Amber Archive Dec 2023: by date

Thursday, 30 November 2023
- [AMBER] Re weighting trajectory file Dulal Mondal via AMBER
- [AMBER] Reproduce a Simulation Xuebin Feng via AMBER
Friday, 1 December 2023
- Re: [AMBER] [Sender Not Verified] Would AMBER suit my purpose? Steinbrecher, Thomas via AMBER
- Re: [AMBER] Looking for a force field with ester linkages between protein chains permitted. FyD via AMBER
- [AMBER] Cpptraj output problem Rimóczi Aliz via AMBER
- Re: [AMBER] Cpptraj output problem Daniel Roe via AMBER
- Re: [AMBER] Would AMBER suit my purpose? David A Case via AMBER
- [AMBER] Fwd: antechamber error-- QMMM: System specified with odd number of electrons Todd Minehardt via AMBER
- [AMBER] LeaP error Prithviraj Nandigrami via AMBER
- [AMBER] MD Heat Run-Sander Error Kaleem Arshad via AMBER
Saturday, 2 December 2023
- Re: [AMBER] MD Heat Run-Sander Error Carlos Simmerling via AMBER
- [AMBER] teLeap: Error! Could not find angle parameter SUBHASMITA MAHAPATRA MAHAPATRA via AMBER
- [AMBER] 回复: teLeap: Error! Could not find angle parameter 郭家藩 via AMBER
Sunday, 3 December 2023
- [AMBER] Fwd: Re weighting trajectory file Dulal Mondal via AMBER
- Re: [AMBER] Fwd: Re weighting trajectory file Carlos Simmerling via AMBER
- Re: [AMBER] Compiling Amber 22 (+ AT 23) with Intel compiler filip fratev via AMBER
- Re: [AMBER] Compiling Amber 22 (+ AT 23) with Intel compiler filip fratev via AMBER
- [AMBER] MCPB, Unrecognized OW type for water Matthew Guberman-Pfeffer via AMBER
- [AMBER] 回复: MCPB, Unrecognized OW type for water 郭家藩 via AMBER
- Re: [AMBER] MCPB, Unrecognized OW type for water Matthew Guberman-Pfeffer via AMBER
- [AMBER] Restarting simulations with Langevin dynamics Martin Juhás via AMBER
- Re: [AMBER] Restarting simulations with Langevin dynamics Thomas Cheatham via AMBER
- [AMBER] How to solve the DOPI force field? Zhang Yongqi via AMBER
Monday, 4 December 2023
- Re: [AMBER] MD Heat Run-Sander Error Carlos Simmerling via AMBER
- [AMBER] Lateral Stress Profiles for Membrane Protein Systems Gentile, Rocco via AMBER
- Re: [AMBER] Seeking Clarification on Twist Angle and Force Field Compatibility David A Case via AMBER
- Re: [AMBER] Seeking Clarification on Twist Angle and Force Field Compatibility Chris Neale via AMBER
- Re: [AMBER] Compiling Amber 22 (+ AT 23) with Intel compiler David A Case via AMBER
- Re: [AMBER] Fwd: Re weighting trajectory file Carlos Simmerling via AMBER
- [AMBER] amber 22 serial installation in local cluster. Dulal Mondal via AMBER
- Re: [AMBER] amber 22 serial installation in local cluster. Todd Minehardt via AMBER
- [AMBER] MCPC.py Iron Sulfur Cluster Parameterization Issus Kaleem Arshad via AMBER
- [AMBER] Parameters for palmitoyl-cysteine, myristoyl-glycine and geranylgeranyl-cysteine in the AMBER force field Eduard Neu via AMBER
Tuesday, 5 December 2023
- [AMBER] pi-pi interaction of the protein-ligand complex: Kankana Bhattacharjee via AMBER
- [AMBER] 回复: MCPB, Unrecognized OW type for water 郭家藩 via AMBER
- [AMBER] 回复: MCPC.py Iron Sulfur Cluster Parameterization Issus 郭家藩 via AMBER
- [AMBER] Fwd: pi-pi interaction of the protein-ligand complex: Kankana Bhattacharjee via AMBER
- [AMBER] 回复: Fwd: pi-pi interaction of the protein-ligand complex: 郭家藩 via AMBER
- Re: [AMBER] Fwd: pi-pi interaction of the protein-ligand complex: Kankana Bhattacharjee via AMBER
- [AMBER] Handaling External Libraries Dulal Mondal via AMBER
- [AMBER] amber22 installation with plumed patched in MPI Dulal Mondal via AMBER
- [AMBER] cpptraj: removing pereodicity from the membrane system Enrico Martinez via AMBER
- [AMBER] tleap and bridged cyclobutyl groups Bennion, Brian via AMBER
- Re: [AMBER] MCPB, negative force constant? Pengfei Li via AMBER
- Re: [AMBER] MCPB, Unrecognized OW type for water Pengfei Li via AMBER
Wednesday, 6 December 2023
- Re: [AMBER] tleap and bridged cyclobutyl groups FyD via AMBER
- Re: [AMBER] tleap and bridged cyclobutyl groups David A Case via AMBER
- Re: [AMBER] MCPC.py Iron Sulfur Cluster Parameterization Issus Pengfei Li via AMBER
Thursday, 7 December 2023
- [AMBER] Inquiry Regarding MMPBSA.py SASA Calculation Method kefun via AMBER
- [AMBER] Error while using plumed Munazzah Fatima Ansari via AMBER
- Re: [AMBER] Error while using plumed Giovanni Bussi via AMBER
- Re: [AMBER] Error while using plumed Daniel Roe via AMBER
- [AMBER] error when compiling Amber22 Irene Maffucci via AMBER
- Re: [AMBER] Error while using plumed Todd Minehardt via AMBER
- Re: [AMBER] error when compiling Amber22 Todd Minehardt via AMBER
- [AMBER] TLEaP question Matthew Guberman-Pfeffer via AMBER
- Re: [AMBER] TLEaP question Carlos Simmerling via AMBER
- Re: [AMBER] TLEaP question Matthew Guberman-Pfeffer via AMBER
- Re: [AMBER] Inquiry Regarding MMPBSA.py SASA Calculation Method Ray Luo via AMBER
- Re: [AMBER] error when compiling Amber22 Scott Brozell via AMBER
Friday, 8 December 2023
- [AMBER] Error: an illegal memory access was encountered launching kernel kNLSkinTest Hoang, Oanh Tu via AMBER
- [AMBER] Calculation of the entropy of active site water molecules Dulal Mondal via AMBER
- Re: [AMBER] Calculation of the entropy of active site water molecules Carlos Simmerling via AMBER
- Re: [AMBER] Error while using plumed Todd Minehardt via AMBER
- [AMBER] : QMMM error - odd number of electrons Yang, Li-Yen via AMBER
- Re: [AMBER] : QMMM error - odd number of electrons David A Case via AMBER
Sunday, 10 December 2023
- [AMBER] H++ Server Down. Setyanto Md via AMBER
Monday, 11 December 2023
- [AMBER] Cmake error Dulal Mondal via AMBER
- [AMBER] Protein analysis VERONICA MARTIN HERNANDEZ via AMBER
- Re: [AMBER] Protein analysis Dr. Anselm Horn via AMBER
- [AMBER] MCPB-related Gaussian error Mario Lopez Martin via AMBER
- Re: [AMBER] MCPB-related Gaussian error Matthew Guberman-Pfeffer via AMBER
- Re: [AMBER] Cmake error David A Case via AMBER
- [AMBER] Error in MMGBSA tutorial Abhilash J via AMBER
Tuesday, 12 December 2023
- [AMBER] normal mode error: Kankana Bhattacharjee via AMBER
- [AMBER] periodic molecules of graphene oxide Victor Nazarychev via AMBER
- Re: [AMBER] periodic molecules of graphene oxide Arun Srikanth via AMBER
- Re: [AMBER] H++ Server Down. Setyanto Md via AMBER
Wednesday, 13 December 2023
- Re: [AMBER] Cmake error Dulal Mondal via AMBER
- Re: [AMBER] normal mode error: Kankana Bhattacharjee via AMBER
- Re: [AMBER] [Sender Not Verified] Re: normal mode error: Steinbrecher, Thomas via AMBER
- [AMBER] Inquiry About Nonbonded Parameters for AMBER Force Field in GROMACS Fadaei Fatemeh Mgr. via AMBER
Thursday, 14 December 2023
- Re: [AMBER] H++ Server Down. Setyanto Md via AMBER
- [AMBER] MMPBSA error: Kankana Bhattacharjee via AMBER
- Re: [AMBER] MMPBSA error: Dr. Anselm Horn via AMBER
- Re: [AMBER] MMPBSA error: Kankana Bhattacharjee via AMBER
Friday, 15 December 2023
- Re: [AMBER] periodic molecules of graphene oxide Arun Srikanth via AMBER
Saturday, 16 December 2023
- [AMBER] calculating average number of water in the binding site: Kankana Bhattacharjee via AMBER
- [AMBER] Armed API Syntax Question Matthew Guberman-Pfeffer via AMBER
- Re: [AMBER] calculating average number of water in the binding site: Skanda Sastry via AMBER
Sunday, 17 December 2023
- [AMBER] [LEaP] Atom does not have a type Thompson, Emma via AMBER
Monday, 18 December 2023
- Re: [AMBER] [Sender Not Verified] [LEaP] Atom does not have a type Steinbrecher, Thomas via AMBER
- [AMBER] Entropy of active site water molecules using matrix and diagmatrix Dulal Mondal via AMBER
- [AMBER] Treecode Summation for Electrostatic Interactions Dulal Mondal via AMBER
- Re: [AMBER] Entropy of active site water molecules using matrix and diagmatrix Dulal Mondal via AMBER
- Re: [AMBER] Entropy of active site water molecules using matrix and diagmatrix Daniel Roe via AMBER
Tuesday, 19 December 2023
- Re: [AMBER] normal mode error: David A Case via AMBER
- Re: [AMBER] Inquiry About Nonbonded Parameters for AMBER Force Field in GROMACS David A Case via AMBER
- Re: [AMBER] Treecode Summation for Electrostatic Interactions David A Case via AMBER
- [AMBER] Titration of non-standard diprotic acid Mainas, Eleftherios via AMBER
- Re: [AMBER] Treecode Summation for Electrostatic Interactions Dulal Mondal via AMBER
Wednesday, 20 December 2023
- [AMBER] MSD calculation Dulal Mondal via AMBER
- Re: [AMBER] [Sender Not Verified] MSD calculation Steinbrecher, Thomas via AMBER
- Re: [AMBER] [Sender Not Verified] MSD calculation Dulal Mondal via AMBER
- Re: [AMBER] [Sender Not Verified] MSD calculation Dulal Mondal via AMBER
- Re: [AMBER] Treecode Summation for Electrostatic Interactions David A Case via AMBER
Thursday, 21 December 2023
- Re: [AMBER] [Sender Not Verified] MSD calculation Dulal Mondal via AMBER
- [AMBER] ligand-protein interaction Jaime Rubio Martinez via AMBER
- Re: [AMBER] ligand-protein interaction VERONICA MARTIN HERNANDEZ via AMBER
- Re: [AMBER] ligand-protein interaction Dr. Anselm Horn via AMBER
- [AMBER] GPU performance with pmemd.cuda Enrico Martinez via AMBER
- [AMBER] Best practices for comparing parameters? Matthew Guberman-Pfeffer via AMBER
- Re: [AMBER] Best practices for comparing parameters? Carlos Simmerling via AMBER
Friday, 22 December 2023
- Re: [AMBER] GPU performance with pmemd.cuda Enrico Martinez via AMBER
- [AMBER] Problems with mdgx for fitting parameters (conformations do not seem to be the minima) David DELLEMME via AMBER
- [AMBER] Query regarding nmode module: Kankana Bhattacharjee via AMBER
- Re: [AMBER] Query regarding nmode module: Todd Minehardt via AMBER
- [AMBER] nativecontact analysis speedup suggestion Delwakkada Liyanage, Senal Dinuka via AMBER
- [AMBER] MCPB.py message for Fe2S2 cluster; help needed Ralph Roberts via AMBER
Saturday, 23 December 2023
- Re: [AMBER] MCPB.py message for Fe2S2 cluster; help needed Matthew Guberman-Pfeffer via AMBER
Monday, 25 December 2023
- [AMBER] Query regarding preparation of protein system having zinc ion using ZAFF Sayan Poddar via AMBER
- Re: [AMBER] Query regarding preparation of protein system having zinc ion using ZAFF SATYAJIT KHATUA via AMBER
Tuesday, 26 December 2023
- [AMBER] Gamess small model geometry optimization from MCPB.py output Ralph Roberts via AMBER
- Re: [AMBER] Gamess small model geometry optimization from MCPB.py output James Kress via AMBER
Wednesday, 27 December 2023
- [AMBER] amber22 installation error Dulal Mondal via AMBER
- Re: [AMBER] amber22 installation error Scott Brozell via AMBER
- [AMBER] Error while performing MMPBSA Kriti Shukla via AMBER
- Re: [AMBER] Error while performing MMPBSA Elvis Martis via AMBER
Thursday, 28 December 2023
- [AMBER] Using tleap sequence command with non-protein Mohd Farid Ismail via AMBER
- Re: [AMBER] amber22 installation error K A SIVASANKER via AMBER
- Re: [AMBER] amber22 installation error Dulal Mondal via AMBER
- [AMBER] TLEaP, torsion error, duplicated bond definitions Matthew Guberman-Pfeffer via AMBER
Friday, 29 December 2023
- [AMBER] Specifying Restraints Question Matthew Guberman-Pfeffer via AMBER
- [AMBER] 回复: Specifying Restraints Question Huang ZiJian via AMBER
- [AMBER] Problem with Installing mpi4py Kriti Shukla via AMBER
- [AMBER] Failed to genarate parameters in Tleap BILASH MAITY via AMBER
- Re: [AMBER] Failed to genarate parameters in Tleap Todd Minehardt via AMBER
- Re: [AMBER] Specifying Restraints Question Matthew Guberman-Pfeffer via AMBER
- Re: [AMBER] tleap and bridged cyclobutyl groups David A Case via AMBER
- Re: [AMBER] Specifying Restraints Question David A Case via AMBER
- [AMBER] minout.perl produces empty files James Kress via AMBER
Saturday, 30 December 2023
- [AMBER] CpHMD, Amber22, MAX_TITR_RES overflow Matthew Guberman-Pfeffer via AMBER
- Re: [AMBER] CpHMD, Amber22, MAX_TITR_RES overflow Matthew Guberman-Pfeffer via AMBER
- Re: [AMBER] Failed to genarate parameters in Tleap Todd Minehardt via AMBER
- [AMBER] tleap output question James Kress via AMBER
Sunday, 31 December 2023
- Re: [AMBER] tleap output question Matthew Guberman-Pfeffer via AMBER
- Re: [AMBER] nativecontact analysis speedup suggestion Delwakkada Liyanage, Senal Dinuka via AMBER
- Re: [AMBER] tleap output question James Kress via AMBER

Last message date: Sun Dec 31 2023 - 14:00:02 PST
Archived on: Sun Dec 22 2024 - 05:56:15 PST

Amber Archive Dec 2023 by date