Amber Archive Dec 2023: by subject

[AMBER] : QMMM error - odd number of electrons
- David A Case via AMBER (Fri Dec 08 2023 - 15:07:05 PST)
- Yang, Li-Yen via AMBER (Fri Dec 08 2023 - 12:35:47 PST)
[AMBER] [LEaP] Atom does not have a type
- Thompson, Emma via AMBER (Sun Dec 17 2023 - 15:02:32 PST)
[AMBER] [Sender Not Verified] [LEaP] Atom does not have a type
- Steinbrecher, Thomas via AMBER (Mon Dec 18 2023 - 01:01:19 PST)
[AMBER] [Sender Not Verified] MSD calculation
- Dulal Mondal via AMBER (Thu Dec 21 2023 - 00:49:34 PST)
- Dulal Mondal via AMBER (Wed Dec 20 2023 - 08:07:01 PST)
- Dulal Mondal via AMBER (Wed Dec 20 2023 - 06:27:41 PST)
- Steinbrecher, Thomas via AMBER (Wed Dec 20 2023 - 04:51:27 PST)
[AMBER] [Sender Not Verified] Would AMBER suit my purpose?
- Steinbrecher, Thomas via AMBER (Fri Dec 01 2023 - 00:01:34 PST)
[AMBER] amber 22 serial installation in local cluster.
- Todd Minehardt via AMBER (Mon Dec 04 2023 - 10:36:00 PST)
- Dulal Mondal via AMBER (Mon Dec 04 2023 - 10:01:46 PST)
[AMBER] amber22 installation error
- Dulal Mondal via AMBER (Thu Dec 28 2023 - 07:38:15 PST)
- K A SIVASANKER via AMBER (Thu Dec 28 2023 - 02:10:56 PST)
- Scott Brozell via AMBER (Wed Dec 27 2023 - 17:40:38 PST)
- Dulal Mondal via AMBER (Wed Dec 27 2023 - 01:18:52 PST)
[AMBER] amber22 installation with plumed patched in MPI
- Dulal Mondal via AMBER (Tue Dec 05 2023 - 06:01:13 PST)
[AMBER] Armed API Syntax Question
- Matthew Guberman-Pfeffer via AMBER (Sat Dec 16 2023 - 09:44:09 PST)
[AMBER] Best practices for comparing parameters?
- Carlos Simmerling via AMBER (Thu Dec 21 2023 - 12:58:33 PST)
- Matthew Guberman-Pfeffer via AMBER (Thu Dec 21 2023 - 10:54:31 PST)
[AMBER] calculating average number of water in the binding site:
- Skanda Sastry via AMBER (Sat Dec 16 2023 - 12:00:36 PST)
- Kankana Bhattacharjee via AMBER (Sat Dec 16 2023 - 03:34:32 PST)
[AMBER] Calculation of the entropy of active site water molecules
- Carlos Simmerling via AMBER (Fri Dec 08 2023 - 05:29:23 PST)
- Dulal Mondal via AMBER (Fri Dec 08 2023 - 05:23:53 PST)
[AMBER] Cmake error
- Dulal Mondal via AMBER (Wed Dec 13 2023 - 00:31:45 PST)
- David A Case via AMBER (Mon Dec 11 2023 - 12:28:30 PST)
- Dulal Mondal via AMBER (Mon Dec 11 2023 - 00:04:29 PST)
[AMBER] Compiling Amber 22 (+ AT 23) with Intel compiler
- David A Case via AMBER (Mon Dec 04 2023 - 08:53:47 PST)
- filip fratev via AMBER (Sun Dec 03 2023 - 07:16:26 PST)
- filip fratev via AMBER (Sun Dec 03 2023 - 07:13:43 PST)
[AMBER] CpHMD, Amber22, MAX_TITR_RES overflow
- Matthew Guberman-Pfeffer via AMBER (Sat Dec 30 2023 - 05:18:34 PST)
- Matthew Guberman-Pfeffer via AMBER (Sat Dec 30 2023 - 05:09:34 PST)
[AMBER] Cpptraj output problem
- Daniel Roe via AMBER (Fri Dec 01 2023 - 07:38:20 PST)
- Rimóczi Aliz via AMBER (Fri Dec 01 2023 - 01:23:51 PST)
[AMBER] cpptraj: removing pereodicity from the membrane system
- Enrico Martinez via AMBER (Tue Dec 05 2023 - 06:27:01 PST)
[AMBER] Entropy of active site water molecules using matrix and diagmatrix
- Daniel Roe via AMBER (Mon Dec 18 2023 - 06:56:40 PST)
- Dulal Mondal via AMBER (Mon Dec 18 2023 - 05:53:44 PST)
- Dulal Mondal via AMBER (Mon Dec 18 2023 - 04:26:10 PST)
[AMBER] Error in MMGBSA tutorial
- Abhilash J via AMBER (Mon Dec 11 2023 - 13:46:59 PST)
[AMBER] error when compiling Amber22
- Scott Brozell via AMBER (Thu Dec 07 2023 - 13:10:52 PST)
- Todd Minehardt via AMBER (Thu Dec 07 2023 - 07:47:58 PST)
- Irene Maffucci via AMBER (Thu Dec 07 2023 - 07:17:21 PST)
[AMBER] Error while performing MMPBSA
- Elvis Martis via AMBER (Wed Dec 27 2023 - 21:57:20 PST)
- Kriti Shukla via AMBER (Wed Dec 27 2023 - 21:46:36 PST)
[AMBER] Error while using plumed
- Todd Minehardt via AMBER (Fri Dec 08 2023 - 07:13:49 PST)
- Todd Minehardt via AMBER (Thu Dec 07 2023 - 07:25:24 PST)
- Daniel Roe via AMBER (Thu Dec 07 2023 - 06:03:18 PST)
- Giovanni Bussi via AMBER (Thu Dec 07 2023 - 05:41:52 PST)
- Munazzah Fatima Ansari via AMBER (Thu Dec 07 2023 - 03:14:47 PST)
[AMBER] Error: an illegal memory access was encountered launching kernel kNLSkinTest
- Hoang, Oanh Tu via AMBER (Fri Dec 08 2023 - 02:31:56 PST)
[AMBER] Failed to genarate parameters in Tleap
- Todd Minehardt via AMBER (Sat Dec 30 2023 - 10:09:05 PST)
- Todd Minehardt via AMBER (Fri Dec 29 2023 - 07:40:16 PST)
- BILASH MAITY via AMBER (Fri Dec 29 2023 - 06:58:37 PST)
[AMBER] Fwd: antechamber error-- QMMM: System specified with odd number of electrons
- Todd Minehardt via AMBER (Fri Dec 01 2023 - 15:01:43 PST)
[AMBER] Fwd: pi-pi interaction of the protein-ligand complex:
- Kankana Bhattacharjee via AMBER (Tue Dec 05 2023 - 04:10:27 PST)
- Kankana Bhattacharjee via AMBER (Tue Dec 05 2023 - 03:47:37 PST)
[AMBER] Fwd: Re weighting trajectory file
- Carlos Simmerling via AMBER (Mon Dec 04 2023 - 09:23:06 PST)
- Carlos Simmerling via AMBER (Sun Dec 03 2023 - 03:40:48 PST)
- Dulal Mondal via AMBER (Sun Dec 03 2023 - 03:29:43 PST)
[AMBER] Gamess small model geometry optimization from MCPB.py output
- James Kress via AMBER (Tue Dec 26 2023 - 16:00:45 PST)
- Ralph Roberts via AMBER (Tue Dec 26 2023 - 15:48:24 PST)
[AMBER] GPU performance with pmemd.cuda
- Enrico Martinez via AMBER (Fri Dec 22 2023 - 00:48:18 PST)
- Enrico Martinez via AMBER (Thu Dec 21 2023 - 09:11:32 PST)
[AMBER] H++ Server Down.
- Setyanto Md via AMBER (Thu Dec 14 2023 - 01:07:02 PST)
- Setyanto Md via AMBER (Tue Dec 12 2023 - 02:21:22 PST)
- Setyanto Md via AMBER (Sun Dec 10 2023 - 19:00:57 PST)
[AMBER] Handaling External Libraries
- Dulal Mondal via AMBER (Tue Dec 05 2023 - 04:17:55 PST)
[AMBER] How to solve the DOPI force field?
- Zhang Yongqi via AMBER (Sun Dec 03 2023 - 17:47:34 PST)
[AMBER] Inquiry About Nonbonded Parameters for AMBER Force Field in GROMACS
- David A Case via AMBER (Tue Dec 19 2023 - 11:02:09 PST)
- Fadaei Fatemeh Mgr. via AMBER (Wed Dec 13 2023 - 08:52:01 PST)
[AMBER] Inquiry Regarding MMPBSA.py SASA Calculation Method
- Ray Luo via AMBER (Thu Dec 07 2023 - 11:16:37 PST)
- kefun via AMBER (Thu Dec 07 2023 - 02:50:04 PST)
[AMBER] Lateral Stress Profiles for Membrane Protein Systems
- Gentile, Rocco via AMBER (Mon Dec 04 2023 - 07:27:35 PST)
[AMBER] LeaP error
- Prithviraj Nandigrami via AMBER (Fri Dec 01 2023 - 16:01:50 PST)
[AMBER] ligand-protein interaction
- Dr. Anselm Horn via AMBER (Thu Dec 21 2023 - 08:41:38 PST)
- VERONICA MARTIN HERNANDEZ via AMBER (Thu Dec 21 2023 - 02:59:54 PST)
- Jaime Rubio Martinez via AMBER (Thu Dec 21 2023 - 02:38:23 PST)
[AMBER] Looking for a force field with ester linkages between protein chains permitted.
- FyD via AMBER (Fri Dec 01 2023 - 00:00:59 PST)
[AMBER] MCPB, negative force constant?
- Pengfei Li via AMBER (Tue Dec 05 2023 - 14:39:19 PST)
[AMBER] MCPB, Unrecognized OW type for water
- Pengfei Li via AMBER (Tue Dec 05 2023 - 14:48:31 PST)
- Matthew Guberman-Pfeffer via AMBER (Sun Dec 03 2023 - 08:53:34 PST)
- Matthew Guberman-Pfeffer via AMBER (Sun Dec 03 2023 - 07:22:37 PST)
[AMBER] MCPB-related Gaussian error
- Matthew Guberman-Pfeffer via AMBER (Mon Dec 11 2023 - 07:23:42 PST)
- Mario Lopez Martin via AMBER (Mon Dec 11 2023 - 03:22:45 PST)
[AMBER] MCPB.py message for Fe2S2 cluster; help needed
- Matthew Guberman-Pfeffer via AMBER (Sat Dec 23 2023 - 00:51:21 PST)
- Ralph Roberts via AMBER (Fri Dec 22 2023 - 23:11:58 PST)
[AMBER] MCPC.py Iron Sulfur Cluster Parameterization Issus
- Pengfei Li via AMBER (Wed Dec 06 2023 - 07:52:56 PST)
- Kaleem Arshad via AMBER (Mon Dec 04 2023 - 19:15:18 PST)
[AMBER] MD Heat Run-Sander Error
- Carlos Simmerling via AMBER (Mon Dec 04 2023 - 07:16:32 PST)
- Carlos Simmerling via AMBER (Sat Dec 02 2023 - 02:41:43 PST)
- Kaleem Arshad via AMBER (Fri Dec 01 2023 - 22:45:23 PST)
[AMBER] minout.perl produces empty files
- James Kress via AMBER (Fri Dec 29 2023 - 11:17:36 PST)
[AMBER] MMPBSA error:
- Kankana Bhattacharjee via AMBER (Thu Dec 14 2023 - 08:51:15 PST)
- Dr. Anselm Horn via AMBER (Thu Dec 14 2023 - 04:19:05 PST)
- Kankana Bhattacharjee via AMBER (Thu Dec 14 2023 - 03:56:36 PST)
[AMBER] MSD calculation
- Dulal Mondal via AMBER (Wed Dec 20 2023 - 02:29:58 PST)
[AMBER] nativecontact analysis speedup suggestion
- Delwakkada Liyanage, Senal Dinuka via AMBER (Sun Dec 31 2023 - 10:41:21 PST)
- Delwakkada Liyanage, Senal Dinuka via AMBER (Fri Dec 22 2023 - 12:41:27 PST)
[AMBER] normal mode error:
- David A Case via AMBER (Tue Dec 19 2023 - 10:57:50 PST)
- Kankana Bhattacharjee via AMBER (Wed Dec 13 2023 - 00:36:57 PST)
- Kankana Bhattacharjee via AMBER (Tue Dec 12 2023 - 01:21:26 PST)
[AMBER] Parameters for palmitoyl-cysteine, myristoyl-glycine and geranylgeranyl-cysteine in the AMBER force field
- Eduard Neu via AMBER (Mon Dec 04 2023 - 19:33:20 PST)
[AMBER] periodic molecules of graphene oxide
- Arun Srikanth via AMBER (Fri Dec 15 2023 - 05:12:57 PST)
- Arun Srikanth via AMBER (Tue Dec 12 2023 - 02:09:17 PST)
- Victor Nazarychev via AMBER (Tue Dec 12 2023 - 01:43:48 PST)
[AMBER] pi-pi interaction of the protein-ligand complex:
- Kankana Bhattacharjee via AMBER (Tue Dec 05 2023 - 00:14:37 PST)
[AMBER] Problem with Installing mpi4py
- Kriti Shukla via AMBER (Fri Dec 29 2023 - 04:23:16 PST)
[AMBER] Problems with mdgx for fitting parameters (conformations do not seem to be the minima)
- David DELLEMME via AMBER (Fri Dec 22 2023 - 03:17:03 PST)
[AMBER] Protein analysis
- Dr. Anselm Horn via AMBER (Mon Dec 11 2023 - 03:01:04 PST)
- VERONICA MARTIN HERNANDEZ via AMBER (Mon Dec 11 2023 - 02:31:35 PST)
[AMBER] Query regarding nmode module:
- Todd Minehardt via AMBER (Fri Dec 22 2023 - 07:41:54 PST)
- Kankana Bhattacharjee via AMBER (Fri Dec 22 2023 - 05:30:11 PST)
[AMBER] Query regarding preparation of protein system having zinc ion using ZAFF
- SATYAJIT KHATUA via AMBER (Mon Dec 25 2023 - 09:48:28 PST)
- Sayan Poddar via AMBER (Mon Dec 25 2023 - 09:38:00 PST)
[AMBER] Re weighting trajectory file
- Dulal Mondal via AMBER (Thu Nov 30 2023 - 11:11:42 PST)
[AMBER] Reproduce a Simulation
- Xuebin Feng via AMBER (Thu Nov 30 2023 - 18:19:40 PST)
[AMBER] Restarting simulations with Langevin dynamics
- Thomas Cheatham via AMBER (Sun Dec 03 2023 - 13:02:26 PST)
- Martin Juhás via AMBER (Sun Dec 03 2023 - 12:51:53 PST)
[AMBER] Seeking Clarification on Twist Angle and Force Field Compatibility
- Chris Neale via AMBER (Mon Dec 04 2023 - 08:22:51 PST)
- David A Case via AMBER (Mon Dec 04 2023 - 08:11:33 PST)
[AMBER] Specifying Restraints Question
- David A Case via AMBER (Fri Dec 29 2023 - 10:13:00 PST)
- Matthew Guberman-Pfeffer via AMBER (Fri Dec 29 2023 - 08:15:18 PST)
- Matthew Guberman-Pfeffer via AMBER (Fri Dec 29 2023 - 00:17:46 PST)
[AMBER] teLeap: Error! Could not find angle parameter
- SUBHASMITA MAHAPATRA MAHAPATRA via AMBER (Sat Dec 02 2023 - 04:46:57 PST)
[AMBER] Titration of non-standard diprotic acid
- Mainas, Eleftherios via AMBER (Tue Dec 19 2023 - 15:51:15 PST)
[AMBER] tleap and bridged cyclobutyl groups
- David A Case via AMBER (Fri Dec 29 2023 - 10:07:18 PST)
- David A Case via AMBER (Wed Dec 06 2023 - 07:29:28 PST)
- FyD via AMBER (Wed Dec 06 2023 - 05:45:24 PST)
- Bennion, Brian via AMBER (Tue Dec 05 2023 - 13:04:04 PST)
[AMBER] tleap output question
- James Kress via AMBER (Sun Dec 31 2023 - 13:48:13 PST)
- Matthew Guberman-Pfeffer via AMBER (Sun Dec 31 2023 - 06:15:45 PST)
- James Kress via AMBER (Sat Dec 30 2023 - 22:15:16 PST)
[AMBER] TLEaP question
- Matthew Guberman-Pfeffer via AMBER (Thu Dec 07 2023 - 09:57:30 PST)
- Carlos Simmerling via AMBER (Thu Dec 07 2023 - 08:07:57 PST)
- Matthew Guberman-Pfeffer via AMBER (Thu Dec 07 2023 - 08:04:47 PST)
[AMBER] TLEaP, torsion error, duplicated bond definitions
- Matthew Guberman-Pfeffer via AMBER (Thu Dec 28 2023 - 09:16:08 PST)
[AMBER] Treecode Summation for Electrostatic Interactions
- David A Case via AMBER (Wed Dec 20 2023 - 10:38:09 PST)
- Dulal Mondal via AMBER (Tue Dec 19 2023 - 22:35:29 PST)
- David A Case via AMBER (Tue Dec 19 2023 - 11:06:51 PST)
- Dulal Mondal via AMBER (Mon Dec 18 2023 - 05:46:01 PST)
[AMBER] Using tleap sequence command with non-protein
- Mohd Farid Ismail via AMBER (Thu Dec 28 2023 - 02:11:22 PST)
[AMBER] Would AMBER suit my purpose?
- David A Case via AMBER (Fri Dec 01 2023 - 08:05:49 PST)
[AMBER] 回复: Fwd: pi-pi interaction of the protein-ligand complex:
- 郭家藩 via AMBER (Tue Dec 05 2023 - 04:08:01 PST)
[AMBER] 回复: MCPB, Unrecognized OW type for water
- 郭家藩 via AMBER (Tue Dec 05 2023 - 00:54:21 PST)
- 郭家藩 via AMBER (Sun Dec 03 2023 - 07:56:27 PST)
[AMBER] 回复: MCPC.py Iron Sulfur Cluster Parameterization Issus
- 郭家藩 via AMBER (Tue Dec 05 2023 - 01:20:08 PST)
[AMBER] 回复: Specifying Restraints Question
- Huang ZiJian via AMBER (Fri Dec 29 2023 - 03:35:48 PST)
[AMBER] 回复: teLeap: Error! Could not find angle parameter
- 郭家藩 via AMBER (Sat Dec 02 2023 - 05:07:07 PST)
normal mode error:
- Steinbrecher, Thomas via AMBER (Wed Dec 13 2023 - 00:51:16 PST)

Amber Archive Dec 2023 by subject