Amber Archive Aug 2021: by subject

[AMBER] "An All-Atom Force Field for Metallocenes"
- Gustaf Olsson (Tue Aug 10 2021 - 05:13:06 PDT)
- Gustaf Olsson (Tue Aug 10 2021 - 01:28:34 PDT)
[AMBER] [Amber] Convert pqr to pdb
- Rohanizeidanlou, Sahar (Thu Aug 19 2021 - 17:43:41 PDT)
- Daniel Roe (Wed Aug 18 2021 - 09:17:30 PDT)
- Rohanizeidanlou, Sahar (Sat Aug 14 2021 - 14:39:59 PDT)
- Daniel Roe (Fri Aug 13 2021 - 12:11:03 PDT)
- Rohanizeidanlou, Sahar (Fri Aug 13 2021 - 11:21:01 PDT)
[AMBER] [UCE] Combining MCPB.py results using tleap
- Anthony Nash (Wed Aug 18 2021 - 13:19:46 PDT)
- Sarah Lefave (Wed Aug 18 2021 - 12:59:35 PDT)
[AMBER] Adding distance restraint in amber
- Daniel Roe (Mon Aug 16 2021 - 12:07:55 PDT)
- David A Case (Mon Aug 16 2021 - 05:08:49 PDT)
- Sadaf Rani (Mon Aug 16 2021 - 00:40:19 PDT)
[AMBER] AMBER 18 and A100?
- Ilyas Yildirim (Thu Aug 12 2021 - 23:00:30 PDT)
[AMBER] Amber parmeters for ACE-CYX bond
- Ali Saad Kusay (Mon Aug 23 2021 - 03:50:03 PDT)
- Carlos Simmerling (Thu Aug 05 2021 - 05:19:00 PDT)
- Ali Kusay (Tue Aug 03 2021 - 21:59:41 PDT)
[AMBER] Amber20 installation, pip not installed in Miniconda
- David A Case (Mon Aug 09 2021 - 06:57:06 PDT)
- Setyanto Md (Sun Aug 08 2021 - 23:34:43 PDT)
[AMBER] An question about Tutorial
- Carlos Simmerling (Tue Aug 31 2021 - 05:34:04 PDT)
- wangwei1669 (Mon Aug 30 2021 - 18:22:53 PDT)
[AMBER] Boron containing molecules in GAFF
- Brian Radak (Wed Aug 04 2021 - 09:41:40 PDT)
- David A Case (Wed Aug 04 2021 - 08:20:11 PDT)
- Brian Radak (Tue Aug 03 2021 - 08:01:15 PDT)
[AMBER] Building pmemd.cuda.MPI with NCCL support
- James Kress (Mon Aug 23 2021 - 17:15:06 PDT)
[AMBER] Chloride ion atom type issue in tleap
- David A Case (Sun Aug 01 2021 - 18:41:09 PDT)
- Aliakbartehrani Zahra (Sat Jul 31 2021 - 23:48:38 PDT)
[AMBER] CMake Error
- David A Case (Thu Aug 12 2021 - 17:40:46 PDT)
- Rodrigo da Silva Bitzer (Thu Aug 12 2021 - 10:58:31 PDT)
[AMBER] Combining MCPB.py results using tleap
- Anthony Nash (Wed Aug 18 2021 - 12:12:55 PDT)
[AMBER] constant ph md
- David A Case (Thu Aug 12 2021 - 04:10:41 PDT)
- Abhik Ghosh Moulick (Wed Aug 11 2021 - 22:22:41 PDT)
[AMBER] CPPTRAJ and data from PQR files
- Matthew Guberman-Pfeffer (Wed Aug 18 2021 - 10:27:23 PDT)
[AMBER] CUDA installation for use with AMBER20
- James Kress (Sun Aug 15 2021 - 12:23:30 PDT)
[AMBER] descrepancy in net charge - TI output
- Delwakkada Liyanage, Senal Dinuka (Tue Aug 31 2021 - 15:15:10 PDT)
- David A Case (Mon Aug 30 2021 - 13:07:52 PDT)
- Delwakkada Liyanage, Senal Dinuka (Mon Aug 30 2021 - 07:02:57 PDT)
- David A Case (Mon Aug 30 2021 - 05:58:38 PDT)
- Delwakkada Liyanage, Senal Dinuka (Sun Aug 29 2021 - 19:28:28 PDT)
[AMBER] Developing Parameters for Bad Atom Types
- Carlos Simmerling (Wed Aug 11 2021 - 16:03:29 PDT)
- Matthew Guberman-Pfeffer (Mon Aug 09 2021 - 07:15:35 PDT)
[AMBER] EEE_INVALID_FLAG IEEE_OVERFLOW_FLAG IEEE_UNDERFLOW_FLAG IEEE_DENORMAL.
- David A Case (Mon Aug 09 2021 - 18:05:07 PDT)
- Akinyemi Omoniyi (Mon Aug 09 2021 - 13:43:58 PDT)
[AMBER] Error 11 Paramfit
- Dr. Anselm Horn (Tue Aug 31 2021 - 06:50:06 PDT)
- Robin Betz (Thu Aug 26 2021 - 13:26:06 PDT)
- Swisher, Justin S (Wed Aug 25 2021 - 12:34:46 PDT)
- Swisher, Justin S (Thu Aug 19 2021 - 10:23:07 PDT)
[AMBER] Error open-mai
- David A Case (Sat Aug 14 2021 - 04:37:25 PDT)
- Rodrigo da Silva Bitzer (Fri Aug 13 2021 - 15:15:41 PDT)
[AMBER] ERROR: I could not find enough velocities
- David A Case (Tue Aug 03 2021 - 13:43:16 PDT)
- ankita mehta (Tue Aug 03 2021 - 06:51:12 PDT)
[AMBER] Freezing atoms in MCPB gaussian small_opt calculations
- David William Kastner (Wed Aug 04 2021 - 12:02:39 PDT)
[AMBER] Fwd:
- Lida Cheng (Tue Aug 10 2021 - 07:58:48 PDT)
[AMBER] Fwd: leap error for modified amino acid
- Ipsita Basu (Tue Aug 24 2021 - 07:58:26 PDT)
- David A Case (Tue Aug 24 2021 - 06:13:41 PDT)
- Ipsita Basu (Tue Aug 24 2021 - 04:14:12 PDT)
[AMBER] Grumpy GROMBER over a ZeroDivisionError
- Jason Swails (Wed Aug 25 2021 - 10:07:44 PDT)
- David A Case (Mon Aug 23 2021 - 05:56:57 PDT)
- Matthew Guberman-Pfeffer (Sun Aug 22 2021 - 08:06:52 PDT)
- Matthew Guberman-Pfeffer (Thu Aug 19 2021 - 22:21:49 PDT)
[AMBER] How to cap the residue/ nucleotide atoms
- David A Case (Sat Aug 28 2021 - 13:47:33 PDT)
- Rana Rehan Khalid (Sat Aug 28 2021 - 12:28:42 PDT)
- David A Case (Sat Aug 14 2021 - 04:41:15 PDT)
- Rana Rehan Khalid (Fri Aug 13 2021 - 19:16:53 PDT)
[AMBER] How to get code modifications into AmberTools
- David A Case (Mon Aug 30 2021 - 12:58:13 PDT)
- Tharrington, Arnold (Mon Aug 30 2021 - 10:54:50 PDT)
[AMBER] How to set a replusive force between two drug molecules or two atoms.
- neildancer.sina.com (Sat Aug 07 2021 - 20:28:27 PDT)
[AMBER] how to set distance restraints in amber
- Sadaf Rani (Sat Aug 14 2021 - 12:59:28 PDT)
[AMBER] How to use parmed in Amber20 tools
- neildancer.sina.com (Wed Aug 18 2021 - 05:22:14 PDT)
[AMBER] How to visualize the protein-implicit solvent boundary
- Matthew Guberman-Pfeffer (Thu Aug 05 2021 - 00:37:34 PDT)
[AMBER] Installation Problem
- David A Case (Thu Aug 12 2021 - 17:37:01 PDT)
- Lida Cheng (Thu Aug 12 2021 - 08:04:00 PDT)
- David A Case (Tue Aug 10 2021 - 09:44:48 PDT)
- Lida Cheng (Tue Aug 10 2021 - 09:08:59 PDT)
[AMBER] iron-sulfur clusters parameters
- Gerald Monard (Fri Aug 27 2021 - 05:33:55 PDT)
- David A Case (Fri Aug 27 2021 - 05:08:15 PDT)
- Patsch David (patc) (Thu Aug 26 2021 - 09:50:03 PDT)
[AMBER] Issue running sander
- Clorice Reinhardt (Wed Aug 25 2021 - 14:01:10 PDT)
- Vento, Gabby (Wed Aug 25 2021 - 13:22:09 PDT)
[AMBER] Issue with MM/PBSA calculations on membrane system
- Ray Luo (Mon Aug 23 2021 - 12:52:33 PDT)
- Gilberto Pereira (Mon Aug 23 2021 - 07:57:06 PDT)
[AMBER] Lite Hash Rate and pmemd.cuda
- Ross Walker (Thu Aug 05 2021 - 10:18:59 PDT)
- Sergei Izmailov (Thu Aug 05 2021 - 02:07:31 PDT)
[AMBER] Loading RNA nucleotide (ADE) tleap error
- David A Case (Thu Aug 05 2021 - 12:28:01 PDT)
- Rana Rehan Khalid (Thu Aug 05 2021 - 09:44:58 PDT)
[AMBER] Lone Pair Issue
- Li,Haoxi (Sun Aug 22 2021 - 12:28:36 PDT)
[AMBER] Maximum coordination exceeded
- Gustaf Olsson (Fri Aug 13 2021 - 07:33:49 PDT)
- David A Case (Fri Aug 13 2021 - 07:17:18 PDT)
- Gustaf Olsson (Fri Aug 13 2021 - 06:18:46 PDT)
- Gustaf Olsson (Fri Aug 13 2021 - 06:16:56 PDT)
- Carlos Simmerling (Fri Aug 13 2021 - 06:13:43 PDT)
- Gustaf Olsson (Fri Aug 13 2021 - 05:16:58 PDT)
- Gustaf Olsson (Fri Aug 13 2021 - 03:22:23 PDT)
- Gustaf Olsson (Fri Aug 13 2021 - 03:14:09 PDT)
- Gustaf Olsson (Fri Aug 13 2021 - 03:02:59 PDT)
- Gustaf Olsson (Fri Aug 13 2021 - 02:56:54 PDT)
- Gustaf Olsson (Fri Aug 13 2021 - 02:17:16 PDT)
[AMBER] MCPB.py - ComplexWarning: Casting complex values to real discards the imaginary part
- Anthony Nash (Sun Aug 15 2021 - 12:00:06 PDT)
- Anthony Nash (Wed Aug 11 2021 - 04:58:30 PDT)
- Anthony Nash (Mon Aug 09 2021 - 03:46:11 PDT)
[AMBER] Missing mtkpp directory after installation of AmberTools21
- Pengfei Li (Fri Aug 06 2021 - 16:11:36 PDT)
[AMBER] Missing name.ncrst and name.nc files.
- David A Case (Wed Aug 18 2021 - 05:18:22 PDT)
- Carlos Simmerling (Tue Aug 17 2021 - 14:37:29 PDT)
- Bruno Cramer (Tue Aug 17 2021 - 14:32:39 PDT)
[AMBER] MMGBSA_MPI for membrane-bound proteins
- Rafał Madaj (Fri Aug 20 2021 - 01:58:46 PDT)
[AMBER] N_OF_BONDS colvar and PBC
- Feng Pan (Sun Aug 01 2021 - 20:20:25 PDT)
[AMBER] Need help with MMPBSA-per residue decomp
- Yen Nguyen (Mon Aug 30 2021 - 19:45:54 PDT)
[AMBER] PCA and K-mean together scripting in CPPTRAJ
- Nisha Amarnath Jonniya (Fri Aug 13 2021 - 05:51:52 PDT)
- Christina Bergonzo (Thu Aug 12 2021 - 06:24:58 PDT)
- Nisha Amarnath Jonniya (Thu Aug 12 2021 - 02:14:30 PDT)
[AMBER] Positive value of electrostatic and negative value of EPB
- David A Case (Tue Aug 17 2021 - 04:42:45 PDT)
- assawin daducale (Mon Aug 16 2021 - 14:24:33 PDT)
[AMBER] query about MD analysis
- Clorice Reinhardt (Tue Aug 10 2021 - 04:40:37 PDT)
- Sadaf Rani (Mon Aug 09 2021 - 17:41:30 PDT)
[AMBER] Question about thermodynamic integration.
- neildancer (Mon Aug 23 2021 - 22:21:35 PDT)
- David A Case (Mon Aug 23 2021 - 08:39:37 PDT)
- neildancer.sina.com (Sun Aug 22 2021 - 23:48:05 PDT)
[AMBER] Question about using C-F with iRED
- David A Case (Tue Aug 03 2021 - 05:14:10 PDT)
- Darian Yang (Mon Aug 02 2021 - 21:41:56 PDT)
[AMBER] Question on Paramfit QM File
- Robin Betz (Wed Aug 04 2021 - 15:35:28 PDT)
- Swisher, Justin S (Tue Aug 03 2021 - 09:48:55 PDT)
[AMBER] Questions about the TI methods in binding free energy calculations.
- neildancer (Mon Aug 02 2021 - 06:31:40 PDT)
- David A Case (Mon Aug 02 2021 - 05:06:53 PDT)
- neildancer.sina.com (Mon Aug 02 2021 - 02:27:05 PDT)
[AMBER] Regarding filling missing residues in a DNA strand
- Carlos Simmerling (Wed Aug 25 2021 - 07:43:58 PDT)
- Sruthi Sudhakar (Wed Aug 25 2021 - 05:58:53 PDT)
- David A Case (Wed Aug 18 2021 - 05:28:25 PDT)
- Sruthi Sudhakar (Tue Aug 17 2021 - 06:21:15 PDT)
[AMBER] Regarding standard deviation and SEM in hbond analysis
- Rajarshi Roy (Tue Aug 17 2021 - 03:58:04 PDT)
- Daniel Roe (Mon Aug 16 2021 - 12:09:50 PDT)
- Rajarshi Roy (Mon Aug 16 2021 - 01:10:05 PDT)
[AMBER] resp2.chg file is missing whilst processing 3rd stage of MCPB.py
- Anthony Nash (Mon Aug 16 2021 - 04:33:03 PDT)
- Aashish Bhatt (Mon Aug 16 2021 - 04:25:21 PDT)
- Anthony Nash (Mon Aug 16 2021 - 03:56:14 PDT)
[AMBER] Restart interrupted sander.MPI calculation
- David A Case (Sun Aug 22 2021 - 07:59:20 PDT)
- Bruno Cramer (Sat Aug 21 2021 - 08:36:53 PDT)
[AMBER] Restraint weight in minimization
- Adrian Roitberg (Fri Aug 13 2021 - 10:58:07 PDT)
- Carlos Simmerling (Thu Aug 12 2021 - 20:03:50 PDT)
- Sadaf Rani (Thu Aug 12 2021 - 17:11:50 PDT)
[AMBER] Rodrigues' rotation about a specified vector
- David A Case (Sun Aug 15 2021 - 18:02:43 PDT)
- Vaibhav Dixit (Wed Aug 11 2021 - 22:35:05 PDT)
- David A Case (Tue Aug 10 2021 - 12:09:48 PDT)
- Vaibhav Dixit (Tue Aug 10 2021 - 11:31:23 PDT)
[AMBER] run_cmake with -DMPI=TRUE fails to produce MPI version of Amber20
- James Kress (Sun Aug 22 2021 - 18:15:31 PDT)
- David A Case (Sun Aug 22 2021 - 17:39:58 PDT)
- James Kress (Sun Aug 22 2021 - 17:28:00 PDT)
- James Kress (Sun Aug 22 2021 - 13:40:27 PDT)
- James Kress (Sun Aug 22 2021 - 09:55:35 PDT)
[AMBER] Solvate and manipulate order of atoms in Leap
- David A Case (Tue Aug 03 2021 - 05:20:32 PDT)
[AMBER] SolvateOct box volume and cubic box information
- Umesh Roy (Wed Aug 04 2021 - 21:57:15 PDT)
- James Kress (Wed Aug 04 2021 - 21:36:39 PDT)
- Daniel Roe (Wed Aug 04 2021 - 13:07:07 PDT)
- David A Case (Wed Aug 04 2021 - 05:09:44 PDT)
- Carlos Simmerling (Wed Aug 04 2021 - 04:16:16 PDT)
- Umesh Roy (Tue Aug 03 2021 - 22:52:30 PDT)
- James Kress (Tue Aug 03 2021 - 21:31:17 PDT)
- David A Case (Tue Aug 03 2021 - 18:08:14 PDT)
- Umesh Roy (Tue Aug 03 2021 - 12:54:48 PDT)
[AMBER] Steered MD simulation
- Prithvi Raj Pandey (Tue Aug 03 2021 - 12:53:26 PDT)
[AMBER] Suggestions for Mn3O4
- Subhadip Basu (Thu Aug 26 2021 - 23:07:49 PDT)
[AMBER] system preparation error
- Carlos Simmerling (Thu Aug 12 2021 - 06:13:54 PDT)
- Renato Araujo (Thu Aug 12 2021 - 04:55:27 PDT)
- Stephan Schott (Thu Aug 12 2021 - 04:31:24 PDT)
- David A Case (Thu Aug 12 2021 - 04:19:10 PDT)
- Renato Araujo (Wed Aug 11 2021 - 20:49:11 PDT)
[AMBER] The paramters of TI
- neildancer.sina.com (Mon Aug 30 2021 - 20:55:36 PDT)
[AMBER] tleap urea "[atom] does not have a type"
- Hector A. Baldoni (Mon Aug 09 2021 - 14:38:36 PDT)
- Daniel Konstantinovsky (Mon Aug 09 2021 - 13:01:14 PDT)
[AMBER] Unit cell size has changed in trajcetory
- Daniel Roe (Tue Aug 31 2021 - 06:15:48 PDT)
- Daniel Roe (Fri Aug 27 2021 - 03:54:46 PDT)
- Sadaf Rani (Thu Aug 26 2021 - 23:32:32 PDT)
[AMBER] Why is self-correlation with atomiccorr in cpptraj zero?
- Daniel Roe (Thu Aug 05 2021 - 11:23:55 PDT)
- Matthew Guberman-Pfeffer (Wed Aug 04 2021 - 16:35:44 PDT)
[AMBER] X-aligned.Box
- Daniel Roe (Wed Aug 11 2021 - 06:39:14 PDT)
- Elvis A F Martis (Mon Aug 09 2021 - 20:32:21 PDT)
- 刘保艳 (Mon Aug 09 2021 - 18:37:58 PDT)
[AMBER] Yet again, MCPB.py for a ferrocene terminated monomer.
- Gustaf Olsson (Thu Aug 12 2021 - 07:32:31 PDT)
- Gustaf Olsson (Wed Aug 11 2021 - 03:02:01 PDT)
- Gustaf Olsson (Tue Aug 10 2021 - 06:58:27 PDT)
[AMBER] {SPAM?} An question about Tutorial
- Matthew Guberman-Pfeffer (Mon Aug 30 2021 - 18:29:55 PDT)

Amber Archive Aug 2021 by subject