Amber Archive Mar 2018 by thread
- Re: [AMBER] AMBER/ORCA for QM/MM minyuan.mail.ustc.edu.cn (Wed Feb 28 2018 - 19:23:16 PST)
- [AMBER] ABMD write error to MDOUT Hugo Macdermott-Opeskin (Wed Feb 28 2018 - 20:28:49 PST)
- [AMBER] Creating gaff-suitable PDB file for SO2 M Conte (Wed Feb 28 2018 - 22:24:30 PST)
- Re: [AMBER] Question about using cpptraj - Script Daniel Roe (Thu Mar 01 2018 - 03:30:53 PST)
- [AMBER] vlimit exceeded for step ASMITA SEN (Thu Mar 01 2018 - 05:31:26 PST)
- [AMBER] vlimit exceeded for step ASMITA SEN (Thu Mar 01 2018 - 05:32:53 PST)
- [AMBER] Question about Parmbsc1 Force Field Dan Gil (Thu Mar 01 2018 - 07:09:53 PST)
- Re: [AMBER] How to generate parameters for two MG 2+ ions ---GTP Rana Rehan Khalid (Thu Mar 01 2018 - 08:09:52 PST)
- [AMBER] After running MD, the number of atom in mdcrd file becomes 0 Gu, Wenze (Thu Mar 01 2018 - 11:16:09 PST)
- Re: [AMBER] After running MD, the number of atom in mdcrd file becomes 0 Carlos Simmerling (Thu Mar 01 2018 - 11:37:46 PST)
- Re: [AMBER] After running MD, the number of atom in mdcrd file becomes 0 Gu, Wenze (Thu Mar 01 2018 - 15:43:56 PST)
- Re: [AMBER] After running MD, the number of atom in mdcrd file becomes 0 Carlos Simmerling (Thu Mar 01 2018 - 16:02:16 PST)
- Re: [AMBER] After running MD, the number of atom in mdcrd file becomes 0 Carlos Simmerling (Thu Mar 01 2018 - 16:02:45 PST)
- Re: [AMBER] After running MD, the number of atom in mdcrd file becomes 0 Gu, Wenze (Thu Mar 01 2018 - 16:20:21 PST)
- Re: [AMBER] After running MD, the number of atom in mdcrd file becomes 0 Carlos Simmerling (Fri Mar 02 2018 - 14:51:06 PST)
- Re: [AMBER] After running MD, the number of atom in mdcrd file becomes 0 koushik kasavajhala (Fri Mar 02 2018 - 14:57:50 PST)
- Re: [AMBER] After running MD, the number of atom in mdcrd file becomes 0 Gu, Wenze (Sat Mar 03 2018 - 06:57:22 PST)
- Re: [AMBER] After running MD, the number of atom in mdcrd file becomes 0 David A Case (Sat Mar 03 2018 - 14:07:35 PST)
- Re: [AMBER] After running MD, the number of atom in mdcrd file becomes 0 Gu, Wenze (Sun Mar 04 2018 - 07:45:20 PST)
- Re: [AMBER] PB Bomb in pb_aaradi(): No radius assigned for atom 7 CB 3C Morrow,John Kenneth (Thu Mar 01 2018 - 14:15:24 PST)
- [AMBER] Turn of SMD after reaching target. David Sáez (Fri Mar 02 2018 - 08:19:40 PST)
- [AMBER] Replica Exchange Cut > 999.0 - Necessitates Very Large Water Box? Jason Ku Wang (Fri Mar 02 2018 - 14:42:31 PST)
- [AMBER] Using center of mass dihedral restraints using PMEMD Lenz, Stefan (Fri Mar 02 2018 - 15:34:42 PST)
- [AMBER] created a new atom named (is an error or we can ignore it) Rana Rehan Khalid (Sat Mar 03 2018 - 02:43:16 PST)
- [AMBER] Regarding PLP and Lys parameter Aashish Bhatt (Sat Mar 03 2018 - 03:35:05 PST)
- [AMBER] Created a new atom named: Rana Rehan Khalid (Sat Mar 03 2018 - 06:23:22 PST)
- [AMBER] How to Develop New Amber ForceField For Borons Barış Kurt (Sat Mar 03 2018 - 08:00:20 PST)
- [AMBER] mm_pbsa.pl error Wu Xu (Sat Mar 03 2018 - 08:08:26 PST)
- [AMBER] Penalty score Henrik Hariman (Sat Mar 03 2018 - 11:24:34 PST)
- [AMBER] reaidt.f problem Barış Kurt (Sat Mar 03 2018 - 14:50:40 PST)
- [AMBER] Energy Calculations in Amber minyuan.mail.ustc.edu.cn (Sun Mar 04 2018 - 06:10:54 PST)
- [AMBER] disulfide bridge -reg Jeyaram R A (Mon Mar 05 2018 - 01:46:14 PST)
- Re: [AMBER] Amber16/AmberTools17 CUDA version David A Case (Mon Mar 05 2018 - 05:17:28 PST)
- [AMBER] Additional Ph.D. and Post-doc positions in MD simulations of enzymes Jan Brezovsky (Mon Mar 05 2018 - 09:04:16 PST)
- [AMBER] Slab of water M Conte (Mon Mar 05 2018 - 15:28:18 PST)
- Re: [AMBER] Simulation does not restart from restart file written in previous step. Abhilash J (Tue Mar 06 2018 - 05:53:01 PST)
- [AMBER] vlimit exceed error sangita kachhap (Tue Mar 06 2018 - 07:47:16 PST)
- [AMBER] van der Waals interactions, electrostatic interactions and long-range corrections balaahme (Tue Mar 06 2018 - 12:37:42 PST)
- [AMBER] Force Fields and Water Models meryem m'hachi (Wed Mar 07 2018 - 02:08:07 PST)
- Re: [AMBER] amber16 sander can't read the box information from restart file David A Case (Wed Mar 07 2018 - 05:47:41 PST)
- [AMBER] Suitability of amber force fields for very low temperature MD simulations? Carolin Berner (Wed Mar 07 2018 - 06:28:43 PST)
- [AMBER] can't compile Ryan Richter (Wed Mar 07 2018 - 07:02:05 PST)
- [AMBER] QM/MM with Orca: selected input parameters not taken into account Ruth Helena Tichauer (Thu Mar 08 2018 - 01:54:35 PST)
- [AMBER] When will you update this tutorial? Barış Kurt (Thu Mar 08 2018 - 06:04:12 PST)
- [AMBER] constant pH simulations pemed.cuda Jacopo Sgrignani (Thu Mar 08 2018 - 07:45:53 PST)
- [AMBER] radial distribution function results Lizelle Lubbe (Thu Mar 08 2018 - 09:52:45 PST)
- [AMBER] FW: AMBER support and extra-point of charge (RESP) issue Jonathan David (Thu Mar 08 2018 - 23:33:53 PST)
- [AMBER] How to Convert gaussian force constant to Gaff? Barış Kurt (Fri Mar 09 2018 - 08:02:05 PST)
- [AMBER] Lennard Jones 12-6-4 with Multiple Ion Types Seitz, Anthony Joseph (Fri Mar 09 2018 - 11:28:19 PST)
- [AMBER] Help With tinker_to_amber Angelo Rossi (Sat Mar 10 2018 - 10:49:03 PST)
- [AMBER] Problem with cphstat Tasneem Kausar (Sun Mar 11 2018 - 22:29:49 PDT)
- [AMBER] error while installing AMBER for GPU malkeet singh Bahia (Mon Mar 12 2018 - 07:59:33 PDT)
- [AMBER] TI simulation with a solvateCap: vlimit exceeded for step Meiting Wang (Tue Mar 13 2018 - 08:31:38 PDT)
- [AMBER] Fwd: ACS COMP Boston awards deadline set Carlos Simmerling (Tue Mar 13 2018 - 12:00:21 PDT)
- [AMBER] NFE, PMD, and MULTI_RMSD questions Russell Davidson (Tue Mar 13 2018 - 16:26:53 PDT)
- [AMBER] restraintmask, error in reading namelist cntrl Nikolay N. Kuzmich (Wed Mar 14 2018 - 08:10:37 PDT)
- [AMBER] Reaction Coordinate that is the Difference of two Distances diego.soler.uam.es (Wed Mar 14 2018 - 08:24:01 PDT)
- [AMBER] Query regarding minimization Rakesh Srivastava (Thu Mar 15 2018 - 00:37:44 PDT)
- [AMBER] center of mass restraint in pmemd.cuda Rajarshi Roy (Thu Mar 15 2018 - 03:07:49 PDT)
- [AMBER] Count water in active site Lizelle Lubbe (Thu Mar 15 2018 - 06:22:57 PDT)
- [AMBER] Volume occupied during MD Lizelle Lubbe (Thu Mar 15 2018 - 06:31:28 PDT)
- [AMBER] Convertion between Gaussian and Gaff ANGULAR Force Constant Units micheal lop (Thu Mar 15 2018 - 09:43:15 PDT)
- [AMBER] Inconsistency with the number of counter ions required for neutralization maryam azimzadehirani (Mon Mar 19 2018 - 04:01:35 PDT)
- [AMBER] 3D-RISM solvation free energy of a molecule in an organic solvent (not water) Smith, Micholas D. (Mon Mar 19 2018 - 07:40:12 PDT)
- Re: [AMBER] Can I include Mg ions in receptor mask when using MMPBSA.py Pengfei Li (Mon Mar 19 2018 - 15:29:59 PDT)
- [AMBER] force-filed parametrization for dichloromethane daniele selli (Wed Mar 21 2018 - 02:27:08 PDT)
- [AMBER] Sudden termination of the heating simulation with sander.MPI Nikolay N. Kuzmich (Wed Mar 21 2018 - 05:24:44 PDT)
- [AMBER] upper limit of water with solvateBox Ikuo KURISAKI (Wed Mar 21 2018 - 06:06:28 PDT)
- [AMBER] Resume AMD simulation Rosellen, Martin (Wed Mar 21 2018 - 06:24:35 PDT)
- Re: [AMBER] FE atom in PARMCHK.DAT file David A Case (Wed Mar 21 2018 - 07:32:20 PDT)
- [AMBER] PMEMD error: "Increase lin__limit in nb_pairlist.F90!!!" Colin Brown (Wed Mar 21 2018 - 07:42:01 PDT)
- [AMBER] Temperature-Based Replica Exchange: Number of Replicas Jason Ku Wang (Wed Mar 21 2018 - 16:15:12 PDT)
- [AMBER] MM-GBSA for membrane protein jixiaofeng (Wed Mar 21 2018 - 18:59:02 PDT)
- [AMBER] Normal Mode Analysis in Amber Robert DeLisle (Wed Mar 21 2018 - 19:59:24 PDT)
- [AMBER] prep to mol2 conversion Rana Rehan Khalid (Thu Mar 22 2018 - 04:45:03 PDT)
- Re: [AMBER] pysmst code David A Case (Thu Mar 22 2018 - 05:21:00 PDT)
- [AMBER] Accelerated MD - Please advice maryam azimzadehirani (Thu Mar 22 2018 - 07:41:41 PDT)
- [AMBER] MCPB.py Thakur, Abhishek (Thu Mar 22 2018 - 12:12:54 PDT)
- [AMBER] generating solvated Fe2+ Thomas Pochapsky (Thu Mar 22 2018 - 12:48:53 PDT)
- [AMBER] pmemd.MPI with a single-entry group file? Kevin Keane (Thu Mar 22 2018 - 16:12:25 PDT)
- [AMBER] which geometry is used in am1bcc charge in antechamber in amber tools 17? Dai, Shuo (Thu Mar 22 2018 - 17:03:06 PDT)
- [AMBER] Problems with creating prmtop file from Charmm-GUI generated membrane system Chetna Tyagi (Fri Mar 23 2018 - 03:55:00 PDT)
- [AMBER] AMBER qualitatively compared to other packages Dmitry Suplatov (Fri Mar 23 2018 - 04:24:37 PDT)
- [AMBER] ERROR TUTORIAL AMBER - creating PDB files from the AMBER coordinate files Edjan Silva (Fri Mar 23 2018 - 10:16:30 PDT)
- [AMBER] Position of amino acid from surface roja rahmani (Sat Mar 24 2018 - 05:21:46 PDT)
- [AMBER] Normal Mode Analysis - output from nmode? Robert DeLisle (Sat Mar 24 2018 - 10:42:51 PDT)
- [AMBER] Calculating ligand contribution is failing- MMPBSA method varun dewaker (Sun Mar 25 2018 - 22:20:24 PDT)
- [AMBER] Calculate water density in the protein water channel by Amber 16 张玥 (Mon Mar 26 2018 - 06:20:26 PDT)
- [AMBER] Selection of interactions that persisted for over 75% of MD time Manivel Panneerselvam (Mon Mar 26 2018 - 22:39:30 PDT)
- [AMBER] Calculate water density in the protein water channel by Amber 16 张玥 (Mon Mar 26 2018 - 22:52:22 PDT)
- [AMBER] WESTPA workshop August 2-3, 2018 Lillian Chong (Tue Mar 27 2018 - 10:54:13 PDT)
- [AMBER] RMSD of individual sub unit of a protein complex. Jag Silwal (Tue Mar 27 2018 - 14:40:20 PDT)
- [AMBER] peptide and bilayer membrane simulations Chetna Tyagi (Wed Mar 28 2018 - 02:30:27 PDT)
- [AMBER] Random seed reproducibility Sergey Samsonov (Thu Mar 29 2018 - 01:32:04 PDT)
- [AMBER] MacOS pmemd.cuda Kadir Ozcan (Thu Mar 29 2018 - 12:21:22 PDT)
- [AMBER] cpptraj mask for hbond analysis Michael Yonkunas (Fri Mar 30 2018 - 09:09:27 PDT)
- [AMBER] CUDA (GPU): Implementation does not currently support the use of COM simulations.Require iat(1) >= 0. rabi1993.iitg.ernet.in (Fri Mar 30 2018 - 22:03:23 PDT)
- [AMBER] Query for force field parameters of 'R' and 'S' enantiomers rabi1993.iitg.ernet.in (Fri Mar 30 2018 - 22:05:17 PDT)
- [AMBER] Need advice with GPU choice. Setyanto Md (Sat Mar 31 2018 - 01:54:08 PDT)
- [AMBER] Help with mdcrd in VMD Vikram Dalal (Sat Mar 31 2018 - 10:16:49 PDT)
- Last message date: Sat Mar 31 2018 - 10:30:03 PDT
- Archived on: Mon Nov 25 2024 - 05:55:33 PST
