Amber Archive Feb 2021 by thread
- Re: [AMBER] Non zero ligand warning Ayesha Fatima (Sun Jan 31 2021 - 08:12:55 PST)
- [AMBER] how does tleap choose missing side chain conformations Vaibhav Dixit (Sun Jan 31 2021 - 19:51:51 PST)
- [AMBER] configure_mpich error Nikolay N. Kuzmich (Mon Feb 01 2021 - 03:36:23 PST)
- [AMBER] erro free energy calculation Renato Araujo (Mon Feb 01 2021 - 03:56:21 PST)
- [AMBER] Solution to the replica exchange SGLD restart bug Charo del Genio (Mon Feb 01 2021 - 13:40:41 PST)
- Re: [AMBER] max pairlist cutoff must be less than unit cell max sphere radius! Pinky Mazumder (Mon Feb 01 2021 - 14:27:11 PST)
- [AMBER] QM/MM in Amber Женя Елизарова (Tue Feb 02 2021 - 01:25:23 PST)
- [AMBER] Hydrogen bond analysis tutorial Renato Araujo (Tue Feb 02 2021 - 11:13:29 PST)
- [AMBER] error while building Amber20 with Intel + CUDA Susan Chacko (Tue Feb 02 2021 - 12:20:43 PST)
- Re: [AMBER] Found bug in sander in restarting SGLD replica exchange runs Carlos Simmerling (Tue Feb 02 2021 - 17:03:28 PST)
- [AMBER] Random seed for restart files that have velocities? Liao (Tue Feb 02 2021 - 18:15:57 PST)
- [AMBER] ModuleNotFoundError: No module named 'MMPBSA_mods' Ch Bilal (Wed Feb 03 2021 - 00:35:26 PST)
- [AMBER] Nudged Elastic Band solvent choice and initial heating problem 李明玉 (Wed Feb 03 2021 - 04:12:45 PST)
- [AMBER] AMBER HREMD replica trajectory Richard Kullmann (Wed Feb 03 2021 - 06:34:11 PST)
- [AMBER] GPU power usage drop for igb = 8 compared to igb = 2 Demian Riccardi (Wed Feb 03 2021 - 14:48:45 PST)
- [AMBER] Prepare pbd file modified cyclodextrin Игорь Злотников (Thu Feb 04 2021 - 00:52:45 PST)
- [AMBER] CUDE upgrade question and AMBER Seibold, Steve Allan (Thu Feb 04 2021 - 10:00:30 PST)
- [AMBER] MMPBSA.py Error: Could not import Amber Python modules Vitor Rabelo (Thu Feb 04 2021 - 11:08:49 PST)
- Re: [AMBER] Bug in the Mol2 format: space converted into a new oxygen atom liu junjun (Thu Feb 04 2021 - 12:22:25 PST)
- [AMBER] decompose running error Nisha Amarnath Jonniya (Thu Feb 04 2021 - 22:23:23 PST)
- [AMBER] RAMD question (Xiaodong Wu) 吴晓东 (Fri Feb 05 2021 - 01:19:57 PST)
- [AMBER] Prmtop missing resid and resname info Violeta Burns Casamayor (Fri Feb 05 2021 - 01:55:31 PST)
- Re: [AMBER] Fwd: unreadable *.mdcrd David A Case (Fri Feb 05 2021 - 05:51:40 PST)
- [AMBER] curiosity about sander reading a traj being written by GPU code Vaibhav Dixit (Fri Feb 05 2021 - 08:39:10 PST)
- [AMBER] External electric fields cannot be used when npt > 0 李明玉 (Fri Feb 05 2021 - 09:19:49 PST)
- [AMBER] suggestion of a patch for building MPI version of MMPBSA.py Yoshitaka Moriwaki (Fri Feb 05 2021 - 09:43:17 PST)
- [AMBER] problem deriving implicit polarised charges charges with mdgx Luis Simon (Fri Feb 05 2021 - 13:10:59 PST)
- [AMBER] About changes in frcmod.parmbsc0 Alan (Sat Feb 06 2021 - 00:12:55 PST)
- [AMBER] RAMD simulation (Xiaodong) 吴晓东 (Sat Feb 06 2021 - 23:00:28 PST)
- [AMBER] Fix the dihedral angle during the simulation Rinsha Chk (Sun Feb 07 2021 - 01:06:16 PST)
- [AMBER] polarizable FF in amber18 or 20 Vaibhav Dixit (Sun Feb 07 2021 - 02:01:37 PST)
- [AMBER] CPPTRAJ cannot open RXSGLD trajectories out of the box Charo del Genio (Sun Feb 07 2021 - 05:59:33 PST)
- [AMBER] multi source calls in tleap Alan (Sun Feb 07 2021 - 11:50:12 PST)
- [AMBER] mdgx ipolQ charges of a charged residue Luis Simon (Mon Feb 08 2021 - 01:23:05 PST)
- Re: [AMBER] Probmlems compiling under macOS Gustaf Olsson (Mon Feb 08 2021 - 02:26:48 PST)
- [AMBER] TI with igb. = 6 Holly Freedman (Mon Feb 08 2021 - 09:47:02 PST)
- Re: [AMBER] CPPTRAJ - KMeans Value for K Piotr Fajer (Mon Feb 08 2021 - 10:15:33 PST)
- [AMBER] IEEE_OVERFLOW_FLAG Mudrovcic, Korana (Tue Feb 09 2021 - 06:22:56 PST)
- [AMBER] Preparation of i-Motif structures Sruthi Sudhakar (Tue Feb 09 2021 - 13:30:41 PST)
- [AMBER] single strand RNA parameters Jorge Iulek (Wed Feb 10 2021 - 09:41:56 PST)
- [AMBER] maximum no of atoms for simulation Pinky Mazumder (Wed Feb 10 2021 - 14:11:14 PST)
- [AMBER] Questions about loading FF02 and MMGBSA Matthew Guberman-Pfeffer (Wed Feb 10 2021 - 18:40:46 PST)
- [AMBER] Parameters for Iron Oxide Matthew Guberman-Pfeffer (Thu Feb 11 2021 - 02:42:10 PST)
- [AMBER] High value for force constant is acceptable? Rinsha Chk (Thu Feb 11 2021 - 03:50:58 PST)
- [AMBER] leap hangs on dihedral in frcmod? Kenneth Huang (Thu Feb 11 2021 - 14:08:58 PST)
- [AMBER] Testing pmemd.cuda.MPI - how many failed file comparisons are innocuous? Nikolay N. Kuzmich (Fri Feb 12 2021 - 01:44:56 PST)
- [AMBER] Amber20 GPU plus PLUMED Domenico Marson (Fri Feb 12 2021 - 04:02:46 PST)
- [AMBER] Fwd: MMPBSA Error Sadaf Rani (Fri Feb 12 2021 - 05:13:17 PST)
- [AMBER] tLeap, Fatal: Atom does not have a type Alysia Mandato (Fri Feb 12 2021 - 11:08:52 PST)
- [AMBER] Using divalent ions in LEaP Sam Walsworth (Researcher) (Fri Feb 12 2021 - 13:30:36 PST)
- [AMBER] Error while setting up constant pH MD simulations Yashraj Kulkarni (Sat Feb 13 2021 - 06:55:57 PST)
- Re: [AMBER] OPC monovalent ion parameters Cavender, Chapin (Sat Feb 13 2021 - 11:50:31 PST)
- [AMBER] Disparities between dG solv from GB and PB Models mish (Sat Feb 13 2021 - 13:55:33 PST)
- [AMBER] Altering ligand positions in Xleap Sruthi Sudhakar (Tue Feb 16 2021 - 02:44:10 PST)
- [AMBER] Membrane protein-ligand simulation - application of multiple FF - compatibility and reliability Prasanth G, Research Scholar (Tue Feb 16 2021 - 09:49:09 PST)
- [AMBER] error with AMBER installation Mohammad Alaraby (Wed Feb 17 2021 - 04:50:46 PST)
- [AMBER] theoretical doubt about TI Gabriel Jara (Wed Feb 17 2021 - 05:54:14 PST)
- Re: [AMBER] Help with installation David A Case (Thu Feb 18 2021 - 05:16:32 PST)
- [AMBER] Making sense of tip3p.frcmod Paul, Austin (Thu Feb 18 2021 - 16:18:12 PST)
- [AMBER] GaMD output (gamd.log) file analysis jacob wick (Fri Feb 19 2021 - 01:08:20 PST)
- [AMBER] query regarding heme forcefield parameters Patil Pranita Uttamrao (Fri Feb 19 2021 - 02:07:27 PST)
- [AMBER] Thermodynamic integration for protein-protein interactions WW (Fri Feb 19 2021 - 06:35:25 PST)
- [AMBER] tip3p water model in amber14 Swisher, Justin S (Fri Feb 19 2021 - 08:48:24 PST)
- [AMBER] Interaction energy by MM-PBSA for a superantigen with important Zn(II) center SATYAJIT KHATUA (Fri Feb 19 2021 - 09:56:53 PST)
- [AMBER] MAXPR error in sander sp job Vaibhav Dixit (Fri Feb 19 2021 - 20:06:57 PST)
- [AMBER] Stacking energy calculation Athena N (Sat Feb 20 2021 - 00:52:04 PST)
- [AMBER] Why do trajectories get corrupted? Victoria E Hill (Sat Feb 20 2021 - 08:36:44 PST)
- [AMBER] Sufficiently equilibrated or not Delwakkada Liyanage, Senal Dinuka (Sat Feb 20 2021 - 11:17:14 PST)
- [AMBER] case studies of MD based drug discovery Vaibhav Dixit (Sun Feb 21 2021 - 05:05:28 PST)
- [AMBER] Odd number of electrons divyabharathi korlepara (Mon Feb 22 2021 - 05:57:27 PST)
- [AMBER] Acpype error: Timed out process killed Shilpa Gupta (Mon Feb 22 2021 - 07:24:04 PST)
- [AMBER] Regarding restarting of Gaussian Accelerated MD. Sruthi Sudhakar (Mon Feb 22 2021 - 20:39:04 PST)
- [AMBER] Problem with pmemd.MPI Pranjal Bhuyan (Tue Feb 23 2021 - 02:36:56 PST)
- [AMBER] Multiple Harmonic Restraints Li,Haoxi (Tue Feb 23 2021 - 08:44:27 PST)
- [AMBER] How to recompile AmberTools Matthew Guberman-Pfeffer (Tue Feb 23 2021 - 21:41:46 PST)
- [AMBER] MDGX charge fitting with some charges fixed or restrained Luis Simon (Wed Feb 24 2021 - 00:34:30 PST)
- Re: [AMBER] [lsimon.usal.es: MDGX charge fitting with some charges fixed or restrained] David Cerutti (Wed Feb 24 2021 - 05:25:12 PST)
- [AMBER] Apply Lennar-Jones potential between small molecules Ming Tang (Wed Feb 24 2021 - 14:51:46 PST)
- Re: [AMBER] Calculating forces Daniel Roe (Thu Feb 25 2021 - 02:32:52 PST)
- [AMBER] AmberTools20 parallel test errors Alain Arsene (Thu Feb 25 2021 - 02:53:50 PST)
- [AMBER] GPU TI PROBLEM Umut Çağan Uçar (Thu Feb 25 2021 - 05:36:25 PST)
- [AMBER] Amber18 + Ambertools20 Rafał Bachorz (Thu Feb 25 2021 - 06:04:39 PST)
- [AMBER] MMPBSA, signal SIGSEGV failure Matthew Guberman-Pfeffer (Thu Feb 25 2021 - 08:11:29 PST)
- [AMBER] help with cpptraj error (segmentation fault) Cato, Lee (Thu Feb 25 2021 - 10:12:20 PST)
- [AMBER] Molecule volume in cpptraj? Gustavo Seabra (Thu Feb 25 2021 - 10:56:10 PST)
- [AMBER] Steered MD Pinky Mazumder (Thu Feb 25 2021 - 12:14:30 PST)
- [AMBER] dimer shifts under NPT ensemble Qinghua Liao (Thu Feb 25 2021 - 16:04:23 PST)
- [AMBER] Calculating pairwise RMSD of two proteins Sadaf Rani (Fri Feb 26 2021 - 10:31:20 PST)
- [AMBER] cpptraj CMAP flag issue with charmm-gui parm7 files Wesley Michael Botello-Smith (Fri Feb 26 2021 - 13:40:53 PST)
- Re: [AMBER] ZAFF force field Pengfei Li (Fri Feb 26 2021 - 15:12:51 PST)
- [AMBER] atom number difference in topology and simulated trajectory Ayesha Fatima (Sat Feb 27 2021 - 00:10:20 PST)
- Last message date: Sun Feb 28 2021 - 03:30:02 PST
- Archived on: Fri Jul 11 2025 - 05:56:19 PDT
