Amber Archive Aug 2020 by thread
- Re: [AMBER] Error in Gausian file preparation using MCPB.py gagandeep singh (Fri Jul 31 2020 - 14:01:14 PDT)
- Re: [AMBER] Problems with MC barostat Gomez, Yessica (Fri Jul 31 2020 - 17:51:23 PDT)
- [AMBER] Reduced Performance with pmemd.cuda Compared With Benchmarks. 李奕言 (Sun Aug 02 2020 - 20:21:55 PDT)
- Re: [AMBER] Issue about "... . RESTARTED DUE TO LINMIN FAILURE..." (???) 辛志宏 (Sun Aug 02 2020 - 21:04:16 PDT)
- [AMBER] Regarding the backup of amber nc files Jenny 148 (Sun Aug 02 2020 - 22:44:34 PDT)
- [AMBER] Are Amber program can running using AMD processor? Setyanto Md (Mon Aug 03 2020 - 20:25:18 PDT)
- Re: [AMBER] Structure Artifact After Autoimage Daniel Roe (Tue Aug 04 2020 - 06:25:10 PDT)
- Re: [AMBER] Tracking lifetime distance by closest of specific water IDs? Daniel Roe (Tue Aug 04 2020 - 06:28:49 PDT)
- Re: [AMBER] Problem installing AmberMD with MPI support on Cray XC40 Daniel Roe (Tue Aug 04 2020 - 06:32:11 PDT)
- Re: [AMBER] fixatomorder Daniel Roe (Tue Aug 04 2020 - 07:27:20 PDT)
- Re: [AMBER] Lipid bilayer imaging problem Daniel Roe (Tue Aug 04 2020 - 07:29:01 PDT)
- [AMBER] open valence problem Ayesha Fatima (Tue Aug 04 2020 - 07:34:19 PDT)
- Re: [AMBER] Regarding RMSD calculation and Clustering Daniel Roe (Tue Aug 04 2020 - 07:54:54 PDT)
- Re: [AMBER] Usage of the Density Peaks Algorithm. Daniel Roe (Tue Aug 04 2020 - 08:13:19 PDT)
- [AMBER] conversion of tripose mol2 to amber type Nikhil Maroli (Tue Aug 04 2020 - 05:21:08 PDT)
- [AMBER] How to make amber/antechamber type mol2 from syble mol2 Nikhil Maroli (Wed Aug 05 2020 - 00:05:03 PDT)
- [AMBER] gnuplot MYRIAN TORRES RICO (Wed Aug 05 2020 - 01:25:03 PDT)
- [AMBER] weird energy histograms with REMD Diego Morone (Wed Aug 05 2020 - 05:35:04 PDT)
- [AMBER] implicit solvent calculations with calcium ion Piotr Fajer (Wed Aug 05 2020 - 17:56:06 PDT)
- [AMBER] Fatal error on running GAMESS for parameters of FE ion gagandeep singh (Thu Aug 06 2020 - 08:59:52 PDT)
- [AMBER] asking about "timlim" in accelerated MD Setyanto Md (Thu Aug 06 2020 - 09:22:24 PDT)
- [AMBER] tleap.in error Ayesha Fatima (Thu Aug 06 2020 - 09:41:19 PDT)
- Re: [AMBER] Issue heating system in equilibration step Samuel A. Ratliff (Thu Aug 06 2020 - 09:58:04 PDT)
- [AMBER] Parmed: Residues cannot be part of 2 molecules! Molecule section will not be correctly set. Samuel A. Ratliff (Thu Aug 06 2020 - 10:10:58 PDT)
- Re: [AMBER] Caping error mohamed marzouk (Thu Aug 06 2020 - 22:39:44 PDT)
- [AMBER] problem in 3DRISM angad sharma (Fri Aug 07 2020 - 06:32:51 PDT)
- Re: [AMBER] Amber20 Performance on RTX (Turing): known problems, with a patch forthcoming David A Case (Fri Aug 07 2020 - 17:41:25 PDT)
- [AMBER] Help with MDCRD file for calculating binding energy Ram Koganti (Fri Aug 07 2020 - 18:36:34 PDT)
- [AMBER] CALL FOR PAPER - 16th German Conference on Cheminformatics (GCC) and the SAMPL satellite workshop Guessregen, Stefan /DE (Sat Aug 08 2020 - 03:45:10 PDT)
- [AMBER] Problem about ADP-Protein complex simulation neildancer.sina.com (Sat Aug 08 2020 - 06:58:49 PDT)
- [AMBER] Assigning new velocities from Maxwell-Boltzmann distribution (ntx = 1) German P. Barletta (Sun Aug 09 2020 - 13:43:20 PDT)
- [AMBER] Amber20 with PLUMED not working with multiple CPUs Amanda Buyan (Sun Aug 09 2020 - 16:25:13 PDT)
- [AMBER] about pressure calculation in Amber18 Li, Min (Sun Aug 09 2020 - 21:16:35 PDT)
- [AMBER] Defining/Selecting BLAS with cmake Gustaf Olsson (Mon Aug 10 2020 - 03:19:03 PDT)
- [AMBER] Using cpptraj to generate rst7 files from trajectory Liao (Tue Aug 11 2020 - 14:47:47 PDT)
- [AMBER] Amazon Cloud services and Amber Debarati DasGupta (Wed Aug 12 2020 - 05:24:31 PDT)
- [AMBER] Compiling AmberTools on macOS Gustaf Olsson (Wed Aug 12 2020 - 07:08:23 PDT)
- [AMBER] tleap error ankita mehta (Wed Aug 12 2020 - 09:43:03 PDT)
- Re: [AMBER] Assigning new velocities from Maxwell-Boltzmann distribution German P. Barletta (Wed Aug 12 2020 - 12:16:19 PDT)
- [AMBER] GlycoTools Webinar tomorrow Lachele Foley (Thu Aug 13 2020 - 07:34:28 PDT)
- [AMBER] Running Paramfit with 300 + structures Samuel Himes (Fri Aug 14 2020 - 14:58:14 PDT)
- [AMBER] Time numbering problem with constant-pH simulations Jonee Lillard (Sat Aug 15 2020 - 07:31:14 PDT)
- [AMBER] Error searching for compatible GPU Camila Clemente (Sat Aug 15 2020 - 18:01:37 PDT)
- [AMBER] Number of atoms in the coordinate file does not match the parm file when assigning ntwprt value 李奕言 (Sat Aug 15 2020 - 21:00:28 PDT)
- [AMBER] AMBER18 pmemd.MPI installation error Shubhandra Tripathi (Mon Aug 17 2020 - 06:43:47 PDT)
- [AMBER] preparing complexes Ayesha Fatima (Mon Aug 17 2020 - 13:25:14 PDT)
- [AMBER] no collective variables output for infe=1 and abfqmmm FLORA, JOSEPH (Mon Aug 17 2020 - 18:52:20 PDT)
- [AMBER] Few workflow-LIE Neha Gandhi (Tue Aug 18 2020 - 06:15:04 PDT)
- Re: [AMBER] How to deal with oxygen atom on Fe=O of Compound I (heme enzyme, P450) Mohamed M. Aboelnga (Tue Aug 18 2020 - 09:10:11 PDT)
- [AMBER] 转发: Amber20 install problem （Geng Dong） 东庚 (Tue Aug 18 2020 - 18:25:04 PDT)
- [AMBER] Antechamber and parmchk2 problem in case of processing mol2 input files Marek Maly (Thu Aug 20 2020 - 03:21:08 PDT)
- [AMBER] converting prmtop to psf with improper and cross-term info stripped off Lod King (Thu Aug 20 2020 - 13:22:41 PDT)
- [AMBER] Force Field ankita mehta (Fri Aug 21 2020 - 07:03:21 PDT)
- [AMBER] trouble with pdb4amber Mattia Cavallaro (Fri Aug 21 2020 - 07:10:45 PDT)
- [AMBER] Questions (and a small bug report) about SIRAH in Amber Charo del Genio (Fri Aug 21 2020 - 13:43:18 PDT)
- [AMBER] Missing (ATTN, need revision) and poor parameters (high penalty score) for small molecule parameters and hard time with paramfit Állan Ferrari (Sat Aug 22 2020 - 13:59:45 PDT)
- [AMBER] amber14 cuda code does not work Carlos (Sat Aug 22 2020 - 21:52:26 PDT)
- [AMBER] How to deal with oxygen atom on Fe=O of Compound I (heme enzyme) using MCPB tool Mohamed M. Aboelnga (Sun Aug 23 2020 - 08:31:58 PDT)
- [AMBER] error while running tutorial B5 Ayesha Fatima (Sun Aug 23 2020 - 11:08:48 PDT)
- [AMBER] Problem with MMPBSA.py Camila Clemente (Sun Aug 23 2020 - 21:23:36 PDT)
- [AMBER] Request .nc to MMPBSA.py? Camila Mara Clemente (Mon Aug 24 2020 - 10:38:37 PDT)
- [AMBER] ANTECHAMBER error: Fatal Error! Weird atomic valence (5) for atom (ID: 7, Name: C5). Pooja Kesari (Tue Aug 25 2020 - 01:33:01 PDT)
- [AMBER] novel residue from Glutamine alex rayevsky (Tue Aug 25 2020 - 05:24:29 PDT)
- [AMBER] Fundamentals of LEaP Tutorial Gustaf Olsson (Tue Aug 25 2020 - 05:36:19 PDT)
- [AMBER] plumed does not work with pmemd.cuda but it works with sander Dmitry Karlov (Wed Aug 26 2020 - 12:04:11 PDT)
- [AMBER] Change covar matrix precision when crdaction is used Guadalupe Alvarez (Wed Aug 26 2020 - 12:56:39 PDT)
- [AMBER] Help for building cross linking polymer using graphic antechamber Pinky Mazumder (Wed Aug 26 2020 - 13:16:26 PDT)
- [AMBER] Tutorial B0 Gustaf Olsson (Thu Aug 27 2020 - 00:52:38 PDT)
- [AMBER] Confusion regarding Center of mass coordinates for protein, with CPPTRAJ Prathit Chatterjee (Thu Aug 27 2020 - 04:58:48 PDT)
- [AMBER] Help for building two different salt concentration system using tLeap module Fulbabu Sk (Thu Aug 27 2020 - 05:55:29 PDT)
- [AMBER] MMPBSA.py with saline environment Camila Clemente (Thu Aug 27 2020 - 07:10:24 PDT)
- [AMBER] Unable to complete heating stage Ramanathan Rajesh (Thu Aug 27 2020 - 10:37:54 PDT)
- [AMBER] Fw: covalent molecule and modified residue parameters Sarah Jane (Thu Aug 27 2020 - 12:44:59 PDT)
- [AMBER] Stripping Protocol in Cpptraj An Ta (Thu Aug 27 2020 - 12:50:39 PDT)
- [AMBER] "Atom does not have a type" despite adding .frcmod parameters Erika Davidoff (Thu Aug 27 2020 - 12:56:25 PDT)
- [AMBER] "After the fact" lifetime analysis with CPPTRAJ Gustaf Olsson (Fri Aug 28 2020 - 05:11:52 PDT)
- [AMBER] facing problem in 3DRISM angad sharma (Fri Aug 28 2020 - 05:27:59 PDT)
- [AMBER] "FATAL: Atom *** does not have a type" Error Jatin Kashyap (Fri Aug 28 2020 - 22:44:11 PDT)
- [AMBER] FATAL atom does not have a type crispr cas9 pdb Jisha B (Sat Aug 29 2020 - 20:37:47 PDT)
- Re: [AMBER] new to amber20 aishen (Sun Aug 30 2020 - 00:53:16 PDT)
- [AMBER] How to select groups for energy calculations-CPPtraj Nikhil Maroli (Sun Aug 30 2020 - 12:44:25 PDT)
- [AMBER] EXTENDED DEADLINE for Submissions - 16th German Conference on Cheminformatics (GCC) and the SAMPL satellite workshop Guessregen, Stefan /DE (Sun Aug 30 2020 - 23:16:41 PDT)
- [AMBER] Fatal error atom type work around Ayesha Fatima (Mon Aug 31 2020 - 04:32:19 PDT)
- [AMBER] azobenzene atoms name in amber format Aashish Bhatt (Mon Aug 31 2020 - 04:42:26 PDT)
- [AMBER] Attention: All CPPTRAJ Questions Daniel Roe (Mon Aug 31 2020 - 09:55:20 PDT)
- [AMBER] Asking for Fe2-S2 cluster and Molybdopterin AMBER force field parameters Maghsoud, Yazdan (Mon Aug 31 2020 - 11:53:51 PDT)
- Last message date: Mon Aug 31 2020 - 13:00:04 PDT
- Archived on: Fri Nov 15 2024 - 05:56:04 PST
