Amber Archive May 2020 by thread
- [AMBER] SHAKE ALgorithm and frcmod file Elif Çiğdem Calvin (Thu Apr 30 2020 - 14:14:10 PDT)
- Re: [AMBER] TI simulations Song, Lin (Thu Apr 30 2020 - 17:18:02 PDT)
- [AMBER] timestep dt for higher temperatures Liao (Fri May 01 2020 - 00:41:54 PDT)
- Re: [AMBER] wrong geometry amide nitrogen Arnaud Bondon (Fri May 01 2020 - 03:54:42 PDT)
- [AMBER] QM/MM with finite temperature string Pratul Agarwal (Fri May 01 2020 - 11:17:57 PDT)
- [AMBER] Leaprc error janardhanan c (Sat May 02 2020 - 03:11:07 PDT)
- [AMBER] Simulation stops during NPT Sunita Patel (Sat May 02 2020 - 03:18:09 PDT)
- [AMBER] NPT 2 ns of equilibration Debarati DasGupta (Sat May 02 2020 - 11:27:21 PDT)
- [AMBER] Free energy calculation and system crash Sadaf Rani (Sat May 02 2020 - 15:54:14 PDT)
- [AMBER] CPPTRAJ: distance between atoms emanuele falbo (Mon May 04 2020 - 03:55:27 PDT)
- [AMBER] Release of Amber20 and AmberTools20 David A Case (Mon May 04 2020 - 05:34:13 PDT)
- [AMBER] Abasic Site and Errant OH Group on Sugar Robert Molt (Mon May 04 2020 - 05:40:40 PDT)
- [AMBER] Mass-weighted RMSD one-liner with cpptraj - possible? Martin Mielke (Mon May 04 2020 - 06:23:09 PDT)
- [AMBER] creating parameters for a thioglycoside rosaester.forgione.unina.it (Mon May 04 2020 - 09:59:39 PDT)
- [AMBER] cpptraj PCA PC-mode pseudo traj Schröder, David Christopher (Mon May 04 2020 - 13:19:23 PDT)
- [AMBER] AmberTools20 comilation on macOS Gustaf Olsson (Tue May 05 2020 - 01:07:11 PDT)
- [AMBER] The lipid section in the 2020 manual require updating Zhiyi Wu (Tue May 05 2020 - 03:38:05 PDT)
- [AMBER] C4 parameters for Au0 from INTERFACE FF sbojarowski.chem.uw.edu.pl (Tue May 05 2020 - 05:58:34 PDT)
- [AMBER] CO atom type missing in PARMCHK.DAT Casalini Tommaso (Tue May 05 2020 - 11:53:42 PDT)
- [AMBER] FRCMOD FILE DATABASE Jenny 148 (Tue May 05 2020 - 22:33:20 PDT)
- [AMBER] MM-PBSA calculation error Serena Vittorio (Wed May 06 2020 - 02:01:38 PDT)
- [AMBER] Flags to Turn off Charges in pmemd Sharif Nada (Wed May 06 2020 - 03:44:24 PDT)
- [AMBER] MMGBSA-DECOM calculation Renato Araujo (Wed May 06 2020 - 04:17:46 PDT)
- [AMBER] Amber20 sander speed difference between cmake and old configure method Charo del Genio (Wed May 06 2020 - 05:07:51 PDT)
- [AMBER] can i analysis number of water molecules in protein by watershell 石娜 (Wed May 06 2020 - 06:21:50 PDT)
- [AMBER] Amber20 sander speed difference between cmake and old configure method (addendum) Charo del Genio (Wed May 06 2020 - 06:35:18 PDT)
- [AMBER] addions Jisha B (Wed May 06 2020 - 08:55:28 PDT)
- [AMBER] RMSD discontinuity between NPT and NVT with restraints Thomas Gaillard (Wed May 06 2020 - 08:57:00 PDT)
- [AMBER] about charmmgen Francesco Pietra (Wed May 06 2020 - 09:28:01 PDT)
- [AMBER] Minimum recommended hardware specs for AmberTools20 and Amber20 Adrianne Lee (Wed May 06 2020 - 14:57:49 PDT)
- [AMBER] How to merge GLYCAM06 and lipid17 to generate force field for simple g; ycolipids? Vijay Achari (Thu May 07 2020 - 01:30:37 PDT)
- [AMBER] Thermodynamic integration by parameter interpolation (PI-TI) Veenis, Andrew Jay (Thu May 07 2020 - 07:01:05 PDT)
- [AMBER] MD and MD-tar restrictions MYRIAN TORRES RICO (Fri May 08 2020 - 03:53:54 PDT)
- [AMBER] OHE residue and crashing Piia Kokkonen (Fri May 08 2020 - 06:49:50 PDT)
- [AMBER] Xmin minimisation Athena N (Fri May 08 2020 - 10:18:41 PDT)
- [AMBER] how to compute the protein interaction surface with the ligand Thomas Evangelidis (Fri May 08 2020 - 15:57:39 PDT)
- [AMBER] Temperature and total energy keeps dropping with NVE ensemble Liao (Fri May 08 2020 - 21:38:15 PDT)
- [AMBER] GPU based TI runs Debarati DasGupta (Sat May 09 2020 - 04:56:04 PDT)
- [AMBER] the error from make test.serial 谢信锐 (Sun May 10 2020 - 05:28:34 PDT)
- [AMBER] Neutralizing a system Jenny 148 (Sun May 10 2020 - 05:56:45 PDT)
- Re: [AMBER] tlea Lachele Foley (Sun May 10 2020 - 11:14:40 PDT)
- [AMBER] Ewald grid size question Yuliana Bosken (Sun May 10 2020 - 16:10:01 PDT)
- [AMBER] error MMPBSA MYRIAN TORRES RICO (Mon May 11 2020 - 03:12:38 PDT)
- [AMBER] MMPBSA - Ternary System = protein-ligand-1-ligand-2 Marcelo Andrade Chagas (Mon May 11 2020 - 04:17:38 PDT)
- [AMBER] 2 aminpurine parameter from Bryce reference? Kenneth Huang (Mon May 11 2020 - 13:15:55 PDT)
- [AMBER] 2 aminpurine parameter from Bryce reference? Kenneth Huang (Mon May 11 2020 - 13:31:37 PDT)
- [AMBER] How to perameterize peptide like compound Rana Rehan Khalid (Tue May 12 2020 - 05:38:00 PDT)
- [AMBER] help MYRIAN TORRES RICO (Tue May 12 2020 - 09:21:29 PDT)
- [AMBER] Topology and parameters for the T4 - Thyroxine Marcelo Andrade Chagas (Tue May 12 2020 - 15:08:35 PDT)
- [AMBER] Open a hole into an equilibrated lipid bilayer Eduardo R. Almeida (Tue May 12 2020 - 19:44:54 PDT)
- [AMBER] pmemd simulation Sofia Vasilakaki (Tue May 12 2020 - 23:01:28 PDT)
- [AMBER] autoimage waters Hector A. Baldoni (Wed May 13 2020 - 12:46:38 PDT)
- [AMBER] About having an auto-restart keyword for the amber/orca interface. Zhiyi Wu (Wed May 13 2020 - 14:41:11 PDT)
- [AMBER] installation problem Arthur Glasfeld (Wed May 13 2020 - 16:05:06 PDT)
- [AMBER] Steered MD with COM_ANGLE Amanda Buyan (Wed May 13 2020 - 16:32:22 PDT)
- [AMBER] AMBER 18 GPU Renato Araujo (Thu May 14 2020 - 09:53:40 PDT)
- [AMBER] differences in EGB energies sander vs. pmemd Niransha Kumarachchi (Thu May 14 2020 - 16:20:28 PDT)
- [AMBER] Fwd: Fw: Amber18 - MPI version error on HPC Cluster Sivanandam Magudeeswaran (Thu May 14 2020 - 21:04:53 PDT)
- [AMBER] Questions about PCA Kat G (Thu May 14 2020 - 21:27:24 PDT)
- [AMBER] Query regarding calculating RMSF. DHEERAJ CHITARA (Thu May 14 2020 - 23:51:19 PDT)
- [AMBER] Installation error Hrishikesh Dhondge (Fri May 15 2020 - 03:09:44 PDT)
- [AMBER] updating to ambertools 20 from version 19 Homeo Morphism (Fri May 15 2020 - 03:57:48 PDT)
- [AMBER] Installation Error while linking C executable xaLeap Hrishikesh Dhondge (Fri May 15 2020 - 06:33:14 PDT)
- [AMBER] Similar RESP1 and RESP2 fitting outputs Kodituwakku,Dimuthu Nirmani (Fri May 15 2020 - 07:16:21 PDT)
- [AMBER] Mol2 to generatee prepc and frcmod fo using Antechamer Lod King (Fri May 15 2020 - 08:36:08 PDT)
- Re: [AMBER] cellulose chain Pinky Mazumder (Fri May 15 2020 - 10:00:57 PDT)
- [AMBER] Query regarding force fields SHAUNAK BADANI (Fri May 15 2020 - 11:10:15 PDT)
- [AMBER] upgrade to 19 Scott Brozell (Fri May 15 2020 - 15:01:29 PDT)
- [AMBER] Amber20 MPIC location problem Filip Fratev (Fri May 15 2020 - 20:54:11 PDT)
- [AMBER] Could not find control namelist error Jisha B (Sat May 16 2020 - 04:31:11 PDT)
- [AMBER] Absolute free energy calculation-GitHub Sadaf Rani (Sat May 16 2020 - 17:03:00 PDT)
- [AMBER] Amber20 pmemd.cuda installation and performance problems Filip Fratev (Sun May 17 2020 - 01:43:26 PDT)
- [AMBER] Galactosylation of 5-Hydroxylysine Harald Lanig (Thu May 14 2020 - 09:05:08 PDT)
- [AMBER] parameter for modified residue sangita kachhap (Mon May 18 2020 - 09:32:01 PDT)
- [AMBER] COM position mohamed marzouk (Tue May 19 2020 - 02:41:30 PDT)
- [AMBER] How to use set pert=true Dawid das (Wed May 20 2020 - 09:32:27 PDT)
- [AMBER] AMBER Tools 20: Bug in libraries of modified amino acids prevents force field load Matias Machado (Wed May 20 2020 - 10:13:34 PDT)
- [AMBER] MMPBSA - per residue decomposition Prasanth G, Research Scholar (Thu May 21 2020 - 01:09:47 PDT)
- [AMBER] paramfit - negative energy for 1 of the 2 term Erdem Yeler (Thu May 21 2020 - 05:26:07 PDT)
- [AMBER] Amber20 serial make test FAILUREs on IBM Power9 Cong Liu (Thu May 21 2020 - 07:03:12 PDT)
- [AMBER] TI production runs(20ns) NVT query Debarati DasGupta (Thu May 21 2020 - 07:05:42 PDT)
- [AMBER] QM/MM MD: Error reading box emanuele falbo (Thu May 21 2020 - 07:42:33 PDT)
- [AMBER] Free energy of solvation using polarizable force fields Carl Heroneme (Thu May 21 2020 - 14:11:06 PDT)
- [AMBER] Different LJ parameters in .dat file and 'atominfo' output José Daniel Martinez (Sat May 23 2020 - 05:17:50 PDT)
- [AMBER] Changing hydrogen atom radius to optimize saltbridge in GB-OBC model Sunita Patel (Sat May 23 2020 - 07:01:04 PDT)
- [AMBER] Amber18 with AmberTools20 test.serial FAILURES and ERRORS Samanta M (Sat May 23 2020 - 07:02:03 PDT)
- [AMBER] Help with Acpype on AMberTools19 Prapasiri Pongprayoon (Sun May 24 2020 - 23:02:50 PDT)
- [AMBER] Help with Acpype in AmberTools19 Prapasiri Pongprayoon (Sun May 24 2020 - 23:07:32 PDT)
- [AMBER] Questions about QM Ignjat Filipović (Mon May 25 2020 - 07:23:45 PDT)
- [AMBER] clustering parameter files Ranim Maaieh (Mon May 25 2020 - 07:36:39 PDT)
- [AMBER] What would you like to see in visualization of chemical data? Jan Mičan (Tue May 26 2020 - 09:59:39 PDT)
- [AMBER] installation failed libsanderles.dir amd plumed Andrew Waight (Tue May 26 2020 - 21:07:59 PDT)
- [AMBER] Missing bond parameters after MCPB.py Oleksandr Kravchenko (Wed May 27 2020 - 03:29:31 PDT)
- [AMBER] Tool to calculate CSP and NOE for DNA trajectory? Kenneth Huang (Wed May 27 2020 - 16:47:41 PDT)
- [AMBER] Installing latest ambertools (2020) with conda Alan (Thu May 28 2020 - 02:41:50 PDT)
- [AMBER] Small molecules paramters Athena N (Thu May 28 2020 - 05:47:24 PDT)
- [AMBER] Amber99SB force field Seketoulie Keretsu (Thu May 28 2020 - 05:51:12 PDT)
- [AMBER] AMBER 16 NFE MULTI_RMSD Question on the Output of reaction variable Xiaoyong Zhang (Thu May 28 2020 - 08:39:38 PDT)
- [AMBER] Simulating pyridine in water TIP3P Debarati DasGupta (Thu May 28 2020 - 09:22:57 PDT)
- Re: [AMBER] adding hydrogen to pdbqt ligand files Eduardo Mayo (Thu May 28 2020 - 23:25:00 PDT)
- [AMBER] Amber20 Performance on RTX (Turing): known problems, with a patch forthcoming David Cerutti (Thu May 28 2020 - 23:30:20 PDT)
- [AMBER] questions for mdgx-virtual site Gao J (Fri May 29 2020 - 01:29:44 PDT)
- [AMBER] igb for non-aqueous solvent? Timothy Schutt (Fri May 29 2020 - 06:40:59 PDT)
- [AMBER] how to identify lipids around a protein Sally Pias (Fri May 29 2020 - 17:53:48 PDT)
- Re: [AMBER] Amber for help 马海川 (Sat May 30 2020 - 06:04:02 PDT)
- Re: [AMBER] AMBER Digest, Vol 3017, Issue 1 Gao J (Sat May 30 2020 - 19:18:36 PDT)
- [AMBER] amber20 output header Baker, Joseph (Sat May 30 2020 - 19:18:49 PDT)
- Re: [AMBER] Using pytraj with jupyter notebook Rangarajan, Amith (Sun May 31 2020 - 12:44:17 PDT)
- Last message date: Sun May 31 2020 - 17:00:02 PDT
- Archived on: Wed Dec 25 2024 - 05:55:58 PST
