Amber Archive Apr 2017: by subject

[AMBER] 3 GPUs ?
- Chris Neale (Wed Apr 05 2017 - 17:04:27 PDT)
- Ross Walker (Wed Apr 05 2017 - 12:41:33 PDT)
- Chris Neale (Tue Apr 04 2017 - 17:06:04 PDT)
- Ross Walker (Tue Apr 04 2017 - 16:46:34 PDT)
- Chris Neale (Tue Apr 04 2017 - 13:28:43 PDT)
- Ross Walker (Tue Apr 04 2017 - 08:26:57 PDT)
- Andreas Tosstorff (Tue Apr 04 2017 - 00:18:53 PDT)
- Chris Neale (Mon Apr 03 2017 - 19:43:01 PDT)
[AMBER] 3D-RISM centering 0
- Lucia Fusani (Wed Apr 26 2017 - 08:45:30 PDT)
- Tyler Luchko (Lists) (Thu Apr 20 2017 - 11:18:04 PDT)
- Lucia Fusani (Thu Apr 20 2017 - 10:05:42 PDT)
[AMBER] 4.5 fold increase in memory consumption for nmr restraints going from amber14 to amber16
- Paul Westphaelinger (Wed Apr 05 2017 - 13:03:53 PDT)
- Charles Lin (Wed Apr 05 2017 - 12:46:03 PDT)
[AMBER] About Tutorial B3
- David Case (Thu Apr 13 2017 - 18:44:17 PDT)
- Hadeer ELHabashy (Thu Apr 13 2017 - 15:40:12 PDT)
[AMBER] Acetonitrile Water Mix
- Marcos Serrou do Amaral (Fri Apr 07 2017 - 06:44:44 PDT)
- Andreas Tosstorff (Fri Apr 07 2017 - 06:32:01 PDT)
- Marcos Serrou do Amaral (Fri Apr 07 2017 - 05:58:51 PDT)
- Andreas Tosstorff (Wed Apr 05 2017 - 09:08:53 PDT)
- David Cerutti (Wed Apr 05 2017 - 08:00:55 PDT)
- Sowmya Indrakumar (Wed Apr 05 2017 - 07:48:34 PDT)
- David A Case (Wed Apr 05 2017 - 07:37:58 PDT)
- Andreas Tosstorff (Wed Apr 05 2017 - 05:50:55 PDT)
- Marcos Serrou do Amaral (Wed Apr 05 2017 - 05:46:25 PDT)
- Andreas Tosstorff (Wed Apr 05 2017 - 05:35:31 PDT)
[AMBER] Adding hydrogens to a ligand
- jacob wick (Tue Apr 18 2017 - 03:27:54 PDT)
- Hannes Loeffler (Tue Apr 18 2017 - 02:22:38 PDT)
- Bill Ross (Tue Apr 18 2017 - 02:22:20 PDT)
- jacob wick (Tue Apr 18 2017 - 01:57:34 PDT)
[AMBER] Amber 16 does not read the "ncsu_smd" from a QMMM input file
- Samaneh Ghassabi Kondalaji (Mon Apr 17 2017 - 11:36:58 PDT)
- Goetz, Andreas (Mon Apr 17 2017 - 11:21:32 PDT)
- Samaneh Ghassabi Kondalaji (Mon Apr 17 2017 - 10:40:37 PDT)
- Samaneh Ghassabi Kondalaji (Mon Apr 17 2017 - 10:19:55 PDT)
- Goetz, Andreas (Mon Apr 17 2017 - 10:15:17 PDT)
- Feng Pan (Mon Apr 17 2017 - 10:11:22 PDT)
- Samaneh Ghassabi Kondalaji (Mon Apr 17 2017 - 09:50:20 PDT)
- Samaneh Ghassabi Kondalaji (Thu Apr 13 2017 - 09:56:02 PDT)
- Hannes Loeffler (Thu Apr 13 2017 - 09:35:02 PDT)
- Samaneh Ghassabi Kondalaji (Thu Apr 13 2017 - 09:01:35 PDT)
- Hannes Loeffler (Thu Apr 13 2017 - 08:40:22 PDT)
- Samaneh Ghassabi Kondalaji (Thu Apr 13 2017 - 08:29:59 PDT)
[AMBER] AMBER umbrella sampling
- 吴萌 (Fri Apr 14 2017 - 20:02:07 PDT)
- Feng Pan (Thu Apr 13 2017 - 13:04:56 PDT)
- Andreas Tosstorff (Thu Apr 13 2017 - 09:59:01 PDT)
- Hannes Loeffler (Thu Apr 13 2017 - 06:04:10 PDT)
- 吴萌 (Thu Apr 13 2017 - 02:27:20 PDT)
[AMBER] AmberTools17 + intel17 = bug
- Hector A. Baldoni (Wed Apr 19 2017 - 06:09:50 PDT)
- David Case (Tue Apr 18 2017 - 18:19:19 PDT)
- Daniel Roe (Tue Apr 18 2017 - 17:34:24 PDT)
- Hector A. Baldoni (Tue Apr 18 2017 - 16:30:05 PDT)
- Hector A. Baldoni (Tue Apr 18 2017 - 16:02:39 PDT)
[AMBER] AmberTools17: test of mpi configuration with pnetcdf failed on Mac OS X 10.10
- Mooers, Blaine H.M. (HSC) (Wed Apr 26 2017 - 08:06:50 PDT)
- David Case (Sun Apr 23 2017 - 14:57:40 PDT)
- Mooers, Blaine H.M. (HSC) (Sun Apr 23 2017 - 09:10:44 PDT)
- David Case (Sun Apr 23 2017 - 06:00:41 PDT)
- Mooers, Blaine H.M. (HSC) (Sat Apr 22 2017 - 14:01:02 PDT)
- David Case (Fri Apr 21 2017 - 18:42:49 PDT)
- Mooers, Blaine H.M. (HSC) (Fri Apr 21 2017 - 12:36:27 PDT)
[AMBER] Announcement: Release of DOCK 6.8
- Scott Brozell (Thu Apr 27 2017 - 13:23:57 PDT)
[AMBER] antechamber convergence problem.
- David Case (Tue Apr 25 2017 - 05:07:34 PDT)
- Vatsal Purohit (Mon Apr 24 2017 - 13:32:52 PDT)
[AMBER] antechamber problem
- Maura Malinska (Thu Apr 13 2017 - 00:25:10 PDT)
- Niel Henriksen (Wed Apr 12 2017 - 09:54:53 PDT)
- Gerald Monard (Wed Apr 12 2017 - 08:00:39 PDT)
- David Case (Wed Apr 12 2017 - 07:47:07 PDT)
- Maura Malinska (Wed Apr 12 2017 - 06:59:37 PDT)
[AMBER] Atom types for Baaden Hydronium Ion
- Samaneh Ghassabi Kondalaji (Wed Apr 05 2017 - 13:11:21 PDT)
- David A Case (Wed Apr 05 2017 - 12:17:21 PDT)
- Samaneh Ghassabi Kondalaji (Wed Apr 05 2017 - 09:06:39 PDT)
- David A Case (Wed Apr 05 2017 - 04:51:49 PDT)
- Samaneh Ghassabi Kondalaji (Tue Apr 04 2017 - 18:51:26 PDT)
[AMBER] barostat=1 error at Stampede
- Elvis Martis (Thu Apr 27 2017 - 07:05:42 PDT)
- Ross Walker (Thu Apr 27 2017 - 04:33:35 PDT)
- Bill Ross (Thu Apr 27 2017 - 00:23:15 PDT)
- Elvis Martis (Wed Apr 26 2017 - 23:53:12 PDT)
- Elvis Martis (Wed Apr 26 2017 - 23:51:56 PDT)
- Tarsis (Wed Apr 26 2017 - 13:10:05 PDT)
[AMBER] BCC charge for my HEME
- David Case (Fri Apr 14 2017 - 11:34:28 PDT)
- Elvis Martis (Fri Apr 14 2017 - 09:42:25 PDT)
- Thakur, Abhishek (Fri Apr 14 2017 - 09:16:23 PDT)
- Elvis Martis (Fri Apr 14 2017 - 08:29:23 PDT)
- Thakur, Abhishek (Fri Apr 14 2017 - 07:12:51 PDT)
[AMBER] Binding site volume calculation
- David A Case (Wed Apr 05 2017 - 12:14:29 PDT)
- Thakur, Abhishek (Wed Apr 05 2017 - 08:45:53 PDT)
[AMBER] Can't not run cpptraj
- Khatcharin Siriwong (Thu Apr 20 2017 - 20:04:39 PDT)
- Gulsevin,Alican (Thu Apr 20 2017 - 19:45:42 PDT)
- Khatcharin Siriwong (Thu Apr 20 2017 - 19:21:13 PDT)
- Hai Nguyen (Thu Apr 20 2017 - 19:15:51 PDT)
- Khatcharin Siriwong (Thu Apr 20 2017 - 19:13:06 PDT)
[AMBER] Compilation of MPI 3D-RISM issue in amber1 4
- Nhai (Thu Apr 13 2017 - 22:13:26 PDT)
- Tyler Luchko (Lists) (Thu Apr 13 2017 - 22:03:50 PDT)
- Rakesh Srivastava (Thu Apr 13 2017 - 21:54:07 PDT)
[AMBER] consult about LEaP in amber
- Elvis Martis (Wed Apr 26 2017 - 03:39:01 PDT)
- 张壮壮 (Tue Apr 25 2017 - 20:49:48 PDT)
[AMBER] coordinate bond between them and S and FE
- David Case (Mon Apr 17 2017 - 09:00:50 PDT)
- Thakur, Abhishek (Mon Apr 17 2017 - 08:38:55 PDT)
- Adrian Roitberg (Mon Apr 17 2017 - 08:14:58 PDT)
- Thakur, Abhishek (Mon Apr 17 2017 - 07:45:31 PDT)
- Andrew Schaub (Fri Apr 14 2017 - 14:23:27 PDT)
- Adrian Roitberg (Fri Apr 14 2017 - 13:48:37 PDT)
- Thakur, Abhishek (Fri Apr 14 2017 - 13:44:44 PDT)
- Marcos Serrou do Amaral (Fri Apr 14 2017 - 12:24:54 PDT)
- Thakur, Abhishek (Fri Apr 14 2017 - 12:18:37 PDT)
[AMBER] coordinates in restraint mast
- Daniel Roe (Mon Apr 03 2017 - 10:29:24 PDT)
- Thomas Evangelidis (Sun Apr 02 2017 - 09:25:48 PDT)
[AMBER] cpptraj analysis of two different dsDNA strands.
- James Kress (Sun Apr 09 2017 - 08:43:57 PDT)
- Nhai (Sun Apr 09 2017 - 01:35:49 PDT)
- James Kress (Sat Apr 08 2017 - 11:31:57 PDT)
[AMBER] CPPTRAJ Cluster
- Daniel Roe (Wed Apr 05 2017 - 10:08:46 PDT)
- d00b46022 (Wed Apr 05 2017 - 02:26:09 PDT)
[AMBER] cpptraj configure may fail in AmberTools17
- Daniel Roe (Tue Apr 25 2017 - 06:16:46 PDT)
- Hannes Loeffler (Sat Apr 22 2017 - 03:38:57 PDT)
[AMBER] cpptraj creates pdb file it cannot read
- James Kress (Mon Apr 17 2017 - 13:26:03 PDT)
- Daniel Roe (Mon Apr 17 2017 - 05:40:13 PDT)
- Jason Swails (Sun Apr 16 2017 - 19:56:34 PDT)
- James Kress (Sun Apr 16 2017 - 11:41:41 PDT)
- Daniel Roe (Sun Apr 16 2017 - 08:17:09 PDT)
- James Kress (Sat Apr 15 2017 - 14:09:56 PDT)
- Daniel Roe (Wed Apr 12 2017 - 08:05:56 PDT)
- Hai Nguyen (Wed Apr 12 2017 - 07:47:21 PDT)
- James Kress (Wed Apr 12 2017 - 07:28:47 PDT)
- Elka Firmanda (Tue Apr 11 2017 - 23:00:55 PDT)
- James Kress (Tue Apr 11 2017 - 14:37:10 PDT)
- James Kress (Tue Apr 11 2017 - 14:03:17 PDT)
- Hai Nguyen (Tue Apr 11 2017 - 13:51:49 PDT)
- James Kress (Tue Apr 11 2017 - 13:44:09 PDT)
- Hai Nguyen (Tue Apr 11 2017 - 13:07:16 PDT)
- James Kress (Tue Apr 11 2017 - 12:29:13 PDT)
[AMBER] Creating a pdb of only certain molecules from a frame
- Daniel Roe (Mon Apr 10 2017 - 11:46:20 PDT)
- Aseel Bala (Tue Apr 04 2017 - 09:46:37 PDT)
[AMBER] density plot of Na+ ions using grid
- Mary Varughese (Tue Apr 04 2017 - 23:17:14 PDT)
[AMBER] Dftb3
- David Case (Sat Apr 29 2017 - 14:33:59 PDT)
- Jacopo Sgrignani (Sat Apr 29 2017 - 13:40:28 PDT)
[AMBER] Diffusion and permeability coefficients
- Fabrício Bracht (Thu Apr 06 2017 - 13:21:14 PDT)
- Chris Neale (Thu Apr 06 2017 - 12:16:12 PDT)
- Fabrício Bracht (Thu Apr 06 2017 - 12:01:19 PDT)
[AMBER] Discrepancy in delta G total and per residues decomposition results in MMPBSA.py
- mish (Wed Apr 12 2017 - 01:35:32 PDT)
[AMBER] Discussion questions regarding PyRED FF development
- Iqbal, Muhammad Sajid (Tue Apr 18 2017 - 10:28:40 PDT)
[AMBER] distance calculations - Protein-RNA
- Daniel Roe (Tue Apr 04 2017 - 05:17:02 PDT)
- Bill Ross (Tue Apr 04 2017 - 01:59:59 PDT)
- Sidhu, Khushwant (Dr.) (Tue Apr 04 2017 - 01:50:01 PDT)
[AMBER] DNA Tutorial B1 - Temperature Drop
- Johannes Kalliauer (Tue Apr 11 2017 - 02:42:42 PDT)
[AMBER] Early-bird and bursary deadline April 30: eChemInfo Training and Innovation Course in Drug Design
- Thomas Exner (Mon Apr 24 2017 - 04:09:50 PDT)
[AMBER] eChemInfo Training and Innovation Course in Drug Design
- Thomas Exner (Tue Apr 04 2017 - 02:51:20 PDT)
[AMBER] ERROR in load_lbfgs(): YS=0.
- 杨满意 (Thu Apr 13 2017 - 19:20:45 PDT)
- David A Case (Thu Apr 13 2017 - 04:49:29 PDT)
- 杨满意 (Wed Apr 12 2017 - 20:46:26 PDT)
[AMBER] Error when running MMPBSA calculation using Force field from CHARMM GUI membrane builder running on amber.
- David Case (Sat Apr 29 2017 - 05:28:00 PDT)
- Miguel Rivera (Fri Apr 28 2017 - 15:12:18 PDT)
[AMBER] Error with 'surf' and acetonitrile-water solvent mixture
- Marcel Passon (Thu Apr 27 2017 - 01:21:32 PDT)
[AMBER] Error with MMPSA.py calculation
- Jason Swails (Wed Apr 19 2017 - 17:20:59 PDT)
- Praneeth Bommisetti (Tue Apr 18 2017 - 14:22:16 PDT)
[AMBER] EVB with RPMD
- David Case (Wed Apr 19 2017 - 08:59:58 PDT)
- Rob Arbon (Wed Apr 19 2017 - 08:25:33 PDT)
[AMBER] External electric fields on CUDA enabled PMEMD
- Neville Bethel (Sun Apr 30 2017 - 13:14:00 PDT)
[AMBER] failed to generate parameter and topology file for protein-ligand complex containing zinc
- Elvis Martis (Mon Apr 24 2017 - 00:24:14 PDT)
- Elvis Martis (Sat Apr 22 2017 - 05:53:17 PDT)
- Sharon D. Morris (Sat Apr 22 2017 - 02:00:17 PDT)
[AMBER] Format error in frcmod file of HEME
- Thakur, Abhishek (Fri Apr 14 2017 - 11:46:25 PDT)
- David Case (Fri Apr 14 2017 - 11:41:09 PDT)
- Marcos Serrou do Amaral (Fri Apr 14 2017 - 09:50:57 PDT)
- Thakur, Abhishek (Fri Apr 14 2017 - 09:42:46 PDT)
[AMBER] GB Methodology for Nucleic Acid to calculate Internal energy
- Bill Ross (Thu Apr 06 2017 - 01:57:08 PDT)
- Bill Ross (Thu Apr 06 2017 - 00:41:25 PDT)
- Ramin Salimi (Wed Apr 05 2017 - 19:54:43 PDT)
- Bill Ross (Wed Apr 05 2017 - 10:35:51 PDT)
- Daniel Roe (Wed Apr 05 2017 - 09:20:33 PDT)
- Ramin Salimi (Wed Apr 05 2017 - 03:01:25 PDT)
- Bill Ross (Tue Apr 04 2017 - 21:17:26 PDT)
- Ramin Salimi (Tue Apr 04 2017 - 19:13:38 PDT)
- David Case (Tue Apr 04 2017 - 18:44:22 PDT)
- Carlos Simmerling (Tue Apr 04 2017 - 14:19:54 PDT)
- Ramin Salimi (Tue Apr 04 2017 - 10:50:13 PDT)
- David A Case (Tue Apr 04 2017 - 05:17:39 PDT)
- Ramin Salimi (Mon Apr 03 2017 - 18:02:46 PDT)
[AMBER] GPU performance
- Ross Walker (Wed Apr 05 2017 - 16:26:41 PDT)
- Andreas Tosstorff (Wed Apr 05 2017 - 07:35:54 PDT)
- Sofia Vasilakaki (Wed Apr 05 2017 - 07:27:35 PDT)
[AMBER] GTX 1080 error
- Ross Walker (Thu Apr 06 2017 - 14:30:04 PDT)
- Paul Westphaelinger (Thu Apr 06 2017 - 13:49:44 PDT)
- Jacopo Sgrignani (Thu Apr 06 2017 - 13:41:57 PDT)
[AMBER] HEME-CYS
- Elvis Martis (Wed Apr 19 2017 - 09:50:05 PDT)
- Thakur, Abhishek (Wed Apr 19 2017 - 09:42:58 PDT)
- Elvis Martis (Wed Apr 19 2017 - 09:35:02 PDT)
- Thakur, Abhishek (Wed Apr 19 2017 - 07:19:20 PDT)
- Elvis Martis (Tue Apr 18 2017 - 21:44:33 PDT)
- Thakur, Abhishek (Tue Apr 18 2017 - 09:10:04 PDT)
- Elvis Martis (Tue Apr 18 2017 - 08:22:26 PDT)
- Elvis Martis (Mon Apr 17 2017 - 20:31:14 PDT)
- Elvis Martis (Mon Apr 17 2017 - 20:30:25 PDT)
- Thakur, Abhishek (Mon Apr 17 2017 - 11:37:43 PDT)
- Thakur, Abhishek (Mon Apr 17 2017 - 10:56:41 PDT)
- Elvis Martis (Mon Apr 17 2017 - 10:10:21 PDT)
- Thakur, Abhishek (Mon Apr 17 2017 - 09:45:38 PDT)
[AMBER] How to calculate the solvation free energy using Amber?
- hannes.loeffler.stfc.ac.uk (Mon Apr 17 2017 - 03:19:43 PDT)
- Bill Ross (Mon Apr 17 2017 - 01:52:51 PDT)
- JinpengYang (Mon Apr 17 2017 - 01:05:07 PDT)
[AMBER] How to distinguish between water molecules?
- Jason Swails (Wed Apr 05 2017 - 05:53:56 PDT)
- Markowska (Wed Apr 05 2017 - 05:52:05 PDT)
- Hannes Loeffler (Wed Apr 05 2017 - 05:42:57 PDT)
- Markowska (Wed Apr 05 2017 - 05:11:07 PDT)
- David A Case (Wed Apr 05 2017 - 04:55:30 PDT)
- Hannes Loeffler (Wed Apr 05 2017 - 04:50:34 PDT)
- Markowska (Wed Apr 05 2017 - 04:32:05 PDT)
- Hannes Loeffler (Wed Apr 05 2017 - 02:53:06 PDT)
- Markowska (Wed Apr 05 2017 - 02:11:03 PDT)
[AMBER] How to make sure there is bond in my complex
- Thakur, Abhishek (Thu Apr 20 2017 - 12:23:09 PDT)
- Hai Nguyen (Thu Apr 20 2017 - 12:17:09 PDT)
- Thakur, Abhishek (Thu Apr 20 2017 - 12:06:48 PDT)
- Hai Nguyen (Thu Apr 20 2017 - 11:59:20 PDT)
- Thakur, Abhishek (Thu Apr 20 2017 - 11:56:22 PDT)
[AMBER] How to perform good quality local optimization with Sander
- David Case (Sat Apr 01 2017 - 06:17:22 PDT)
- danil kutov (Sat Apr 01 2017 - 00:48:50 PDT)
[AMBER] How to write an frcmod file
- Hannes Loeffler (Thu Apr 06 2017 - 02:15:43 PDT)
- Andreas Tosstorff (Thu Apr 06 2017 - 01:13:23 PDT)
[AMBER] Incorrect ligand parameterization using GAFF
- Hannes Loeffler (Fri Apr 14 2017 - 01:23:26 PDT)
- David Case (Thu Apr 13 2017 - 18:40:41 PDT)
- Emilia Pecora-de-barros (Thu Apr 13 2017 - 10:16:07 PDT)
[AMBER] Internal dielectric constant and pmemd
- Samaneh Ghassabi Kondalaji (Fri Apr 21 2017 - 14:23:48 PDT)
- Thomas Cheatham (Fri Apr 21 2017 - 13:48:22 PDT)
- James Kress (Fri Apr 21 2017 - 11:19:43 PDT)
- Samaneh Ghassabi Kondalaji (Fri Apr 21 2017 - 11:04:34 PDT)
- James Kress (Fri Apr 21 2017 - 09:55:38 PDT)
- James Kress (Fri Apr 21 2017 - 09:53:13 PDT)
- Samaneh Ghassabi Kondalaji (Fri Apr 21 2017 - 06:36:17 PDT)
- Adrian Roitberg (Fri Apr 21 2017 - 06:26:37 PDT)
- Samaneh Ghassabi Kondalaji (Fri Apr 21 2017 - 06:21:45 PDT)
- Adrian Roitberg (Fri Apr 21 2017 - 06:14:52 PDT)
- Samaneh Ghassabi Kondalaji (Fri Apr 21 2017 - 06:11:47 PDT)
- David Case (Fri Apr 21 2017 - 05:04:49 PDT)
- Samaneh Ghassabi Kondalaji (Thu Apr 20 2017 - 11:02:59 PDT)
[AMBER] intra-residue water bridge with cpptraj
- Joanna Sarzynska (Fri Apr 28 2017 - 03:22:09 PDT)
- Daniel Roe (Wed Apr 26 2017 - 08:25:49 PDT)
- Joanna Sarzynska (Wed Apr 26 2017 - 07:27:36 PDT)
[AMBER] Is Hvib (vibration contribution to enthalpy) considered/calculated in NMA in NAB program?
- Guqin Shi (Sat Apr 22 2017 - 13:43:33 PDT)
- David Case (Sat Apr 22 2017 - 05:38:53 PDT)
- Guqin Shi (Fri Apr 21 2017 - 21:05:34 PDT)
- David Case (Fri Apr 21 2017 - 19:34:03 PDT)
- Guqin Shi (Fri Apr 21 2017 - 07:58:01 PDT)
- David Case (Thu Apr 20 2017 - 18:48:12 PDT)
- Guqin Shi (Thu Apr 20 2017 - 15:59:14 PDT)
[AMBER] Linkage problem in branched oligosaccharide
- Manju Sah (Sat Apr 01 2017 - 03:10:13 PDT)
[AMBER] Membrane Protein Simulation Methodology
- Gulsevin,Alican (Mon Apr 24 2017 - 04:10:18 PDT)
- Elvis Martis (Thu Apr 20 2017 - 22:13:20 PDT)
- Edson Katekawa (Thu Apr 20 2017 - 11:18:24 PDT)
- Gulsevin,Alican (Thu Apr 20 2017 - 08:53:30 PDT)
[AMBER] Minimization fails when switching from steepest descent to conjugate gradient
- Andreas Tosstorff (Sun Apr 09 2017 - 14:40:02 PDT)
- Chris Moth (Sun Apr 09 2017 - 14:06:06 PDT)
- Hai Nguyen (Sat Apr 08 2017 - 22:43:42 PDT)
- Elvis Martis (Sat Apr 08 2017 - 22:23:07 PDT)
- Andreas Tosstorff (Sat Apr 08 2017 - 16:08:36 PDT)
[AMBER] Minor bug with updating Amber/AmberTools with Python3
- Hai Nguyen (Thu Apr 20 2017 - 13:57:28 PDT)
- Rohith Mohan (Thu Apr 20 2017 - 13:52:35 PDT)
[AMBER] MMPBSA - error
- Ray Luo (Thu Apr 20 2017 - 09:06:20 PDT)
- Anna Cebrian Prats (Thu Apr 20 2017 - 08:02:45 PDT)
[AMBER] mmpbsa - stability calculation
- David Case (Mon Apr 03 2017 - 05:11:33 PDT)
- Mary Varughese (Mon Apr 03 2017 - 00:12:32 PDT)
[AMBER] MMPBSA entropy calculation help
- David Case (Mon Apr 10 2017 - 05:29:00 PDT)
- Mary Varughese (Mon Apr 10 2017 - 04:02:21 PDT)
[AMBER] mmpbsa- binding energy between ligand-receptor
- Anna Cebrian Prats (Tue Apr 04 2017 - 06:27:06 PDT)
[AMBER] multinode pmemd.cuda.MPI jac9999 behavior
- Nhai (Tue Apr 25 2017 - 16:10:53 PDT)
- Daniel Roe (Tue Apr 25 2017 - 13:02:46 PDT)
- Ross Walker (Tue Apr 25 2017 - 12:32:21 PDT)
- Scott Brozell (Tue Apr 25 2017 - 10:48:19 PDT)
- David Case (Tue Apr 25 2017 - 10:27:45 PDT)
- Scott Brozell (Tue Apr 25 2017 - 08:44:50 PDT)
- Daniel Roe (Tue Apr 25 2017 - 06:09:14 PDT)
- Scott Brozell (Mon Apr 24 2017 - 13:26:21 PDT)
[AMBER] Pairwise energy calculations in cpptraj
- Daniel Roe (Tue Apr 25 2017 - 06:33:09 PDT)
- Aishani Prem (Mon Apr 24 2017 - 20:07:52 PDT)
[AMBER] parmed doesn't give any output or error message
- Sadegh Faramarzi Ganjabad (Wed Apr 05 2017 - 10:55:59 PDT)
[AMBER] PCA - concatenating trajectories
- George Tzotzos (Mon Apr 17 2017 - 07:12:23 PDT)
- Chris Neale (Mon Apr 17 2017 - 06:58:57 PDT)
- Daniel Roe (Mon Apr 17 2017 - 06:25:47 PDT)
- George Tzotzos (Mon Apr 17 2017 - 06:23:53 PDT)
- Adrian Roitberg (Mon Apr 17 2017 - 06:21:50 PDT)
- George Tzotzos (Mon Apr 17 2017 - 06:19:03 PDT)
[AMBER] Periodic box error for restarting simulations with restraints
- Sadegh Faramarzi Ganjabad (Sun Apr 16 2017 - 00:24:41 PDT)
- Chris Neale (Thu Apr 13 2017 - 13:19:14 PDT)
- Sadegh Faramarzi Ganjabad (Thu Apr 13 2017 - 13:12:21 PDT)
- Bill Ross (Tue Apr 11 2017 - 13:15:59 PDT)
- Sadegh Faramarzi Ganjabad (Tue Apr 11 2017 - 12:39:12 PDT)
- Bill Ross (Fri Apr 07 2017 - 22:13:48 PDT)
- Sadegh Faramarzi Ganjabad (Fri Apr 07 2017 - 22:05:37 PDT)
- Daniel Roe (Fri Apr 07 2017 - 06:08:09 PDT)
- Sadegh Faramarzi Ganjabad (Fri Apr 07 2017 - 00:44:28 PDT)
[AMBER] placing water at specified coordinates with tleap
- David Case (Mon Apr 03 2017 - 09:49:00 PDT)
- Thomas Evangelidis (Mon Apr 03 2017 - 08:14:51 PDT)
[AMBER] PMEMD should halt with error exit after netcdf write failure
- Chris Moth (Thu Apr 20 2017 - 15:30:25 PDT)
[AMBER] pmemd.cuda on an Amber Certified High-End workstation
- Li, Wen (Thu Apr 20 2017 - 12:52:43 PDT)
- David Case (Tue Apr 18 2017 - 10:29:26 PDT)
- Ross Walker (Tue Apr 18 2017 - 10:20:31 PDT)
- Li, Wen (Tue Apr 18 2017 - 09:02:52 PDT)
[AMBER] Post Doc position in Munich, German required
- Andreas Tosstorff (Wed Apr 26 2017 - 09:01:44 PDT)
[AMBER] Post MD minimization
- David Case (Thu Apr 20 2017 - 08:07:50 PDT)
- Bill Ross (Thu Apr 20 2017 - 02:51:25 PDT)
- Manjula Saravanan (Thu Apr 20 2017 - 02:33:48 PDT)
[AMBER] problem about amber install of MMPBSA.py.mpi
- 白正亚 (Tue Apr 11 2017 - 00:38:27 PDT)
[AMBER] problem with temperature after rst
- David A Case (Thu Apr 13 2017 - 04:55:54 PDT)
- Bill Ross (Wed Apr 12 2017 - 23:52:25 PDT)
- Bill Ross (Wed Apr 12 2017 - 23:44:36 PDT)
- Jorgen Simonsen (Wed Apr 12 2017 - 23:10:51 PDT)
- Bill Ross (Wed Apr 12 2017 - 22:57:25 PDT)
- Bill Ross (Wed Apr 12 2017 - 22:52:51 PDT)
- Jorgen Simonsen (Wed Apr 12 2017 - 22:41:45 PDT)
- Bill Ross (Wed Apr 12 2017 - 22:15:49 PDT)
- Jorgen Simonsen (Wed Apr 12 2017 - 22:03:57 PDT)
[AMBER] ptraj hbonds
- Daniel Roe (Wed Apr 05 2017 - 09:45:58 PDT)
- Mary Varughese (Wed Apr 05 2017 - 03:33:55 PDT)
[AMBER] QM/MM equilibration before SMD in vacuum
- Samaneh Ghassabi Kondalaji (Mon Apr 10 2017 - 09:58:49 PDT)
- Samaneh Ghassabi Kondalaji (Mon Apr 10 2017 - 09:04:21 PDT)
[AMBER] Quasi-harmonic entropy calculation ---- Vibrational component of entropy
- David Case (Tue Apr 18 2017 - 05:06:20 PDT)
- David Case (Tue Apr 18 2017 - 05:02:39 PDT)
- George Tzotzos (Tue Apr 18 2017 - 04:42:20 PDT)
[AMBER] Quenstions about Constraints in AMBER
- David Case (Sun Apr 30 2017 - 17:14:40 PDT)
- Hannes Loeffler (Fri Apr 28 2017 - 00:31:50 PDT)
- Pengfei Li (Thu Apr 27 2017 - 21:05:26 PDT)
[AMBER] Query regarding convergence issue of 3D-RISM
- David Case (Mon Apr 24 2017 - 04:50:45 PDT)
- Rakesh Srivastava (Sun Apr 23 2017 - 23:28:53 PDT)
[AMBER] Query regarding energy calcuation using 3D-RISM
- David Case (Mon Apr 24 2017 - 04:55:40 PDT)
- Vertika Gautam (Mon Apr 24 2017 - 01:50:11 PDT)
[AMBER] Query regarding output of 3D-RISM in Amber.
- Rakesh Srivastava (Mon Apr 10 2017 - 02:10:38 PDT)
- David Case (Sun Apr 09 2017 - 17:26:28 PDT)
- Rakesh Srivastava (Fri Apr 07 2017 - 21:48:22 PDT)
[AMBER] Recommended LJ parameters for divalent cations used for negatively charged lipid bilayers simulations ?
- Marek Maly (Thu Apr 20 2017 - 09:02:08 PDT)
[AMBER] Regarding gaussian namelist error
- Budhathoki, Dipesh (Tue Apr 25 2017 - 20:48:12 PDT)
- David Case (Tue Apr 25 2017 - 17:22:08 PDT)
- Budhathoki, Dipesh (Tue Apr 25 2017 - 16:35:45 PDT)
[AMBER] Regarding REMD simulations of Proteins
- Carlos Simmerling (Sun Apr 09 2017 - 09:22:24 PDT)
- MOHD HOMAIDUR RAHMAN (Sun Apr 09 2017 - 08:35:32 PDT)
[AMBER] Release of AmberTools17
- James Kress (Wed Apr 19 2017 - 19:11:09 PDT)
- Bill Ross (Wed Apr 19 2017 - 14:08:30 PDT)
- James Kress (Wed Apr 19 2017 - 13:55:22 PDT)
- James Kress (Wed Apr 19 2017 - 13:52:36 PDT)
- David Case (Wed Apr 19 2017 - 12:27:36 PDT)
- James Kress (Wed Apr 19 2017 - 11:22:54 PDT)
- David Case (Mon Apr 17 2017 - 18:28:04 PDT)
[AMBER] Release of AmberTools17 binary
- David Case (Wed Apr 26 2017 - 12:22:25 PDT)
- Hai Nguyen (Wed Apr 26 2017 - 07:30:04 PDT)
[AMBER] reorientation in rmsd
- Jason Swails (Thu Apr 13 2017 - 06:21:19 PDT)
- Andy Watkins (Wed Apr 12 2017 - 20:18:26 PDT)
- Andy Watkins (Wed Apr 12 2017 - 20:18:23 PDT)
- James Kress (Wed Apr 12 2017 - 19:55:08 PDT)
- David Case (Wed Apr 12 2017 - 19:06:13 PDT)
- James Kress (Wed Apr 12 2017 - 12:08:37 PDT)
- Jason Swails (Wed Apr 12 2017 - 11:41:06 PDT)
- Bill Ross (Wed Apr 12 2017 - 11:28:35 PDT)
- James Kress (Wed Apr 12 2017 - 10:32:31 PDT)
[AMBER] RES: Incorrect ligand parameterization using GAFF
- Hannes Loeffler (Sat Apr 15 2017 - 03:32:12 PDT)
- Emilia Pecora-de-barros (Fri Apr 14 2017 - 13:50:05 PDT)
- Emilia Pecora-de-barros (Thu Apr 13 2017 - 18:53:54 PDT)
[AMBER] residue contribution calculation for covalent inhibitor--- Technical challenge???
- nagakumarb.ccamp.res.in (Sat Apr 15 2017 - 05:24:45 PDT)
- Bill Ross (Fri Apr 14 2017 - 23:48:34 PDT)
- nagakumarb.ccamp.res.in (Fri Apr 14 2017 - 23:32:09 PDT)
- Bill Ross (Fri Apr 14 2017 - 23:01:41 PDT)
- nagakumarb.ccamp.res.in (Fri Apr 14 2017 - 22:47:49 PDT)
- Bill Ross (Fri Apr 14 2017 - 22:22:34 PDT)
- nagakumarb.ccamp.res.in (Fri Apr 14 2017 - 22:02:36 PDT)
[AMBER] residue-based dielectric model in MMGBSA
- Jaime Rubio Martinez (Mon Apr 24 2017 - 00:45:47 PDT)
- David Case (Sat Apr 22 2017 - 05:32:02 PDT)
- Thomas Cheatham (Fri Apr 21 2017 - 18:32:27 PDT)
- Thomas Cheatham (Fri Apr 21 2017 - 18:26:13 PDT)
- David Case (Fri Apr 21 2017 - 18:25:25 PDT)
- Mrinda Jones (Fri Apr 21 2017 - 11:28:44 PDT)
[AMBER] restarting Amber calculations gives abnormal structures
- David Case (Mon Apr 03 2017 - 18:43:03 PDT)
- Chris Neale (Sun Apr 02 2017 - 23:45:00 PDT)
- Sadegh Faramarzi Ganjabad (Sun Apr 02 2017 - 23:37:09 PDT)
- Sadegh Faramarzi Ganjabad (Sun Apr 02 2017 - 23:28:02 PDT)
[AMBER] Restraint in Steered MD/Jarzynski method
- Ramin Salimi (Sun Apr 30 2017 - 11:41:18 PDT)
- Hannes Loeffler (Sun Apr 30 2017 - 09:05:15 PDT)
- Ramin Salimi (Sat Apr 29 2017 - 10:55:20 PDT)
- Ramin Salimi (Sat Apr 29 2017 - 04:02:01 PDT)
[AMBER] Run NPT in a small periodic box
- David Case (Thu Apr 20 2017 - 09:48:44 PDT)
- Xiaoliu Zhang (Thu Apr 20 2017 - 07:44:37 PDT)
[AMBER] Segmentation fault
- David Case (Fri Apr 21 2017 - 19:17:50 PDT)
- sylvester kisembo (Fri Apr 21 2017 - 16:50:39 PDT)
- David Case (Fri Apr 21 2017 - 07:49:16 PDT)
- Adrian Roitberg (Fri Apr 21 2017 - 06:40:34 PDT)
- sylvester kisembo (Fri Apr 21 2017 - 06:35:04 PDT)
[AMBER] simulation energies are exploding
- giulia palermo (Tue Apr 11 2017 - 14:44:28 PDT)
- David Case (Tue Apr 11 2017 - 05:12:59 PDT)
- giulia palermo (Mon Apr 10 2017 - 17:30:28 PDT)
[AMBER] solvateBox for large size of RNA
- George Giambasu (Thu Apr 13 2017 - 09:59:52 PDT)
- David Case (Thu Apr 13 2017 - 07:20:39 PDT)
- Li, Wen (Thu Apr 13 2017 - 07:03:15 PDT)
[AMBER] Steered MD using two reaction coordinates
- Hannes Loeffler (Fri Apr 07 2017 - 23:28:52 PDT)
- Suchetana Gupta (Fri Apr 07 2017 - 21:27:26 PDT)
[AMBER] Stricter convergence Criterion for stretching
- Ramin Salimi (Tue Apr 25 2017 - 16:18:14 PDT)
- Ramin Salimi (Tue Apr 25 2017 - 11:26:43 PDT)
- Adrian Roitberg (Tue Apr 25 2017 - 11:01:02 PDT)
- Ramin Salimi (Tue Apr 25 2017 - 10:57:29 PDT)
[AMBER] Tleap error.
- David A Case (Thu Apr 06 2017 - 20:36:43 PDT)
- Scott Brozell (Thu Apr 06 2017 - 19:26:42 PDT)
- Vatsal Purohit (Thu Apr 06 2017 - 17:11:45 PDT)
[AMBER] tleap input file that fails following upgrade to AmberTools17
- Adams, John E. (Sat Apr 29 2017 - 09:43:27 PDT)
- David Case (Sat Apr 29 2017 - 05:20:13 PDT)
- Nhai (Fri Apr 28 2017 - 15:58:05 PDT)
- Adams, John E. (Fri Apr 28 2017 - 15:49:46 PDT)
- Adams, John E. (Fri Apr 28 2017 - 15:24:10 PDT)
- Hai Nguyen (Fri Apr 28 2017 - 15:15:20 PDT)
- Adams, John E. (Fri Apr 28 2017 - 14:59:15 PDT)
- Hai Nguyen (Fri Apr 28 2017 - 11:55:22 PDT)
- Hai Nguyen (Fri Apr 28 2017 - 11:50:48 PDT)
- Adams, John E. (Fri Apr 28 2017 - 11:03:36 PDT)
- Scott Brozell (Fri Apr 28 2017 - 09:21:35 PDT)
- Adams, John E. (Thu Apr 27 2017 - 08:45:51 PDT)
[AMBER] Too many iterations in routine! in RMSD calculation
- kungking Hanpaibool (Sat Apr 29 2017 - 02:16:06 PDT)
[AMBER] Trouble with simple MD simulation of short peptide and Cu2+ ion
- Bill Ross (Tue Apr 25 2017 - 21:33:07 PDT)
- MOHD HOMAIDUR RAHMAN (Tue Apr 25 2017 - 21:29:30 PDT)
- Bill Ross (Tue Apr 25 2017 - 20:54:58 PDT)
- Eugene Cha (Tue Apr 25 2017 - 20:34:27 PDT)
[AMBER] Tutorial - 3 / MM-PBSA
- Hai Nguyen (Wed Apr 26 2017 - 14:26:51 PDT)
- Marcelo Andrade Chagas (Wed Apr 26 2017 - 14:19:55 PDT)
[AMBER] Using AmberTools17 and Amber14
- Hai Nguyen (Fri Apr 28 2017 - 22:00:48 PDT)
- David Adrian Saez San Martin (Fri Apr 28 2017 - 20:40:38 PDT)
[AMBER] using pmemd.MPI for REMD
- Kris Feher (Thu Apr 13 2017 - 04:01:15 PDT)
- Kris Feher (Thu Apr 13 2017 - 03:38:41 PDT)
- Hannes Loeffler (Wed Apr 12 2017 - 10:31:25 PDT)
- Kris Feher (Wed Apr 12 2017 - 09:48:36 PDT)
[AMBER] Warning message in AmberTools17 upgrade
- Baker, Joseph (Mon Apr 24 2017 - 11:53:37 PDT)
- Hai Nguyen (Mon Apr 24 2017 - 09:54:08 PDT)
- Baker, Joseph (Mon Apr 24 2017 - 09:41:09 PDT)
- Hai Nguyen (Fri Apr 21 2017 - 20:49:02 PDT)
- Baker, Joseph (Fri Apr 21 2017 - 13:53:04 PDT)
- Jason Swails (Fri Apr 21 2017 - 13:48:47 PDT)
- Baker, Joseph (Fri Apr 21 2017 - 13:23:13 PDT)
- Hai Nguyen (Fri Apr 21 2017 - 12:46:30 PDT)
- Baker, Joseph (Fri Apr 21 2017 - 12:43:43 PDT)
- Hai Nguyen (Fri Apr 21 2017 - 12:39:59 PDT)
- Baker, Joseph (Fri Apr 21 2017 - 12:36:56 PDT)
- Baker, Joseph (Fri Apr 21 2017 - 12:30:27 PDT)
- Nhai (Fri Apr 21 2017 - 12:27:24 PDT)
- Baker, Joseph (Fri Apr 21 2017 - 12:23:51 PDT)
- Baker, Joseph (Fri Apr 21 2017 - 12:17:52 PDT)
- Nhai (Fri Apr 21 2017 - 12:07:29 PDT)
- Baker, Joseph (Fri Apr 21 2017 - 11:53:11 PDT)
- Baker, Joseph (Fri Apr 21 2017 - 11:41:19 PDT)
[AMBER] weird asymmetries in solvent box
- Thomas Pochapsky (Wed Apr 19 2017 - 12:03:18 PDT)
- David Case (Mon Apr 17 2017 - 07:32:23 PDT)
- Thomas Pochapsky (Mon Apr 17 2017 - 06:57:34 PDT)
- David Case (Mon Apr 17 2017 - 04:43:39 PDT)
- Thomas Charles Pochapsky (Sat Apr 15 2017 - 05:52:11 PDT)
[AMBER] You won't believe what happens with maximum coordination limits...
- David Poole (Thu Apr 06 2017 - 03:22:04 PDT)
- Marek Maly (Tue Apr 04 2017 - 14:49:21 PDT)
- Ben Roberts (Tue Apr 04 2017 - 12:53:23 PDT)
- Hannes Loeffler (Tue Apr 04 2017 - 07:50:27 PDT)
- David Poole (Tue Apr 04 2017 - 07:23:11 PDT)

Amber Archive Apr 2017 by subject