Amber Archive Aug 2021: by author

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

Amber Archive Aug 2021 by author