Amber Archive Dec 2023 by thread
- [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)
- Re: [AMBER] [Sender Not Verified] Would AMBER suit my purpose? Steinbrecher, Thomas via AMBER (Fri Dec 01 2023 - 00:01:34 PST)
- Re: [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] Cpptraj output problem Rimóczi Aliz via AMBER (Fri Dec 01 2023 - 01:23:51 PST)
- Re: [AMBER] Would AMBER suit my purpose? David A Case via AMBER (Fri Dec 01 2023 - 08:05:49 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] LeaP error Prithviraj Nandigrami via AMBER (Fri Dec 01 2023 - 16:01:50 PST)
- [AMBER] MD Heat Run-Sander Error Kaleem Arshad via AMBER (Fri Dec 01 2023 - 22:45:23 PST)
- [AMBER] teLeap: Error! Could not find angle parameter SUBHASMITA MAHAPATRA MAHAPATRA via AMBER (Sat Dec 02 2023 - 04:46:57 PST)
- Re: [AMBER] Compiling Amber 22 (+ AT 23) with Intel compiler filip fratev via AMBER (Sun Dec 03 2023 - 07:13:43 PST)
- [AMBER] MCPB, Unrecognized OW type for water Matthew Guberman-Pfeffer via AMBER (Sun Dec 03 2023 - 07:22:37 PST)
- [AMBER] Restarting simulations with Langevin dynamics Martin Juhás via AMBER (Sun Dec 03 2023 - 12:51:53 PST)
- [AMBER] How to solve the DOPI force field? Zhang Yongqi via AMBER (Sun Dec 03 2023 - 17:47:34 PST)
- [AMBER] Lateral Stress Profiles for Membrane Protein Systems Gentile, Rocco via AMBER (Mon Dec 04 2023 - 07:27:35 PST)
- Re: [AMBER] Seeking Clarification on Twist Angle and Force Field Compatibility David A Case via AMBER (Mon Dec 04 2023 - 08:11:33 PST)
- [AMBER] amber 22 serial installation in local cluster. Dulal Mondal via AMBER (Mon Dec 04 2023 - 10:01:46 PST)
- [AMBER] MCPC.py Iron Sulfur Cluster Parameterization Issus Kaleem Arshad via AMBER (Mon Dec 04 2023 - 19:15:18 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] pi-pi interaction of the protein-ligand complex: Kankana Bhattacharjee via AMBER (Tue Dec 05 2023 - 00:14:37 PST)
- [AMBER] Handaling External Libraries Dulal Mondal via AMBER (Tue Dec 05 2023 - 04:17:55 PST)
- [AMBER] amber22 installation with plumed patched in MPI Dulal Mondal via AMBER (Tue Dec 05 2023 - 06:01:13 PST)
- [AMBER] cpptraj: removing pereodicity from the membrane system Enrico Martinez via AMBER (Tue Dec 05 2023 - 06:27:01 PST)
- [AMBER] tleap and bridged cyclobutyl groups Bennion, Brian via AMBER (Tue Dec 05 2023 - 13:04:04 PST)
- Re: [AMBER] MCPB, negative force constant? Pengfei Li via AMBER (Tue Dec 05 2023 - 14:39:19 PST)
- [AMBER] Inquiry Regarding MMPBSA.py SASA Calculation Method kefun via AMBER (Thu Dec 07 2023 - 02:50:04 PST)
- [AMBER] Error while using plumed Munazzah Fatima Ansari via AMBER (Thu Dec 07 2023 - 03:14:47 PST)
- [AMBER] error when compiling Amber22 Irene Maffucci via AMBER (Thu Dec 07 2023 - 07:17:21 PST)
- [AMBER] TLEaP question Matthew Guberman-Pfeffer via AMBER (Thu Dec 07 2023 - 08:04:47 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] Calculation of the entropy of active site water molecules Dulal Mondal via AMBER (Fri Dec 08 2023 - 05:23:53 PST)
- [AMBER] : QMMM error - odd number of electrons Yang, Li-Yen via AMBER (Fri Dec 08 2023 - 12:35:47 PST)
- [AMBER] H++ Server Down. Setyanto Md via AMBER (Sun Dec 10 2023 - 19:00:57 PST)
- [AMBER] Cmake error Dulal Mondal via AMBER (Mon Dec 11 2023 - 00:04:29 PST)
- [AMBER] Protein analysis VERONICA MARTIN HERNANDEZ via AMBER (Mon Dec 11 2023 - 02:31:35 PST)
- [AMBER] MCPB-related Gaussian error Mario Lopez Martin via AMBER (Mon Dec 11 2023 - 03:22:45 PST)
- [AMBER] Error in MMGBSA tutorial Abhilash J via AMBER (Mon Dec 11 2023 - 13:46:59 PST)
- [AMBER] normal mode error: Kankana Bhattacharjee via AMBER (Tue Dec 12 2023 - 01:21:26 PST)
- [AMBER] periodic molecules of graphene oxide Victor Nazarychev via AMBER (Tue Dec 12 2023 - 01:43:48 PST)
- [AMBER] Inquiry About Nonbonded Parameters for AMBER Force Field in GROMACS Fadaei Fatemeh Mgr. via AMBER (Wed Dec 13 2023 - 08:52:01 PST)
- [AMBER] MMPBSA error: Kankana Bhattacharjee via AMBER (Thu Dec 14 2023 - 03:56:36 PST)
- [AMBER] calculating average number of water in the binding site: Kankana Bhattacharjee via AMBER (Sat Dec 16 2023 - 03:34:32 PST)
- [AMBER] Armed API Syntax Question Matthew Guberman-Pfeffer via AMBER (Sat Dec 16 2023 - 09:44:09 PST)
- [AMBER] [LEaP] Atom does not have a type Thompson, Emma via AMBER (Sun Dec 17 2023 - 15:02:32 PST)
- [AMBER] Entropy of active site water molecules using matrix and diagmatrix Dulal Mondal via AMBER (Mon Dec 18 2023 - 04:26:10 PST)
- [AMBER] Treecode Summation for Electrostatic Interactions Dulal Mondal via AMBER (Mon Dec 18 2023 - 05:46:01 PST)
- [AMBER] Titration of non-standard diprotic acid Mainas, Eleftherios via AMBER (Tue Dec 19 2023 - 15:51:15 PST)
- [AMBER] MSD calculation Dulal Mondal via AMBER (Wed Dec 20 2023 - 02:29:58 PST)
- Re: [AMBER] [Sender Not Verified] MSD calculation Dulal Mondal via AMBER (Thu Dec 21 2023 - 00:49:34 PST)
- [AMBER] ligand-protein interaction Jaime Rubio Martinez via AMBER (Thu Dec 21 2023 - 02:38:23 PST)
- [AMBER] GPU performance with pmemd.cuda Enrico Martinez via AMBER (Thu Dec 21 2023 - 09:11:32 PST)
- [AMBER] Best practices for comparing parameters? Matthew Guberman-Pfeffer via AMBER (Thu Dec 21 2023 - 10:54:31 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] Query regarding nmode module: Kankana Bhattacharjee via AMBER (Fri Dec 22 2023 - 05:30:11 PST)
- [AMBER] nativecontact analysis speedup suggestion Delwakkada Liyanage, Senal Dinuka via AMBER (Fri Dec 22 2023 - 12:41:27 PST)
- [AMBER] MCPB.py message for Fe2S2 cluster; help needed Ralph Roberts via AMBER (Fri Dec 22 2023 - 23:11:58 PST)
- [AMBER] Query regarding preparation of protein system having zinc ion using ZAFF Sayan Poddar via AMBER (Mon Dec 25 2023 - 09:38:00 PST)
- [AMBER] Gamess small model geometry optimization from MCPB.py output Ralph Roberts via AMBER (Tue Dec 26 2023 - 15:48:24 PST)
- [AMBER] amber22 installation error Dulal Mondal via AMBER (Wed Dec 27 2023 - 01:18:52 PST)
- [AMBER] Error while performing MMPBSA Kriti Shukla via AMBER (Wed Dec 27 2023 - 21:46:36 PST)
- [AMBER] Using tleap sequence command with non-protein Mohd Farid Ismail via AMBER (Thu Dec 28 2023 - 02:11:22 PST)
- [AMBER] TLEaP, torsion error, duplicated bond definitions Matthew Guberman-Pfeffer via AMBER (Thu Dec 28 2023 - 09:16:08 PST)
- [AMBER] Specifying Restraints Question Matthew Guberman-Pfeffer via AMBER (Fri Dec 29 2023 - 00:17:46 PST)
- [AMBER] Problem with Installing mpi4py Kriti Shukla via AMBER (Fri Dec 29 2023 - 04:23:16 PST)
- [AMBER] Failed to genarate parameters in Tleap BILASH MAITY via AMBER (Fri Dec 29 2023 - 06:58:37 PST)
- [AMBER] CpHMD, Amber22, MAX_TITR_RES overflow Matthew Guberman-Pfeffer via AMBER (Sat Dec 30 2023 - 05:09:34 PST)
- Last message date: Sun Dec 31 2023 - 14:00:02 PST
- Archived on: Fri Apr 26 2024 - 05:56:21 PDT
