Guberman-Pfeffer (Tue Jan 11 2022 - 08:42:53 PST)
[AMBER] Multi-GPU Bug in Amber20 James Kress (Tue Jan 11 2022 - 10:51:51 PST)
- Re: [AMBER] Multi-GPU Bug in Amber20 Ross Walker (Tue Jan 11 2022 - 11:22:57 PST)
  - Re: [AMBER] Multi-GPU Bug in Amber20 James Kress (Tue Jan 11 2022 - 12:14:55 PST)
- Re: [AMBER] Multi-GPU Bug in Amber20 James Kress (Tue Jan 11 2022 - 15:57:03 PST)
  - Re: [AMBER] Multi-GPU Bug in Amber20 David A Case (Tue Jan 11 2022 - 18:15:54 PST)
    - Re: [AMBER] Multi-GPU Bug in Amber20 James Kress (Tue Jan 11 2022 - 19:34:47 PST)
[AMBER] RESP giving ridiculous charges Daniel Konstantinovsky (Tue Jan 11 2022 - 11:59:43 PST)
- Re: [AMBER] RESP giving ridiculous charges Dr. Anselm Horn (Wed Jan 12 2022 - 02:23:25 PST)
[AMBER] Question on REMD on GPU/CPU Suchetana Gupta (Tue Jan 11 2022 - 20:22:02 PST)
- Re: [AMBER] Question on REMD on GPU/CPU Vinicius Wilian Cruzeiro (Tue Jan 11 2022 - 21:01:49 PST)
[AMBER] SMD Jacopo Sgrignani (Wed Jan 12 2022 - 00:37:45 PST)
[AMBER] Running AmberTools21 on HPC cluster using distributed memory Manuel Fernandez Merino (Wed Jan 12 2022 - 01:28:56 PST)
- Re: [AMBER] Running AmberTools21 on HPC cluster using distributed memory David A Case (Wed Jan 12 2022 - 06:05:41 PST)
  - Re: [AMBER] Running AmberTools21 on HPC cluster using distributed memory Manuel Fernandez Merino (Thu Jan 13 2022 - 01:23:50 PST)
    - Re: [AMBER] Running AmberTools21 on HPC cluster using distributed memory David A Case (Thu Jan 13 2022 - 06:18:26 PST)
    - Re: [AMBER] Running AmberTools21 on HPC cluster using distributed memory Manuel Fernandez Merino (Thu Jan 13 2022 - 06:54:46 PST)
[AMBER] Thermodynamic integration equilibration Gian Marco ELISI (Wed Jan 12 2022 - 03:23:01 PST)
Re: [AMBER] [External] How to calculate multipole moment？ Scott Boesch (Wed Jan 12 2022 - 04:55:59 PST)
- Re: [AMBER] [External] How to calculate multipole moment？ Scott Boesch (Wed Jan 12 2022 - 04:57:49 PST)
[AMBER] About the drug charge _antechamber Arooma Maryam (Wed Jan 12 2022 - 10:21:36 PST)
- Re: [AMBER] About the drug charge _antechamber David A Case (Wed Jan 12 2022 - 17:51:46 PST)
[AMBER] Restraint removal doesn't seem to be happening Daniel Burns (Wed Jan 12 2022 - 13:42:04 PST)
- Re: [AMBER] Restraint removal doesn't seem to be happening David A Case (Thu Jan 13 2022 - 06:02:57 PST)
  - Re: [AMBER] Restraint removal doesn't seem to be happening Daniel Burns (Thu Jan 13 2022 - 07:30:04 PST)
    - Re: [AMBER] Restraint removal doesn't seem to be happening Rafał Madaj (Fri Jan 14 2022 - 01:24:22 PST)
    - Re: [AMBER] Restraint removal doesn't seem to be happening Daniel Burns (Fri Jan 14 2022 - 16:29:10 PST)
    - Re: [AMBER] Restraint removal doesn't seem to be happening David A Case (Fri Jan 14 2022 - 18:55:11 PST)
    - Re: [AMBER] Restraint removal doesn't seem to be happening Daniel Burns (Sat Jan 15 2022 - 06:17:42 PST)
    - Re: [AMBER] Restraint removal doesn't seem to be happening Daniel Burns (Sat Jan 15 2022 - 09:44:28 PST)
- Re: [AMBER] Restraint removal doesn't seem to be happening David A Case (Wed Jan 19 2022 - 05:06:27 PST)
[AMBER] number of waters near a mask (K+) cpptraj Vaibhav Dixit (Wed Jan 12 2022 - 22:38:55 PST)
- Re: [AMBER] number of waters near a mask (K+) cpptraj Daniel Roe (Thu Jan 13 2022 - 05:43:03 PST)
  - Re: [AMBER] number of waters near a mask (K+) cpptraj Vaibhav Dixit (Thu Jan 13 2022 - 06:32:58 PST)
[AMBER] Single Point Energy: sander x python sander Alan (Thu Jan 13 2022 - 01:26:51 PST)
- Re: [AMBER] Single Point Energy: sander x python sander David A Case (Thu Jan 13 2022 - 06:25:52 PST)
  - Re: [AMBER] Single Point Energy: sander x python sander Alan (Thu Jan 13 2022 - 08:16:13 PST)
    - Re: [AMBER] Single Point Energy: sander x python sander Ray Luo (Thu Jan 13 2022 - 09:06:18 PST)
    - Re: [AMBER] Single Point Energy: sander x python sander David A Case (Thu Jan 13 2022 - 09:37:01 PST)
    - Re: [AMBER] Single Point Energy: sander x python sander Alan (Fri Jan 14 2022 - 03:31:07 PST)
    - Re: [AMBER] Single Point Energy: sander x python sander Alan (Fri Jan 14 2022 - 03:42:17 PST)
    - Re: [AMBER] Single Point Energy: sander x python sander David A Case (Fri Jan 14 2022 - 05:20:38 PST)
[AMBER] QM / MM module query Aashish Bhatt (Thu Jan 13 2022 - 02:56:32 PST)
- Re: [AMBER] QM / MM module query David A Case (Thu Jan 13 2022 - 06:27:40 PST)
  - Re: [AMBER] QM / MM module query Aashish Bhatt (Wed Jan 19 2022 - 10:19:02 PST)
[AMBER] CMAP and NBFIX Charmm36 in amber Burns Casamayor, Violeta (Thu Jan 13 2022 - 10:31:56 PST)
- Re: [AMBER] CMAP and NBFIX Charmm36 in amber David A Case (Thu Jan 13 2022 - 12:34:57 PST)
[AMBER] How to solve Error: an illegal memory access was encountered launching kernel kClearForces on amber? natalia francisca rodriguez cabello (Thu Jan 13 2022 - 13:16:07 PST)
- Re: [AMBER] How to solve Error: an illegal memory access was encountered launching kernel kClearForces on amber? Mohamed Aboelnga (Thu Jan 13 2022 - 16:56:45 PST)
  - Re: [AMBER] How to solve Error: an illegal memory access was encountered launching kernel kClearForces on amber? natalia francisca rodriguez cabello (Fri Jan 14 2022 - 04:24:07 PST)
- Re: [AMBER] How to solve Error: an illegal memory access was encountered launching kernel kClearForces on amber? David A Case (Thu Jan 13 2022 - 18:13:45 PST)
[AMBER] Request for Extra Points Functionality Matthew Guberman-Pfeffer (Thu Jan 13 2022 - 22:01:04 PST)
[AMBER] The application of QM/MMGBSA in the evaluation of protein stability, is it reasonable? Xinheng He (Thu Jan 13 2022 - 22:32:49 PST)
[AMBER] NETCDF problem Björn Karlsson (Fri Jan 14 2022 - 01:28:00 PST)
- Re: [AMBER] NETCDF problem David A Case (Fri Jan 14 2022 - 05:13:34 PST)
  - Re: [AMBER] NETCDF problem Björn Karlsson (Fri Jan 14 2022 - 05:27:46 PST)
    - Re: [AMBER] NETCDF problem David A Case (Fri Jan 14 2022 - 08:38:28 PST)
    - Re: [AMBER] NETCDF problem Björn Karlsson (Fri Jan 14 2022 - 09:51:52 PST)
[AMBER] [MCPB] The force field parameter problem of the MCPB Huimin Tian (Fri Jan 14 2022 - 05:30:34 PST)
[AMBER] Error in MMPBSA calculation Sruthi Sudhakar (Fri Jan 14 2022 - 13:54:15 PST)
- Re: [AMBER] Error in MMPBSA calculation Sruthi Sudhakar (Fri Jan 14 2022 - 23:25:20 PST)
[AMBER] Inquiry on LJ parameters in .mdl file for 3D-RISM Alexis Azucena (Sun Jan 16 2022 - 22:42:17 PST)
- Re: [AMBER] Inquiry on LJ parameters in .mdl file for 3D-RISM tluchko (Mon Jan 17 2022 - 11:02:34 PST)
  - Re: [AMBER] Inquiry on LJ parameters in .mdl file for 3D-RISM Alexis Azucena (Mon Jan 17 2022 - 17:33:07 PST)
[AMBER] Bad atom type error and invalid periodicity error in MMPBSA.py Yi Ren (Mon Jan 17 2022 - 00:13:37 PST)
[AMBER] Protein + DNA, which FF? Alan (Mon Jan 17 2022 - 01:50:18 PST)
- Re: [AMBER] Protein + DNA, which FF? Alan (Mon Jan 17 2022 - 02:05:26 PST)
[AMBER] Distorted water molecules in QM partition (possible bug) Antonio Frances Monerris (Mon Jan 17 2022 - 07:56:26 PST)
- Re: [AMBER] Distorted water molecules in QM partition (possible bug) David A Case (Tue Jan 18 2022 - 04:42:33 PST)
[AMBER] Need help with SMD natalia francisca rodriguez cabello (Mon Jan 17 2022 - 08:33:31 PST)
- Re: [AMBER] Need help with SMD Carlos Simmerling (Mon Jan 17 2022 - 09:41:31 PST)
[AMBER] low-water system, bad NPT and NVT Daniel Konstantinovsky (Mon Jan 17 2022 - 15:01:09 PST)
- Re: [AMBER] low-water system, bad NPT and NVT Carlos Simmerling (Mon Jan 17 2022 - 16:38:29 PST)
[AMBER] Converting %FLAG XVV array found in .xvv file into a readable format similar to other .*vv files Daniel Fowles (Tue Jan 18 2022 - 02:25:44 PST)
[AMBER] A4500 Benchmarks Ross Walker (Tue Jan 18 2022 - 06:50:49 PST)
Re: [AMBER] ?==?utf-8?q? Distorted water molecules in QM partition (possible?==?utf-8?q? bug) Antonio Frances Monerris (Tue Jan 18 2022 - 08:26:31 PST)
[AMBER] how to obtain index of atoms based on residue and atom masks Ming Tang (Tue Jan 18 2022 - 17:01:41 PST)
- Re: [AMBER] how to obtain index of atoms based on residue and atom masks Matthew Guberman-Pfeffer (Tue Jan 18 2022 - 19:12:31 PST)
  - Re: [AMBER] how to obtain index of atoms based on residue and atom masks Dr. Anselm Horn (Wed Jan 19 2022 - 02:23:28 PST)
    - Re: [AMBER] how to obtain index of atoms based on residue and atom masks Hai Nguyen (Wed Jan 19 2022 - 12:31:06 PST)
  - Re: [AMBER] how to obtain index of atoms based on residue and atom masks Ming Tang (Wed Jan 19 2022 - 21:35:31 PST)
[AMBER] Improved speed of CPPTRAJ post-clustering steps for large sets Daniel Roe (Tue Jan 18 2022 - 17:21:12 PST)
- Re: [AMBER] Improved speed of CPPTRAJ post-clustering steps for large sets Robert Molt (Tue Jan 18 2022 - 17:22:14 PST)
- Re: [AMBER] Improved speed of CPPTRAJ post-clustering steps for large sets Daniel Roe (Fri Jan 21 2022 - 15:46:28 PST)
[AMBER] Converting %FLAG XVV array found in .xvv file into a readable format similar to other .*vv files Daniel Fowles (Wed Jan 19 2022 - 04:26:45 PST)
- Re: [AMBER] Converting %FLAG XVV array found in .xvv file into a readable format similar to other .*vv files Jason Swails (Thu Jan 20 2022 - 06:23:31 PST)
[AMBER] How to compute MM/PB(GB)SA with Extra Points 王世玉 (Wed Jan 19 2022 - 05:56:30 PST)
- Re: [AMBER] How to compute MM/PB(GB)SA with Extra Points David A Case (Mon Jan 31 2022 - 10:23:18 PST)
  - Re: [AMBER] How to compute MM/PB(GB)SA with Extra Points Ray Luo (Mon Jan 31 2022 - 10:59:52 PST)
  - Re: [AMBER] How to compute MM/PB(GB)SA with Extra Points Matthew Guberman-Pfeffer (Mon Jan 31 2022 - 11:16:36 PST)
    - Re: [AMBER] How to compute MM/PB(GB)SA with Extra Points David A Case (Mon Jan 31 2022 - 18:17:32 PST)
[AMBER] Comparing trajectories Reza Khayat (Wed Jan 19 2022 - 13:04:17 PST)
- Re: [AMBER] Comparing trajectories Thomas Cheatham (Wed Jan 19 2022 - 13:16:26 PST)
  - Re: [AMBER] Comparing trajectories Reza Khayat (Wed Jan 19 2022 - 13:30:11 PST)
    - Re: [AMBER] Comparing trajectories Rodrigo Galindo-Murillo (Wed Jan 19 2022 - 13:45:14 PST)
- Re: [AMBER] Comparing trajectories Carlos Simmerling (Wed Jan 19 2022 - 13:16:36 PST)
[AMBER] Parameterize SO4 zz sheng (Wed Jan 19 2022 - 21:37:41 PST)
- Re: [AMBER] Parameterize SO4 David A Case (Thu Jan 20 2022 - 04:05:09 PST)
  - Re: [AMBER] Parameterize SO4 Matthew Guberman-Pfeffer (Thu Jan 20 2022 - 04:50:00 PST)
    - Re: [AMBER] Parameterize SO4 zz sheng (Thu Jan 20 2022 - 19:24:20 PST)
    - Re: [AMBER] Parameterize SO4 Matthew Guberman-Pfeffer (Thu Jan 20 2022 - 21:57:57 PST)
    - Re: [AMBER] Parameterize SO4 zz sheng (Fri Jan 21 2022 - 05:48:25 PST)
[AMBER] Installing amber20 in conda Ming Tang (Wed Jan 19 2022 - 22:02:10 PST)
- Re: [AMBER] Installing amber20 in conda David A Case (Thu Jan 20 2022 - 04:07:37 PST)
[AMBER] Adding on terminal hydrogen/phosphate to nucleosides in ff86? Kenneth Huang (Thu Jan 20 2022 - 11:03:01 PST)
[AMBER] Aligning a dimer for PCA analysis Kodituwakku,Dimuthu Nirmani (Fri Jan 21 2022 - 08:19:36 PST)
- Re: [AMBER] Aligning a dimer for PCA analysis Daniel Roe (Fri Jan 21 2022 - 11:23:25 PST)
- Re: [AMBER] Aligning a dimer for PCA analysis Dr. Anselm Horn (Mon Jan 24 2022 - 01:33:09 PST)
[AMBER] GaMD error: cudaMemcpy GpuBuffer::Download failed an illegal memory access was encountered Li,Haoxi (Fri Jan 21 2022 - 08:37:26 PST)
Re: [AMBER] Archive page Thomas Cheatham (Fri Jan 21 2022 - 15:29:52 PST)
- Re: [AMBER] Archive page James Kress (Fri Jan 21 2022 - 15:48:27 PST)
[AMBER] any working singularity or docker recipe? (esp for CUDA and MPI) Michael Coleman (Fri Jan 21 2022 - 21:05:14 PST)
- Re: [AMBER] any working singularity or docker recipe? (esp for CUDA and MPI) Gerald Monard (Sun Jan 23 2022 - 03:31:05 PST)
  - Re: [AMBER] any working singularity or docker recipe? (esp for CUDA and MPI) Gerald Monard (Sun Jan 23 2022 - 03:39:06 PST)
    - Re: [AMBER] any working singularity or docker recipe? (esp for CUDA and MPI) Michael Coleman (Sun Jan 23 2022 - 13:42:39 PST)
    - Re: [AMBER] any working singularity or docker recipe? (esp for CUDA and MPI) Karl Kirschner (Mon Jan 24 2022 - 00:20:57 PST)
    - Re: [AMBER] any working singularity or docker recipe? (esp for CUDA and MPI) David A Case (Mon Jan 24 2022 - 06:27:00 PST)
    - Re: [AMBER] any working singularity or docker recipe? (esp for CUDA and MPI) Michael Coleman (Mon Jan 24 2022 - 15:51:36 PST)
    - Re: [AMBER] any working singularity or docker recipe? (esp for CUDA and MPI) David A Case (Tue Jan 25 2022 - 06:22:07 PST)
[AMBER] ghost pmemd.cuda process ? Jordi Bujons (Sat Jan 22 2022 - 13:02:53 PST)
- Re: [AMBER] ghost pmemd.cuda process ? Ross Walker (Mon Jan 24 2022 - 06:45:16 PST)
- Re: [AMBER] ghost pmemd.cuda process ? Jordi Bujons (Tue Jan 25 2022 - 07:52:59 PST)
[AMBER] Distorted average pdb structure from 10 ns trajectory !!! A R (Sun Jan 23 2022 - 06:03:06 PST)
- Re: [AMBER] Distorted average pdb structure from 10 ns trajectory !!! Carlos Simmerling (Sun Jan 23 2022 - 06:11:04 PST)
[AMBER] hydrogen mass repartitioning with accelerated MD James Kress (Sun Jan 23 2022 - 11:05:32 PST)
[AMBER] Negative DIHEDRAL_PERIODICITY in prmtop for amber20-benchmark FactorIX benchmark John Chodera (Sun Jan 23 2022 - 18:58:51 PST)
- Re: [AMBER] Negative DIHEDRAL_PERIODICITY in prmtop for amber20-benchmark FactorIX benchmark David A Case (Mon Jan 24 2022 - 06:47:41 PST)
  - Re: [AMBER] Negative DIHEDRAL_PERIODICITY in prmtop for amber20-benchmark FactorIX benchmark Piotr Cieplak (Mon Jan 24 2022 - 12:39:44 PST)
    - Re: [AMBER] Negative DIHEDRAL_PERIODICITY in prmtop for amber20-benchmark FactorIX benchmark David A Case (Mon Jan 24 2022 - 13:43:22 PST)
    - Re: [AMBER] Negative DIHEDRAL_PERIODICITY in prmtop for amber20-benchmark FactorIX benchmark John Chodera (Tue Jan 25 2022 - 14:06:35 PST)
    - Re: [AMBER] Negative DIHEDRAL_PERIODICITY in prmtop for amber20-benchmark FactorIX benchmark Dr. Anselm Horn (Wed Jan 26 2022 - 03:15:06 PST)
    - Re: [AMBER] Negative DIHEDRAL_PERIODICITY in prmtop for amber20-benchmark FactorIX benchmark David A Case (Wed Jan 26 2022 - 07:08:27 PST)
    - Re: [AMBER] Negative DIHEDRAL_PERIODICITY in prmtop for amber20-benchmark FactorIX benchmark David A Case (Wed Jan 26 2022 - 12:34:53 PST)
[AMBER] Restraint file for amber20 with pmemd.cuda implementation Prithviraj Nandigrami (Mon Jan 24 2022 - 13:31:04 PST)
- Re: [AMBER] Restraint file for amber20 with pmemd.cuda implementation Carlos Simmerling (Mon Jan 24 2022 - 13:46:26 PST)
- Re: [AMBER] Restraint file for amber20 with pmemd.cuda implementation Prithviraj Nandigrami (Mon Jan 24 2022 - 14:24:21 PST)
  - Re: [AMBER] Restraint file for amber20 with pmemd.cuda implementation David A Case (Tue Jan 25 2022 - 06:06:04 PST)
- Re: [AMBER] Restraint file for amber20 with pmemd.cuda implementation Prithviraj Nandigrami (Tue Jan 25 2022 - 07:16:34 PST)
  - Re: [AMBER] Restraint file for amber20 with pmemd.cuda implementation Carlos Simmerling (Tue Jan 25 2022 - 07:26:00 PST)
  - Re: [AMBER] Restraint file for amber20 with pmemd.cuda implementation David A Case (Tue Jan 25 2022 - 10:11:24 PST)
[AMBER] MEOHBOX/CHCL3BOX not working Daniel Konstantinovsky (Mon Jan 24 2022 - 13:41:54 PST)
- Re: [AMBER] MEOHBOX/CHCL3BOX not working Matthew Guberman-Pfeffer (Mon Jan 24 2022 - 13:59:32 PST)
  - Re: [AMBER] MEOHBOX/CHCL3BOX not working Daniel Konstantinovsky (Mon Jan 24 2022 - 14:17:54 PST)
    - Re: [AMBER] MEOHBOX/CHCL3BOX not working Matthew Guberman-Pfeffer (Mon Jan 24 2022 - 14:21:49 PST)
[AMBER] Regarding targeted md Pranabesh Mandal (PhD, Bioinformatics August-2019) (Mon Jan 24 2022 - 20:30:36 PST)
- Re: [AMBER] Regarding targeted md Carlos Simmerling (Tue Jan 25 2022 - 04:17:16 PST)
- Re: [AMBER] Regarding targeted md Pranabesh Mandal (PhD, Bioinformatics August-2019) (Wed Jan 26 2022 - 23:27:37 PST)
  - Re: [AMBER] Regarding targeted md Carlos Simmerling (Thu Jan 27 2022 - 03:50:43 PST)
[AMBER] adding ions to half the water box Daniel Konstantinovsky (Tue Jan 25 2022 - 08:54:53 PST)
- Re: [AMBER] adding ions to half the water box David A Case (Tue Jan 25 2022 - 10:19:28 PST)
  - Re: [AMBER] adding ions to half the water box Hai Nguyen (Tue Jan 25 2022 - 18:04:42 PST)
[AMBER] CPPTRAJ for Buried SA King Wu (Tue Jan 25 2022 - 16:16:53 PST)
[AMBER] dihedral restraints slowing down simulation Richard Kullmann (Wed Jan 26 2022 - 06:22:50 PST)
- Re: [AMBER] dihedral restraints slowing down simulation David A Case (Wed Jan 26 2022 - 12:13:51 PST)
  - Re: [AMBER] dihedral restraints slowing down simulation Carlos Simmerling (Wed Jan 26 2022 - 13:41:43 PST)
    - Re: [AMBER] dihedral restraints slowing down simulation Kellon Belfon (Thu Jan 27 2022 - 00:46:42 PST)
    - Re: [AMBER] dihedral restraints slowing down simulation Richard Kullmann (Thu Jan 27 2022 - 01:57:40 PST)
    - Re: [AMBER] dihedral restraints slowing down simulation Carlos Simmerling (Thu Jan 27 2022 - 03:43:40 PST)
    - Re: [AMBER] dihedral restraints slowing down simulation Richard Kullmann (Thu Jan 27 2022 - 06:28:19 PST)
    - Re: [AMBER] dihedral restraints slowing down simulation Carlos Simmerling (Fri Jan 28 2022 - 09:30:46 PST)
    - Re: [AMBER] dihedral restraints slowing down simulation Kellon Belfon (Thu Jan 27 2022 - 04:48:34 PST)
    - Re: [AMBER] dihedral restraints slowing down simulation Kellon Belfon (Thu Jan 27 2022 - 05:09:15 PST)
[AMBER] LIE calculation with distance-based mask - reg. Naveen Kumar Vasudevan (Wed Jan 26 2022 - 17:25:52 PST)
[AMBER] The effect of water box size for TI free energy calculation zz sheng (Wed Jan 26 2022 - 21:17:57 PST)
[AMBER] Umbrella Sampling Collective Variable Volkan Findik (Wed Jan 26 2022 - 23:25:09 PST)
[AMBER] Calculating energies per residue pair, rather than per residue Tue (Thu Jan 27 2022 - 18:09:32 PST)
- Re: [AMBER] Calculating energies per residue pair, rather than per residue Matthew Guberman-Pfeffer (Thu Jan 27 2022 - 19:34:24 PST)
- Re: [AMBER] Calculating energies per residue pair, rather than per residue Carlos Simmerling (Fri Jan 28 2022 - 02:09:14 PST)
[AMBER] Issue concerning the AMBER/TeraChem interface Jiang, Yaoyukun (Thu Jan 27 2022 - 19:56:00 PST)
- Re: [AMBER] Issue concerning the AMBER/TeraChem interface Vinicius Wilian Cruzeiro (Thu Jan 27 2022 - 20:40:31 PST)
[AMBER] Torsion parameters Cenk Andac (Fri Jan 28 2022 - 04:30:26 PST)
- Re: [AMBER] Torsion parameters Karl Kirschner (Fri Jan 28 2022 - 04:59:23 PST)
  - Re: [AMBER] Torsion parameters Cenk Andac (Fri Jan 28 2022 - 06:13:33 PST)

Amber Archive Jan 2022 by thread