Amber Archive Sep 2024: by subject

[AMBER] About making Amber code a more standard
- David A Case via AMBER (Fri Sep 06 2024 - 07:08:28 PDT)
[AMBER] amber24 (cuda) installation compilation error
- Dulal Mondal via AMBER (Mon Sep 16 2024 - 09:16:09 PDT)
- Li, Zhen via AMBER (Mon Sep 16 2024 - 09:07:08 PDT)
- David A Case via AMBER (Thu Sep 12 2024 - 06:48:13 PDT)
- Li, Zhen via AMBER (Thu Sep 12 2024 - 06:33:32 PDT)
- Dulal Mondal via AMBER (Thu Sep 12 2024 - 06:17:43 PDT)
- Dulal Mondal via AMBER (Wed Sep 11 2024 - 00:20:09 PDT)
[AMBER] An error in TiMerge?
- Ryan Snyder via AMBER (Fri Sep 20 2024 - 12:11:04 PDT)
- Carlos Simmerling via AMBER (Fri Sep 20 2024 - 10:00:07 PDT)
- Osman, Roman via AMBER (Fri Sep 20 2024 - 09:56:47 PDT)
[AMBER] Announcement: Release of DOCK 6.12
- Scott Brozell via AMBER (Thu Sep 12 2024 - 13:16:13 PDT)
[AMBER] atom does not have a type error, ff15ipq
- Rosa Teijeiro Juiz via AMBER (Wed Sep 11 2024 - 07:14:22 PDT)
- 王世玉 via AMBER (Tue Sep 10 2024 - 18:12:06 PDT)
- Rosa Teijeiro Juiz via AMBER (Tue Sep 10 2024 - 03:14:48 PDT)
[AMBER] atom type error in antechamber
- Shiyu Wang via AMBER (Thu Sep 12 2024 - 18:41:32 PDT)
- David A Case via AMBER (Thu Sep 12 2024 - 06:53:58 PDT)
- 홍종희 via AMBER (Thu Sep 12 2024 - 02:01:46 PDT)
[AMBER] Bug in parmchck2 code (antechamber engine) ...
- Michal Husak via AMBER (Wed Sep 25 2024 - 06:31:06 PDT)
[AMBER] Calculating the number of replicas for h-remd
- Carlos Simmerling via AMBER (Thu Sep 26 2024 - 15:16:20 PDT)
- Carlos Simmerling via AMBER (Thu Sep 26 2024 - 14:53:45 PDT)
- Carlos Simmerling via AMBER (Mon Sep 23 2024 - 11:48:09 PDT)
- Carlos Simmerling via AMBER (Sat Sep 21 2024 - 04:36:21 PDT)
- Liyanage, Risi $MU-Student$ via AMBER (Fri Sep 20 2024 - 13:33:11 PDT)
[AMBER] Cannot find pmemd in $AMBERHOME/bin/
- Shiyu Wang via AMBER (Tue Sep 10 2024 - 17:59:51 PDT)
- Carlos Simmerling via AMBER (Tue Sep 10 2024 - 09:10:57 PDT)
- Wu, Ming Hsiu via AMBER (Tue Sep 10 2024 - 08:55:56 PDT)
[AMBER] cannot properly run sqm on antechamber
- David Case via AMBER (Fri Sep 20 2024 - 09:26:24 PDT)
- Teijeiro Juiz, Rosa via AMBER (Fri Sep 20 2024 - 08:23:48 PDT)
[AMBER] CpH MD in explicit solvent: no switch for CYS although it was in the titratable residues list
- Jason Swails via AMBER (Wed Sep 25 2024 - 14:33:43 PDT)
- Adrian Roitberg via AMBER (Wed Sep 25 2024 - 11:59:09 PDT)
- Jason Swails via AMBER (Wed Sep 25 2024 - 11:30:40 PDT)
- Jason Swails via AMBER (Tue Sep 24 2024 - 09:52:14 PDT)
- Nikolay Kuzmich via AMBER (Mon Sep 23 2024 - 01:09:41 PDT)
[AMBER] Cuda problems - Error: invalid device ordinal
- Pertschy, Florian via AMBER (Tue Sep 10 2024 - 07:48:17 PDT)
- Pertschy, Florian via AMBER (Tue Sep 10 2024 - 06:54:55 PDT)
[AMBER] Custom AA residue missing parameters
- Téletchéa Stéphane via AMBER (Mon Sep 09 2024 - 02:56:31 PDT)
- Téletchéa Stéphane via AMBER (Thu Sep 05 2024 - 03:38:48 PDT)
[AMBER] Direct contact to Antechamber developers ?
- Husak Michal via AMBER (Wed Sep 25 2024 - 12:32:07 PDT)
[AMBER] distance command issues
- David A Case via AMBER (Thu Sep 12 2024 - 06:52:16 PDT)
- Carlos Simmerling via AMBER (Wed Sep 11 2024 - 10:02:37 PDT)
- Debarati DasGupta via AMBER (Wed Sep 11 2024 - 09:56:21 PDT)
[AMBER] Error testing pmemd.cuda: "Illegal instruction (core dumped)"
- Skanda Sastry via AMBER (Fri Sep 27 2024 - 13:59:18 PDT)
[AMBER] Error to run constant pH replica exchange in explicit solvent in amber18
- Vinicius Cruzeiro via AMBER (Wed Sep 04 2024 - 10:54:40 PDT)
- Dulal Mondal via AMBER (Wed Sep 04 2024 - 07:06:09 PDT)
[AMBER] Error while running antechamber on the server
- Dr. Anselm Horn via AMBER (Sun Sep 08 2024 - 08:32:18 PDT)
- Ramesh M via AMBER (Sat Sep 07 2024 - 23:23:34 PDT)
[AMBER] Error while running equilibrium step
- David A Case via AMBER (Thu Sep 12 2024 - 06:40:52 PDT)
- Téletchéa Stéphane via AMBER (Mon Sep 09 2024 - 02:59:11 PDT)
- Ramesh M via AMBER (Sun Sep 08 2024 - 23:29:32 PDT)
[AMBER] Failed minimization for membrane system using pmemd.MPI
- David A Case via AMBER (Wed Sep 25 2024 - 22:01:02 PDT)
- Pengfei Li via AMBER (Wed Sep 25 2024 - 19:58:11 PDT)
[AMBER] Forcefield Builder analogs in Amber
- Carlos Simmerling via AMBER (Thu Sep 19 2024 - 11:54:57 PDT)
- David A Case via AMBER (Thu Sep 19 2024 - 11:00:56 PDT)
- Jones de Andrade via AMBER (Tue Sep 17 2024 - 02:25:30 PDT)
- David A Case via AMBER (Sun Sep 15 2024 - 19:54:02 PDT)
- Nikolay Kuzmich via AMBER (Sun Sep 15 2024 - 09:38:07 PDT)
[AMBER] Fraction in native contacts out file
- Debarati DasGupta via AMBER (Tue Sep 10 2024 - 13:48:10 PDT)
[AMBER] fusing or tiling simulation boxes
- Ryan Woltz via AMBER (Fri Sep 20 2024 - 16:46:41 PDT)
[AMBER] GAFF2 publication with c5 parameterization
- Intravaia, Lauren E via AMBER (Wed Sep 18 2024 - 14:01:33 PDT)
[AMBER] help
- David A Case via AMBER (Sun Sep 29 2024 - 20:42:49 PDT)
- 张丹阳 via AMBER (Sun Sep 29 2024 - 19:23:09 PDT)
[AMBER] Installation Amber24
- Enrico Martinez via AMBER (Tue Sep 24 2024 - 08:30:40 PDT)
- Enrico Martinez via AMBER (Tue Sep 24 2024 - 08:09:43 PDT)
- Enrico Martinez via AMBER (Tue Sep 24 2024 - 05:50:07 PDT)
[AMBER] Issue with Bonds after Ligand Parameterization for MD Simulation
- Carlos Simmerling via AMBER (Mon Sep 16 2024 - 16:26:38 PDT)
- Carlos Simmerling via AMBER (Mon Sep 16 2024 - 12:02:41 PDT)
- Carlos Simmerling via AMBER (Mon Sep 16 2024 - 11:49:39 PDT)
- Maciej Spiegel via AMBER (Mon Sep 16 2024 - 11:34:38 PDT)
[AMBER] Issue with Heating a Solvated Membrane Bilayer System in AMBER
- Carlos Simmerling via AMBER (Fri Sep 20 2024 - 09:37:55 PDT)
- Carlos Simmerling via AMBER (Fri Sep 20 2024 - 08:57:02 PDT)
- Maciej Spiegel via AMBER (Fri Sep 20 2024 - 08:46:06 PDT)
[AMBER] Minimisation Error: LINMIN FAILURE
- Carlos Simmerling via AMBER (Wed Sep 25 2024 - 10:35:27 PDT)
- Carlos Simmerling via AMBER (Wed Sep 25 2024 - 09:13:42 PDT)
- SUBHASMITA MAHAPATRA MAHAPATRA via AMBER (Wed Sep 25 2024 - 08:36:26 PDT)
[AMBER] MMPBSA error : cpptraj failed with prmtop ../../prep/com.top
- 홍종희 via AMBER (Thu Sep 19 2024 - 22:47:38 PDT)
- 홍종희 via AMBER (Thu Sep 19 2024 - 19:23:43 PDT)
- David A Case via AMBER (Thu Sep 19 2024 - 11:07:10 PDT)
- 홍종희 via AMBER (Thu Sep 19 2024 - 07:16:54 PDT)
[AMBER] MMPBSA error: LengthError: length mismatch in energy vectors
- Jason Swails via AMBER (Tue Sep 24 2024 - 09:54:10 PDT)
- 홍종희 via AMBER (Thu Sep 19 2024 - 19:29:14 PDT)
[AMBER] Modification of MMPBSA electrostatic energy
- David A Case via AMBER (Fri Sep 06 2024 - 06:59:50 PDT)
[AMBER] Modifying Topology to Use OPC Water Instead of TIP3P
- Carlos Simmerling via AMBER (Wed Sep 18 2024 - 03:14:59 PDT)
- haiyangzhong via AMBER (Wed Sep 18 2024 - 02:15:17 PDT)
- Maciej Spiegel via AMBER (Wed Sep 18 2024 - 01:54:41 PDT)
[AMBER] Molecules minimized by amber + gaff or gaff2 requiest (for code testing)
- David A Case via AMBER (Sun Sep 29 2024 - 20:36:20 PDT)
- Michal Husak via AMBER (Fri Sep 27 2024 - 07:36:30 PDT)
[AMBER] OPC3 water and ff19SB forcefield for constant pH simulations
- Nikolay Kuzmich via AMBER (Thu Sep 05 2024 - 02:35:54 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] patched plumed with amber24
- SATYAJIT KHATUA via AMBER (Wed Sep 18 2024 - 00:00:04 PDT)
- SATYAJIT KHATUA via AMBER (Mon Sep 16 2024 - 08:36:24 PDT)
- Dulal Mondal via AMBER (Mon Sep 16 2024 - 07:07:04 PDT)
[AMBER] Positive value of MM-GBSA computations
- Maciej Spiegel via AMBER (Wed Sep 11 2024 - 00:39:28 PDT)
- 王世玉 via AMBER (Tue Sep 10 2024 - 18:36:34 PDT)
- Carlos Simmerling via AMBER (Sun Sep 08 2024 - 10:37:50 PDT)
- Maciej Spiegel via AMBER (Sun Sep 08 2024 - 10:26:29 PDT)
[AMBER] Possible error in TiMerge
- Osman, Roman via AMBER (Fri Sep 13 2024 - 07:29:10 PDT)
- Osman, Roman via AMBER (Tue Sep 10 2024 - 10:56:08 PDT)
- Osman, Roman via AMBER (Thu Sep 05 2024 - 07:27:33 PDT)
[AMBER] Problem in TI output
- Tamalika Ash via AMBER (Sun Sep 22 2024 - 12:23:46 PDT)
[AMBER] Problem with Miniconda after executing ./run_cmake
- Daniel Roe via AMBER (Mon Sep 09 2024 - 12:29:48 PDT)
- Nikolay Kuzmich via AMBER (Sat Sep 07 2024 - 07:18:49 PDT)
[AMBER] problem with Python.h while compiling amber24
- Timothy Giese via AMBER (Mon Sep 30 2024 - 07:34:18 PDT)
- David A Case via AMBER (Wed Sep 25 2024 - 16:53:42 PDT)
- LUIS MANUEL SIMÓN RUBIO via AMBER (Wed Sep 25 2024 - 12:26:54 PDT)
- Timothy Giese via AMBER (Wed Sep 25 2024 - 10:15:38 PDT)
- Luis Simon via AMBER (Tue Sep 24 2024 - 10:52:51 PDT)
[AMBER] protein-DNA complex model
- mohamed marzouk via AMBER (Fri Sep 06 2024 - 16:12:41 PDT)
[AMBER] QM/MM error: No parameter for sulfur atom
- Goetz, Andreas via AMBER (Mon Sep 09 2024 - 21:28:03 PDT)
- SUBHASMITA MAHAPATRA MAHAPATRA via AMBER (Mon Sep 09 2024 - 11:25:32 PDT)
[AMBER] Question about the use of MCPB.py(Handling of proteins with non-standard residues in the chain)
- Li, Zhen via AMBER (Wed Sep 25 2024 - 20:06:30 PDT)
- 郑逸非 via AMBER (Mon Sep 23 2024 - 19:30:46 PDT)
[AMBER] reduce command
- Debarati DasGupta via AMBER (Mon Sep 16 2024 - 10:11:51 PDT)
- Carlos Simmerling via AMBER (Mon Sep 16 2024 - 10:03:06 PDT)
- Debarati DasGupta via AMBER (Mon Sep 16 2024 - 09:54:59 PDT)
[AMBER] Regarding a Problem in TI calculation
- David A Case via AMBER (Sun Sep 15 2024 - 19:57:44 PDT)
- Weerawarna Kurukulasooriy, Sandaruwani Tharaka \[CHEM\] via AMBER (Sun Sep 15 2024 - 13:24:38 PDT)
[AMBER] Regarding a problem with TI calculation
- David A Case via AMBER (Thu Sep 12 2024 - 06:44:56 PDT)
- Timothy Giese via AMBER (Mon Sep 09 2024 - 11:42:31 PDT)
- Weerawarna Kurukulasooriy, Sandaruwani Tharaka \[CHEM\] via AMBER (Mon Sep 09 2024 - 11:32:20 PDT)
[AMBER] Regarding DiscoverEdges.py script to get xml files for Advanced TI calculation analysis:
- Kankana Bhattacharjee via AMBER (Tue Sep 10 2024 - 07:46:30 PDT)
- Kankana Bhattacharjee via AMBER (Tue Sep 10 2024 - 05:18:10 PDT)
- Kankana Bhattacharjee via AMBER (Tue Sep 10 2024 - 03:37:10 PDT)
- Kankana Bhattacharjee via AMBER (Tue Sep 10 2024 - 03:35:11 PDT)
[AMBER] Regarding REUS simulations
- Carlos Simmerling via AMBER (Fri Sep 06 2024 - 06:48:33 PDT)
- Carlos Simmerling via AMBER (Fri Sep 06 2024 - 06:34:48 PDT)
- Carlos Simmerling via AMBER (Sun Sep 01 2024 - 05:00:37 PDT)
[AMBER] Saving a frame of a trajectory in pdbqt format.
- Daniel Roe via AMBER (Fri Sep 13 2024 - 14:22:35 PDT)
- saverio lemme via AMBER (Fri Sep 13 2024 - 10:07:35 PDT)
[AMBER] Some comments about vlimit
- David A Case via AMBER (Sun Sep 15 2024 - 19:26:15 PDT)
[AMBER] Some dihedral parameters for HID (ff19SB)
- Peng Zhang via AMBER (Mon Sep 30 2024 - 14:07:21 PDT)
[AMBER] TI simulation with "covalent ligands" for relative binding energy?
- King Wang via AMBER (Sun Sep 15 2024 - 08:01:38 PDT)
[AMBER] tleap changes HETATM to ATOM
- Carlos Simmerling via AMBER (Sun Sep 22 2024 - 04:29:20 PDT)
- Maciej Spiegel via AMBER (Sun Sep 22 2024 - 00:40:55 PDT)
[AMBER] tutorial to run ABFE calculation
- Justice Josiah Mallen via AMBER (Wed Sep 11 2024 - 15:03:40 PDT)
[AMBER] Using Drude with Amber
- David A Case via AMBER (Fri Sep 06 2024 - 07:06:46 PDT)
- Abraham, Rhea C via AMBER (Thu Sep 05 2024 - 10:25:31 PDT)
[AMBER] Water not recgnized correctly by atomtypes in Antechamber
- David A Case via AMBER (Tue Sep 24 2024 - 11:41:39 PDT)
- Carlos Simmerling via AMBER (Sun Sep 22 2024 - 04:54:17 PDT)
- Carlos Simmerling via AMBER (Sun Sep 22 2024 - 04:31:15 PDT)
- Husak Michal via AMBER (Sat Sep 21 2024 - 21:49:36 PDT)
[AMBER] Zn2+ bond angle parameter related error
- SATYAJIT KHATUA via AMBER (Mon Sep 16 2024 - 12:21:17 PDT)
- SATYAJIT KHATUA via AMBER (Mon Sep 16 2024 - 12:17:05 PDT)
- Carlos Simmerling via AMBER (Mon Sep 16 2024 - 12:10:56 PDT)
- Debarati DasGupta via AMBER (Mon Sep 16 2024 - 12:01:57 PDT)

Amber Archive Sep 2024 by subject