Amber Archive Oct 2020 by thread
- Re: [AMBER] controversy in PBSA and GBSA results h_sahakyan.mb.sci.am (Wed Sep 30 2020 - 21:16:05 PDT)
- Re: [AMBER] Modification of dihedral torsion potential David A Case (Thu Oct 01 2020 - 05:03:36 PDT)
- Re: [AMBER] Conversion of Gromacs [atomtypes] and [nonbond_params] to Amber NONBON and LJEDIT Matias Machado (Thu Oct 01 2020 - 05:58:33 PDT)
- [AMBER] pmemd aishen (Thu Oct 01 2020 - 09:44:55 PDT)
- [AMBER] Error: Failed to generate parameters Jatin Kashyap (Thu Oct 01 2020 - 09:57:17 PDT)
- Re: [AMBER] Problem in AMBER18 Installation Mariangela Dametto (Thu Oct 01 2020 - 09:58:09 PDT)
- Re: [AMBER] Query regarding Dialanine peptide 2d ABMD tutorial in the NFE category SHAUNAK BADANI (Thu Oct 01 2020 - 13:26:28 PDT)
- [AMBER] pmemd aishen (Thu Oct 01 2020 - 13:50:45 PDT)
- [AMBER] MMPBSA.py TypeError: a bytes-like object is required, not 'str' سید حامد سادات حیاتشاهی (Thu Oct 01 2020 - 13:52:28 PDT)
- [AMBER] partial charges for modified nucleotide Farkhad Maksudov (Thu Oct 01 2020 - 18:28:28 PDT)
- [AMBER] Additional restraints in Umbrella sampling? Qing Lv (Thu Oct 01 2020 - 18:29:39 PDT)
- [AMBER] Compiling CPPTRAJ from GitHub Gustaf Olsson (Fri Oct 02 2020 - 03:53:11 PDT)
- [AMBER] image protein complex iwrap=1 Ari Zeida (Fri Oct 02 2020 - 07:21:41 PDT)
- [AMBER] how to use one prmtop for two trajectories with just one ion difference Vaibhav Dixit (Fri Oct 02 2020 - 07:55:35 PDT)
- [AMBER] about translation aishen (Sat Oct 03 2020 - 01:21:57 PDT)
- [AMBER] MMGBSA/MMPBSA Help Abdul-Rashid III Sampaco (Sat Oct 03 2020 - 04:33:44 PDT)
- [AMBER] RMSD of ligand in pocket Debarati DasGupta (Sat Oct 03 2020 - 08:08:20 PDT)
- [AMBER] Query regarding ion constraint in MD simulations Nisha Amarnath Jonniya (Sat Oct 03 2020 - 19:33:58 PDT)
- [AMBER] cpptraj unable to write pdb files using Vaibhav Dixit (Sat Oct 03 2020 - 21:32:46 PDT)
- [AMBER] usage of nmr (between COMs) restraints with pmem.cuda Dmitry Karlov (Sun Oct 04 2020 - 06:57:55 PDT)
- [AMBER] controversy in PBSA and GBSA results h_sahakyan.mb.sci.am (Sun Oct 04 2020 - 22:28:30 PDT)
- [AMBER] Different atomic partial charges on OD1/OD2 Margareta Hellmann (Mon Oct 05 2020 - 07:59:37 PDT)
- [AMBER] Hitting the supercomputer wall limit before completion of minimization step Jatin Kashyap (Mon Oct 05 2020 - 08:28:44 PDT)
- [AMBER] REST2 in Amber Qinghua Liao (Mon Oct 05 2020 - 08:30:05 PDT)
- [AMBER] Question about force field for proteins Asaf Farhi (Mon Oct 05 2020 - 08:31:10 PDT)
- [AMBER] controversy in PBSA and GBSA results h_sahakyan.mb.sci.am (Mon Oct 05 2020 - 09:04:26 PDT)
- [AMBER] How does one build MMPBSA.py.MPI on a Centos 7 system? Hamed S. Hayatshahi (Mon Oct 05 2020 - 12:30:44 PDT)
- [AMBER] Which OS/Amber combinations are supported? Kevin Keane (Mon Oct 05 2020 - 13:06:37 PDT)
- [AMBER] Imaging issues with cpptraj Suchetana Gupta (Tue Oct 06 2020 - 00:09:41 PDT)
- Re: [AMBER] A100 and RTX3090 Benchmarks Filip Fratev (Tue Oct 06 2020 - 01:44:54 PDT)
- [AMBER] Amber performance Jonathan Gabriel Canan Gomez (Tue Oct 06 2020 - 15:56:22 PDT)
- [AMBER] controversy in PBSA and GBSA results h_sahakyan.mb.sci.am (Wed Oct 07 2020 - 06:19:19 PDT)
- [AMBER] Problems with using pdb4amber (and possibly other programs) on Ubuntu 20.04 bgostyns.cbmm.lodz.pl (Wed Oct 07 2020 - 06:52:03 PDT)
- [AMBER] Cannot run NPT mohamed marzouk (Wed Oct 07 2020 - 07:05:56 PDT)
- [AMBER] QMMM SCC-DFTB: Convergence could not be achieved Sarah Jane (Wed Oct 07 2020 - 10:22:46 PDT)
- [AMBER] Verbose - Output File Information Not Changing An Ta (Wed Oct 07 2020 - 11:55:43 PDT)
- [AMBER] Amber20 compilation issue (related to boost?) Suman Chakrabarty (Wed Oct 07 2020 - 23:07:08 PDT)
- [AMBER] not writing restart file Erik Zuiderweg (Thu Oct 08 2020 - 09:17:41 PDT)
- [AMBER] ERROR: The file contained 14 atoms not in residue templates Jatin Kashyap (Thu Oct 08 2020 - 12:28:14 PDT)
- [AMBER] Permute dihedrals David Poole (Fri Oct 09 2020 - 04:40:53 PDT)
- [AMBER] NVIDIA GeForce RTX 3080 GPUs Mike Mazanetz (Fri Oct 09 2020 - 08:36:46 PDT)
- [AMBER] CPPTRAJ: Cluster structures keeping only one water, by position? Gustavo Seabra (Fri Oct 09 2020 - 11:14:59 PDT)
- Re: [AMBER] AmberMdPrep github cpptraj not sourced Vaibhav Dixit (Fri Oct 09 2020 - 17:30:17 PDT)
- Re: [AMBER] NVIDIA GeForce RTX 3080 GPUs (Ross Walker) German P. Barletta (Sat Oct 10 2020 - 12:48:39 PDT)
- [AMBER] Conda installation of AmberTools mukesh raval (Sat Oct 10 2020 - 21:00:54 PDT)
- [AMBER] NVIDIA GeForce RTX 3080 GPUs German P. Barletta (Sun Oct 11 2020 - 13:10:54 PDT)
- Re: [AMBER] partial charge calculation (RESP) using gaussian09/antechamber (ambertools17) on a symmetrical molecule BLUNTZER Marie (Mon Oct 12 2020 - 04:09:32 PDT)
- [AMBER] RMSD, Rg density map mohamed marzouk (Mon Oct 12 2020 - 11:00:45 PDT)
- [AMBER] MMGBSA Ligand Mask issues Suchetana Gupta (Tue Oct 13 2020 - 03:03:31 PDT)
- [AMBER] Error running small molecule simulation: "RESTARTED DUE TO LINMIN FAILURE" and "an illegal memory access was encountered launching kernel kClearForces" erros Állan Ferrari (Tue Oct 13 2020 - 07:07:53 PDT)
- [AMBER] vlimit=10 compromise for Amber 20 error: "an illegal memory access was encountered launching kernel kClearForces"? Liao (Tue Oct 13 2020 - 11:29:23 PDT)
- [AMBER] Using parmchk2 with GLYCAM_06j.dat Delwakkada Liyanage, Senal Dinuka (Tue Oct 13 2020 - 12:44:58 PDT)
- [AMBER] Installation of AMBER20 on CentOS 7 Pandey Anwesh (Wed Oct 14 2020 - 06:53:31 PDT)
- [AMBER] assess which structures are similar between two MD-trajectories Vaibhav Dixit (Wed Oct 14 2020 - 20:51:04 PDT)
- Re: [AMBER] PMF calculation somdev pahari (Thu Oct 15 2020 - 10:11:28 PDT)
- [AMBER] mdout issue Alejandro Cagnoni (Thu Oct 15 2020 - 07:01:53 PDT)
- [AMBER] Query about using MMPBSA.py to calculate the binding free energy for a ligand bound enzyme SATYAJIT KHATUA (Thu Oct 15 2020 - 09:41:54 PDT)
- [AMBER] cpptraj's hbond shows hbonds with carbon hydrogens German P. Barletta (Thu Oct 15 2020 - 12:53:21 PDT)
- [AMBER] Adding catalytic Magnesium ion Jisha B (Thu Oct 15 2020 - 15:10:17 PDT)
- [AMBER] KeyError: 'H262' Wu Xu (Thu Oct 15 2020 - 20:25:27 PDT)
- [AMBER] VMD 1.9.4 could not read AMBER16 .mdcrd Wu Xu (Thu Oct 15 2020 - 21:23:17 PDT)
- [AMBER] Loading R.E.D server parameters into xleap Sruthi Sudhakar (Fri Oct 16 2020 - 02:50:13 PDT)
- [AMBER] Fwd: AMBER Digest, Vol 3153, Issue 1 SATYAJIT KHATUA (Thu Oct 15 2020 - 21:59:05 PDT)
- [AMBER] mm-pbsa calculation Serena Vittorio (Fri Oct 16 2020 - 09:21:24 PDT)
- [AMBER] rms(d) or (f) per residue Seibold, Steve Allan (Fri Oct 16 2020 - 09:51:09 PDT)
- [AMBER] NAMD trajectory analysis with cpptraj sangita kachhap (Fri Oct 16 2020 - 12:35:39 PDT)
- [AMBER] cpptraj's hbond shows hbonds with carbon hydrogens German P. Barletta (Fri Oct 16 2020 - 13:03:50 PDT)
- [AMBER] Creating a coordinate bond in Leap Jenny 148 (Fri Oct 16 2020 - 21:53:54 PDT)
- [AMBER] process_mdout.perl for pmemd Jorge Iulek (Sat Oct 17 2020 - 14:31:07 PDT)
- [AMBER] Amber20 compiling warning Tom Wang (Sun Oct 18 2020 - 05:40:44 PDT)
- [AMBER] Bond: Maximum coordination exceeded Sarah Jane (Sun Oct 18 2020 - 11:21:45 PDT)
- [AMBER] Adding missing residues in a pdb file using tleap SUNITA MUDULI (Sun Oct 18 2020 - 12:14:01 PDT)
- [AMBER] RMSD (non mass-weighted) as collective variable in Amber-18 Madhur Aggarwal (Sun Oct 18 2020 - 14:20:09 PDT)
- [AMBER] MD error Kehinde Idowu (Sun Oct 18 2020 - 14:24:14 PDT)
- [AMBER] Metalloprotein-ligand complex modelling for MMPBSA.py SATYAJIT KHATUA (Mon Oct 19 2020 - 00:59:36 PDT)
- [AMBER] mm-pbsa calculation: SA Bomb in circle(): Stored surface arcs over limit Serena Vittorio (Mon Oct 19 2020 - 01:27:56 PDT)
- [AMBER] Steered MD at constant force Vishal Singh (Mon Oct 19 2020 - 05:28:49 PDT)
- [AMBER] NOE analysis with cpptraj Pavlína Pokorná (Mon Oct 19 2020 - 06:17:47 PDT)
- [AMBER] Changing lj_radius without changing lj_14_radius Batuhan Kav (Mon Oct 19 2020 - 08:23:32 PDT)
- [AMBER] Amber 20 compilation with the intel 2019.1.1 compiler Vlad Cojocaru (Mon Oct 19 2020 - 10:47:43 PDT)
- [AMBER] Bacteria cell membrane PDB Loo Kang (Mon Oct 19 2020 - 20:06:53 PDT)
- [AMBER] mdout error Alejandro Cagnoni (Tue Oct 20 2020 - 04:54:13 PDT)
- [AMBER] controversy in PBSA and GBSA results h_sahakyan.mb.sci.am (Tue Oct 20 2020 - 05:27:05 PDT)
- [AMBER] calculating differences in binding energy for enantiomers to amino acid based surfactants Billiot, Eugene (Tue Oct 20 2020 - 05:45:16 PDT)
- [AMBER] Adding Ions Gustaf Olsson (Tue Oct 20 2020 - 05:56:08 PDT)
- [AMBER] TI not compatible with GB on GPU Vaibhav Dixit (Tue Oct 20 2020 - 02:27:07 PDT)
- [AMBER] AMBER16 problem Seibold, Steve Allan (Tue Oct 20 2020 - 07:56:20 PDT)
- Re: [AMBER] Error building Amber Kazuo Ohta (Tue Oct 20 2020 - 19:08:05 PDT)
- [AMBER] ff19SB and OPC, process_(min/md)out.perl and LEaP Gustaf Olsson (Wed Oct 21 2020 - 01:10:10 PDT)
- Re: [AMBER] ff19SB and OPC, process_(min/md)out.perl and LEaP Gustaf Olsson (Wed Oct 21 2020 - 05:36:30 PDT)
- Re: [AMBER] ff19SB and OPC, process_(min/md)out.perl and LEaP Carlos Simmerling (Wed Oct 21 2020 - 06:32:50 PDT)
- Re: [AMBER] ff19SB and OPC, process_(min/md)out.perl and LEaP Gustaf Olsson (Thu Oct 22 2020 - 00:10:34 PDT)
- Re: [AMBER] ff19SB and OPC, process_(min/md)out.perl and LEaP Gustaf Olsson (Thu Oct 22 2020 - 01:53:17 PDT)
- Re: [AMBER] ff19SB and OPC, process_(min/md)out.perl and LEaP Gustaf Olsson (Thu Oct 22 2020 - 02:27:13 PDT)
- Re: [AMBER] ff19SB and OPC, process_(min/md)out.perl and LEaP David A Case (Thu Oct 22 2020 - 05:47:51 PDT)
- Re: [AMBER] ff19SB and OPC, process_(min/md)out.perl and LEaP Carlos Simmerling (Thu Oct 22 2020 - 06:06:06 PDT)
- Re: [AMBER] ff19SB and OPC, process_(min/md)out.perl and LEaP Gustaf Olsson (Fri Oct 23 2020 - 02:26:05 PDT)
- Re: [AMBER] ff19SB and OPC, process_(min/md)out.perl and LEaP Daniel Roe (Fri Oct 23 2020 - 02:36:20 PDT)
- Re: [AMBER] ff19SB and OPC, process_(min/md)out.perl and LEaP Gustaf Olsson (Fri Oct 23 2020 - 04:12:43 PDT)
- Re: [AMBER] ff19SB and OPC, process_(min/md)out.perl and LEaP Daniel Roe (Fri Oct 23 2020 - 04:28:37 PDT)
- Re: [AMBER] ff19SB and OPC, process_(min/md)out.perl and LEaP Daniel Roe (Fri Oct 23 2020 - 07:29:46 PDT)
- Re: [AMBER] ff19SB and OPC, process_(min/md)out.perl and LEaP Carlos Simmerling (Fri Oct 23 2020 - 07:34:22 PDT)
- Re: [AMBER] ff19SB and OPC, process_(min/md)out.perl and LEaP Gustaf Olsson (Fri Oct 23 2020 - 10:23:56 PDT)
- Re: [AMBER] ff19SB and OPC, process_(min/md)out.perl and LEaP Daniel Roe (Fri Oct 23 2020 - 10:19:28 PDT)
- Re: [AMBER] ff19SB and OPC, process_(min/md)out.perl and LEaP Gustaf Olsson (Fri Oct 23 2020 - 10:27:05 PDT)
- Re: [AMBER] ff19SB and OPC, process_(min/md)out.perl and LEaP Carlos Simmerling (Fri Oct 23 2020 - 05:27:34 PDT)
- Re: [AMBER] ff19SB and OPC, process_(min/md)out.perl and LEaP Carlos Simmerling (Fri Oct 23 2020 - 10:28:58 PDT)
- Re: [AMBER] ff19SB and OPC, process_(min/md)out.perl and LEaP Gustaf Olsson (Sat Oct 24 2020 - 12:49:30 PDT)
- Re: [AMBER] ff19SB and OPC, process_(min/md)out.perl and LEaP Carlos Simmerling (Sat Oct 24 2020 - 12:58:16 PDT)
- Re: [AMBER] ff19SB and OPC, process_(min/md)out.perl and LEaP Gustaf Olsson (Mon Oct 26 2020 - 00:46:07 PDT)
- Re: [AMBER] ff19SB and OPC, process_(min/md)out.perl and LEaP Gustaf Olsson (Mon Oct 26 2020 - 01:21:15 PDT)
- [AMBER] MMPBS decomposition error MYRIAN TORRES RICO (Wed Oct 21 2020 - 02:05:27 PDT)
- [AMBER] installing Amber18 and AmberTools20 Seibold, Steve Allan (Wed Oct 21 2020 - 10:40:43 PDT)
- [AMBER] drms comparison in sander during minimization? Kenneth Huang (Wed Oct 21 2020 - 15:03:40 PDT)
- Re: [AMBER] NVIDIA GeForce RTX 3090 GPUs Mike Mazanetz (Thu Oct 22 2020 - 05:11:35 PDT)
- [AMBER] correct md-input & prmtop for TI calculations Vaibhav Dixit (Thu Oct 22 2020 - 02:27:55 PDT)
- [AMBER] Is the amber website down? 9am EST Debarati DasGupta (Thu Oct 22 2020 - 06:13:12 PDT)
- [AMBER] server issues 403 on ambermd.org Mike Mazanetz (Thu Oct 22 2020 - 06:49:11 PDT)
- [AMBER] Cannot access amber website Lang,Lijun (Thu Oct 22 2020 - 08:13:11 PDT)
- [AMBER] error 403 Ayesha Fatima (Thu Oct 22 2020 - 10:57:21 PDT)
- [AMBER] Fwd: MMPBSA calculations with 1 explicit water molecule divyabharathi korlepara (Thu Oct 22 2020 - 11:01:31 PDT)
- [AMBER] Trouble installing pbsa cuda code Wesley Michael Botello-Smith (Thu Oct 22 2020 - 11:47:41 PDT)
- Re: [AMBER] MCPB with OPC water? Pengfei Li (Thu Oct 22 2020 - 13:59:34 PDT)
- Re: [AMBER] ddikick.x error during Fe3+ ion parameter derivation using Gamess Pengfei Li (Thu Oct 22 2020 - 14:14:09 PDT)
- Re: [AMBER] Prmtop for protein + 2 identical ligands has wrong dihedral parameters for the second ligand. LEaP bug? Pengfei Li (Thu Oct 22 2020 - 14:19:21 PDT)
- Re: [AMBER] Tri-coordination environment in zinc Pengfei Li (Thu Oct 22 2020 - 14:22:53 PDT)
- Re: [AMBER] How to deal with oxygen atom on Fe=O of Compound I (heme enzyme, P450) Pengfei Li (Thu Oct 22 2020 - 14:36:01 PDT)
- [AMBER] GaMD Neha Gandhi (Thu Oct 22 2020 - 15:30:03 PDT)
- [AMBER] doubt charges MYRIAN TORRES RICO (Fri Oct 23 2020 - 01:11:27 PDT)
- [AMBER] Is there a way to analyze contact maps of mixtures of more than 2 components? Naxhije Berisha (Fri Oct 23 2020 - 10:44:52 PDT)
- [AMBER] amber14 and amber16 are not working in new installation Marcelo Andrade Chagas (Fri Oct 23 2020 - 19:31:47 PDT)
- Re: [AMBER] [GaMD-discuss] GaMD Neha Gandhi (Sun Oct 25 2020 - 17:11:36 PDT)
- [AMBER] Steered MD at constant force Vishal Singh (Mon Oct 26 2020 - 05:15:01 PDT)
- [AMBER] mmpbsa error MYRIAN TORRES RICO (Mon Oct 26 2020 - 05:53:47 PDT)
- [AMBER] Amber20: Ampere microarchitecture support and next Amber release Kraus, Sebastian (Mon Oct 26 2020 - 12:18:42 PDT)
- [AMBER] AMBER 20 Benchmarks on NVIDIA RTX 3080/3090 and more Jason Hogrefe (Mon Oct 26 2020 - 15:26:13 PDT)
- [AMBER] System preparation for MMPBSA.py SATYAJIT KHATUA (Mon Oct 26 2020 - 21:29:12 PDT)
- [AMBER] TI calculation input clarification Delwakkada Liyanage, Senal Dinuka (Tue Oct 27 2020 - 10:00:51 PDT)
- [AMBER] pmemd with hybrid mpi/mp Bill Abbott (Tue Oct 27 2020 - 12:28:53 PDT)
- [AMBER] pmemd.cuda and CPU cores Abdul Basit (Tue Oct 27 2020 - 20:13:46 PDT)
- [AMBER] Amber20 and RNA simulations Piia Kokkonen (Wed Oct 28 2020 - 03:31:13 PDT)
- [AMBER] Help with parameterization of non-standard amino acid Amit Sharma (Asstt. Prof., MCARS) (Wed Oct 28 2020 - 05:43:59 PDT)
- [AMBER] Amber TI - crgmask Delwakkada Liyanage, Senal Dinuka (Wed Oct 28 2020 - 09:02:42 PDT)
- [AMBER] CO2 Michele Vanini (Wed Oct 28 2020 - 09:55:40 PDT)
- [AMBER] a metal bound Met Wu Xu (Wed Oct 28 2020 - 12:33:18 PDT)
- [AMBER] How to import (.pdb) files into xleap of AMBER generated by Cellulose builder Pinky Mazumder (Wed Oct 28 2020 - 22:47:59 PDT)
- [AMBER] cellulose crystal structure ( cellulose bundles) Pinky Mazumder (Thu Oct 29 2020 - 00:59:00 PDT)
- [AMBER] Xleap error Jisha B (Thu Oct 29 2020 - 02:17:22 PDT)
- [AMBER] Force field for IDP mohamed marzouk (Thu Oct 29 2020 - 08:31:29 PDT)
- [AMBER] Normalized eigen values DHEERAJ CHITARA (Thu Oct 29 2020 - 09:51:27 PDT)
- [AMBER] Amber20 installation for MPI, CUDA issues. Luka Bilić (Thu Oct 29 2020 - 12:38:15 PDT)
- [AMBER] MM/PBSA after minimization h_sahakyan.mb.sci.am (Thu Oct 29 2020 - 12:56:21 PDT)
- [AMBER] Constant Force SMD simulation Vishal Singh (Thu Oct 29 2020 - 21:05:24 PDT)
- [AMBER] how find Es from mdout to estimate vertical energy gap Vaibhav Dixit (Fri Oct 30 2020 - 10:05:07 PDT)
- [AMBER] NMR restraints Debarati DasGupta (Fri Oct 30 2020 - 12:37:48 PDT)
- [AMBER] Problem with acpype Michele Vanini (Sat Oct 31 2020 - 02:08:54 PDT)
- Last message date: Sat Oct 31 2020 - 09:30:02 PDT
- Archived on: Wed Nov 13 2024 - 05:55:59 PST
