Amber Archive Sep 2024 by thread
- Re: [AMBER] Regarding REUS simulations Carlos Simmerling via AMBER (Sun Sep 01 2024 - 05:00:37 PDT)
- Re: [AMBER] Error to run constant pH replica exchange in explicit solvent in amber18 Dulal Mondal via AMBER (Wed Sep 04 2024 - 07:06:09 PDT)
- [AMBER] OPC3 water and ff19SB forcefield for constant pH simulations Nikolay Kuzmich via AMBER (Thu Sep 05 2024 - 02:35:54 PDT)
- Re: [AMBER] Custom AA residue missing parameters Téletchéa Stéphane via AMBER (Thu Sep 05 2024 - 03:38:48 PDT)
- [AMBER] Possible error in tiMerge Osman, Roman via AMBER (Thu Sep 05 2024 - 07:27:33 PDT)
- [AMBER] Using Drude with Amber Abraham, Rhea C via AMBER (Thu Sep 05 2024 - 10:25:31 PDT)
- Re: [AMBER] Modification of MMPBSA electrostatic energy David A Case via AMBER (Fri Sep 06 2024 - 06:59:50 PDT)
- Re: [AMBER] About making Amber code a more standard David A Case via AMBER (Fri Sep 06 2024 - 07:08:28 PDT)
- [AMBER] protein-DNA complex model mohamed marzouk via AMBER (Fri Sep 06 2024 - 16:12:41 PDT)
- [AMBER] Problem with Miniconda after executing ./run_cmake Nikolay Kuzmich via AMBER (Sat Sep 07 2024 - 07:18:49 PDT)
- [AMBER] Error while running antechamber on the server Ramesh M via AMBER (Sat Sep 07 2024 - 23:23:34 PDT)
- [AMBER] Positive value of MM-GBSA computations Maciej Spiegel via AMBER (Sun Sep 08 2024 - 10:26:29 PDT)
- [AMBER] Error while running equilibrium step Ramesh M via AMBER (Sun Sep 08 2024 - 23:29:32 PDT)
- [AMBER] QM/MM error: No parameter for sulfur atom SUBHASMITA MAHAPATRA MAHAPATRA via AMBER (Mon Sep 09 2024 - 11:25:32 PDT)
- [AMBER] Regarding a problem with TI calculation Weerawarna Kurukulasooriy, Sandaruwani Tharaka \[CHEM\] via AMBER (Mon Sep 09 2024 - 11:32:20 PDT)
- [AMBER] atom does not have a type error, ff15ipq Rosa Teijeiro Juiz via AMBER (Tue Sep 10 2024 - 03:14:48 PDT)
- [AMBER] Regarding DiscoverEdges.py script to get xml files for Advanced TI calculation analysis: Kankana Bhattacharjee via AMBER (Tue Sep 10 2024 - 03:35:11 PDT)
- [AMBER] Cuda problems - Error: invalid device ordinal Pertschy, Florian via AMBER (Tue Sep 10 2024 - 06:54:55 PDT)
- [AMBER] Cannot find pmemd in $AMBERHOME/bin/ Wu, Ming Hsiu via AMBER (Tue Sep 10 2024 - 08:55:56 PDT)
- [AMBER] Possible error in tiMerge Osman, Roman via AMBER (Tue Sep 10 2024 - 10:56:08 PDT)
- [AMBER] Fraction in native contacts out file Debarati DasGupta via AMBER (Tue Sep 10 2024 - 13:48:10 PDT)
- [AMBER] amber24 (cuda) installation compilation error Dulal Mondal via AMBER (Wed Sep 11 2024 - 00:20:09 PDT)
- [AMBER] distance command issues Debarati DasGupta via AMBER (Wed Sep 11 2024 - 09:56:21 PDT)
- [AMBER] tutorial to run ABFE calculation Justice Josiah Mallen via AMBER (Wed Sep 11 2024 - 15:03:40 PDT)
- [AMBER] atom type error in antechamber 홍종희 via AMBER (Thu Sep 12 2024 - 02:01:46 PDT)
- [AMBER] Announcement: Release of DOCK 6.12 Scott Brozell via AMBER (Thu Sep 12 2024 - 13:16:13 PDT)
- [AMBER] Possible error in TiMerge Osman, Roman via AMBER (Fri Sep 13 2024 - 07:29:10 PDT)
- [AMBER] Saving a frame of a trajectory in pdbqt format. saverio lemme via AMBER (Fri Sep 13 2024 - 10:07:35 PDT)
- [AMBER] TI simulation with "covalent ligands" for relative binding energy? King Wang via AMBER (Sun Sep 15 2024 - 08:01:38 PDT)
- [AMBER] Forcefield Builder analogs in Amber Nikolay Kuzmich via AMBER (Sun Sep 15 2024 - 09:38:07 PDT)
- [AMBER] Regarding a Problem in TI calculation Weerawarna Kurukulasooriy, Sandaruwani Tharaka \[CHEM\] via AMBER (Sun Sep 15 2024 - 13:24:38 PDT)
- [AMBER] Some comments about vlimit David A Case via AMBER (Sun Sep 15 2024 - 19:26:15 PDT)
- [AMBER] patched plumed with amber24 Dulal Mondal via AMBER (Mon Sep 16 2024 - 07:07:04 PDT)
- [AMBER] reduce command Debarati DasGupta via AMBER (Mon Sep 16 2024 - 09:54:59 PDT)
- [AMBER] Issue with Bonds after Ligand Parameterization for MD Simulation Maciej Spiegel via AMBER (Mon Sep 16 2024 - 11:34:38 PDT)
- [AMBER] Zn2+ bond angle parameter related error Debarati DasGupta via AMBER (Mon Sep 16 2024 - 12:01:57 PDT)
- [AMBER] Modifying Topology to Use OPC Water Instead of TIP3P Maciej Spiegel via AMBER (Wed Sep 18 2024 - 01:54:41 PDT)
- [AMBER] GAFF2 publication with c5 parameterization Intravaia, Lauren E via AMBER (Wed Sep 18 2024 - 14:01:33 PDT)
- [AMBER] MMPBSA error : cpptraj failed with prmtop ../../prep/com.top 홍종희 via AMBER (Thu Sep 19 2024 - 07:16:54 PDT)
- [AMBER] MMPBSA error: LengthError: length mismatch in energy vectors 홍종희 via AMBER (Thu Sep 19 2024 - 19:29:14 PDT)
- [AMBER] cannot properly run sqm on antechamber Teijeiro Juiz, Rosa via AMBER (Fri Sep 20 2024 - 08:23:48 PDT)
- [AMBER] Issue with Heating a Solvated Membrane Bilayer System in AMBER Maciej Spiegel via AMBER (Fri Sep 20 2024 - 08:46:06 PDT)
- [AMBER] An error in TiMerge? Osman, Roman via AMBER (Fri Sep 20 2024 - 09:56:47 PDT)
- [AMBER] Calculating the number of replicas for h-remd Liyanage, Risi \(MU-Student\) via AMBER (Fri Sep 20 2024 - 13:33:11 PDT)
- [AMBER] fusing or tiling simulation boxes Ryan Woltz via AMBER (Fri Sep 20 2024 - 16:46:41 PDT)
- [AMBER] Water not recgnized correctly by atomtypes in Antechamber Husak Michal via AMBER (Sat Sep 21 2024 - 21:49:36 PDT)
- [AMBER] tleap changes HETATM to ATOM Maciej Spiegel via AMBER (Sun Sep 22 2024 - 00:40:55 PDT)
- [AMBER] Problem in TI output Tamalika Ash via AMBER (Sun Sep 22 2024 - 12:23:46 PDT)
- [AMBER] CpH MD in explicit solvent: no switch for CYS although it was in the titratable residues list Nikolay Kuzmich via AMBER (Mon Sep 23 2024 - 01:09:41 PDT)
- [AMBER] Packmol-Memgen tleap error - FATAL: Atom .R<LYS 233>.A<OXT 23> does not have a type. Maciej Spiegel via AMBER (Mon Sep 23 2024 - 01:17:58 PDT)
- [AMBER] Question about the use of MCPB.py(Handling of proteins with non-standard residues in the chain) 郑逸非 via AMBER (Mon Sep 23 2024 - 19:30:46 PDT)
- [AMBER] Installation Amber24 Enrico Martinez via AMBER (Tue Sep 24 2024 - 05:50:07 PDT)
- [AMBER] problem with Python.h while compiling amber24 Luis Simon via AMBER (Tue Sep 24 2024 - 10:52:51 PDT)
- [AMBER] Minimisation Error: LINMIN FAILURE SUBHASMITA MAHAPATRA MAHAPATRA via AMBER (Wed Sep 25 2024 - 08:36:26 PDT)
- [AMBER] Direct contact to Antechamber developers ? Husak Michal via AMBER (Wed Sep 25 2024 - 12:32:07 PDT)
- [AMBER] Failed minimization for membrane system using pmemd.MPI Pengfei Li via AMBER (Wed Sep 25 2024 - 19:58:11 PDT)
- [AMBER] Molecules minimized by amber + gaff or gaff2 requiest (for code testing) Michal Husak via AMBER (Fri Sep 27 2024 - 07:36:30 PDT)
- [AMBER] Error testing pmemd.cuda: "Illegal instruction (core dumped)" Skanda Sastry via AMBER (Fri Sep 27 2024 - 13:59:18 PDT)
- [AMBER] help 张丹阳 via AMBER (Sun Sep 29 2024 - 19:23:09 PDT)
- [AMBER] Some dihedral parameters for HID (ff19SB) Peng Zhang via AMBER (Mon Sep 30 2024 - 14:07:21 PDT)
- Last message date: Mon Sep 30 2024 - 14:30:02 PDT
- Archived on: Mon Oct 14 2024 - 05:56:17 PDT
