Amber Archive Apr 2021 by thread
- [AMBER] error while building non-GPU accelerated mpi version of amber Homeo Morphism (Thu Apr 01 2021 - 04:35:12 PDT)
- [AMBER] Questions about using the command "lie" Marko Sever (Thu Apr 01 2021 - 05:48:02 PDT)
- [AMBER] example files for the hcp option for GB David A Case (Thu Apr 01 2021 - 06:30:49 PDT)
- [AMBER] Great news! Adrian Roitberg (Thu Apr 01 2021 - 07:51:14 PDT)
- [AMBER] D-amino acid library gard nelson (Fri Apr 02 2021 - 11:14:50 PDT)
- [AMBER] Heat Output File Issue Swisher, Justin S (Fri Apr 02 2021 - 12:35:35 PDT)
- Re: [AMBER] MMPBSA per residue decomposition - Calculation speed Jatin Kashyap (Fri Apr 02 2021 - 13:23:43 PDT)
- [AMBER] Protein dimension Samanta M (Sat Apr 03 2021 - 05:42:45 PDT)
- Re: [AMBER] Distance tolerance for identifying common atoms in thermodynamics integration zz sheng (Mon Apr 05 2021 - 08:00:43 PDT)
- [AMBER] force field balance vs accuracy Brent Krueger (Mon Apr 05 2021 - 08:11:47 PDT)
- [AMBER] Discrepancy in experimental and MMPBSA pattern of binding energy Manisha (Tue Apr 06 2021 - 07:55:56 PDT)
- [AMBER] cleaning after installation Thomas Gaillard (Tue Apr 06 2021 - 08:23:44 PDT)
- Re: [AMBER] Discrepancy in experimental and MMPBSA pattern of Matthew Guberman-Pfeffer (Tue Apr 06 2021 - 12:06:43 PDT)
- [AMBER] Add molecule to prmtop/inpcrd ? Gustavo Seabra (Tue Apr 06 2021 - 14:26:19 PDT)
- [AMBER] Help for NETCDF Error :Input/Output error 余鸿艳 (Wed Apr 07 2021 - 04:51:19 PDT)
- [AMBER] parmchk vs. parmchk2 for metal-ligand parameterization SARAH JEANNE LEFAVE (Wed Apr 07 2021 - 08:00:11 PDT)
- [AMBER] Error using MCPB Maschietto, Federica (Wed Apr 07 2021 - 08:08:02 PDT)
- [AMBER] Per residue free energy decomposition is not working ABDUL BASIT (Wed Apr 07 2021 - 08:42:10 PDT)
- [AMBER] moving water away from a residue German P. Barletta (Wed Apr 07 2021 - 11:25:33 PDT)
- [AMBER] molecular-dynamics docking: when everything docks to the receptor's site, how do you deal with it? Homeo Morphism (Thu Apr 08 2021 - 00:34:56 PDT)
- [AMBER] Per residue free energy is not decomposed correctly Abdul Basit (Thu Apr 08 2021 - 10:03:52 PDT)
- Re: [AMBER] Thermodynamic integration for protein-protein interactions WW (Thu Apr 08 2021 - 15:32:04 PDT)
- [AMBER] Erro installing AMBER18 with RTX3070 and CUDA 10.2 and NVIDIA 460.67 driver Giorgos Lambrinidis (Fri Apr 09 2021 - 04:09:23 PDT)
- [AMBER] Error installing AMBER18 with RTX3070 and CUDA 10.2 and NVIDIA 460.67 driver Giorgos Lambrinidis (Fri Apr 09 2021 - 04:47:22 PDT)
- Re: [AMBER] Calculation halted on pmemd.cuda 库米尔 (Fri Apr 09 2021 - 09:44:04 PDT)
- Re: [AMBER] Apply Lennar-Jones potential between small molecules A R (Fri Apr 09 2021 - 09:46:14 PDT)
- [AMBER] cpptraj atom definition bug found during RMSD/distance calculation? Liao (Fri Apr 09 2021 - 13:39:38 PDT)
- [AMBER] Questions about amber-adding counterions 马芳芳 (Sat Apr 10 2021 - 18:54:21 PDT)
- [AMBER] chromophore file. David Gae (Sat Apr 10 2021 - 23:44:22 PDT)
- Re: [AMBER] Questions about amber-adding counterions (Carlos Simmerling) 马芳芳 (Sun Apr 11 2021 - 17:16:00 PDT)
- [AMBER] Obtaining 3D structures from Reweighted PMF plots of accelerated MD Sruthi Sudhakar (Mon Apr 12 2021 - 03:33:48 PDT)
- [AMBER] How to track oxygen molecules in MD Damiano Spadoni (Mon Apr 12 2021 - 09:51:01 PDT)
- Re: [AMBER] Questions about amber-adding counterions (Carlos Simmerling and David A Case) 马芳芳 (Mon Apr 12 2021 - 19:13:55 PDT)
- [AMBER] Problems when installing AMBER20 on CentOS 7: multiple definition of 'cifpin' 石谷沁 (Mon Apr 12 2021 - 20:48:20 PDT)
- [AMBER] 答复: Problems when installing AMBER20 on CentOS 7: multiple definition of 'cifpin' 石谷沁 (Mon Apr 12 2021 - 23:17:53 PDT)
- Re: [AMBER] help with cpptraj error (segmentation fault) Daniel Roe (Tue Apr 13 2021 - 06:09:09 PDT)
- [AMBER] SMD analysing question (Xiaodong) 吴晓东 (Tue Apr 13 2021 - 18:26:04 PDT)
- [AMBER] TI error on last window of calculations Rafał Madaj (Wed Apr 14 2021 - 01:35:43 PDT)
- [AMBER] Nonstandard Residue Fernandez, Joseph P. (Wed Apr 14 2021 - 06:45:21 PDT)
- [AMBER] .rst file not produced during production run Roberts, Amy L2 (Wed Apr 14 2021 - 09:51:07 PDT)
- [AMBER] Forcefield loading order and water parameters Reza Esmaeeli (Wed Apr 14 2021 - 10:24:26 PDT)
- [AMBER] "No module named pytraj" during make test step 石谷沁 (Wed Apr 14 2021 - 18:33:18 PDT)
- [AMBER] Cyclic Peptides: leap keeps adding missing atoms Tainah Dorina Marforio (Thu Apr 15 2021 - 03:34:07 PDT)
- [AMBER] Questions about Principle Component Analysis Li,Haoxi (Thu Apr 15 2021 - 11:56:50 PDT)
- [AMBER] About REMD extracting temperature trajectory Ojet (Thu Apr 15 2021 - 19:32:57 PDT)
- [AMBER] 答复: [ambermd.org代发]Re: "No module named pytraj" during make test step 石谷沁 (Thu Apr 15 2021 - 20:31:59 PDT)
- [AMBER] RMSIP waleed zalloum (Thu Apr 15 2021 - 21:01:28 PDT)
- [AMBER] tleap solvate box problems Gabriel Titchiner (Fri Apr 16 2021 - 01:02:22 PDT)
- Re: [AMBER] Antechamber and mol2 file with .<TRIPOS>UNITY_ATOM_ATTR Scott Brozell (Fri Apr 16 2021 - 19:03:52 PDT)
- [AMBER] halted quasi-harmonic MMPBSA calculation Vaibhav Dixit (Sat Apr 17 2021 - 08:35:44 PDT)
- [AMBER] Umbrella sampling on Amber 18 vs Amber 20 Ramin Mehrani (Sat Apr 17 2021 - 08:59:56 PDT)
- Re: [AMBER] AMBER Digest, Vol 3336, Issue 1 waleed zalloum (Sat Apr 17 2021 - 13:01:10 PDT)
- [AMBER] Amber Experts A. Bakheit (Sun Apr 18 2021 - 03:52:40 PDT)
- [AMBER] unusually high entropy values MMPBSA quasi-harmonic Vaibhav Dixit (Sun Apr 18 2021 - 10:20:59 PDT)
- [AMBER] Hack to install AmberTools20 on macOS Otto Sievert (Sun Apr 18 2021 - 18:45:36 PDT)
- [AMBER] Distance restraints not working jacob wick (Mon Apr 19 2021 - 02:10:44 PDT)
- [AMBER] 2.5 fs integration time step h_sahakyan.mb.sci.am (Mon Apr 19 2021 - 05:48:25 PDT)
- [AMBER] amber manual - non-bonded terms Jutta Rogal (Mon Apr 19 2021 - 08:34:47 PDT)
- [AMBER] Amber Tool Sangita Kachhap (Mon Apr 19 2021 - 09:54:59 PDT)
- [AMBER] 2.5 fs integration time step h_sahakyan.mb.sci.am (Mon Apr 19 2021 - 23:13:34 PDT)
- [AMBER] Will AmberTool21 support gcc10? Gustaf Olsson (Tue Apr 20 2021 - 02:03:36 PDT)
- [AMBER] protein sticking out of solvation box causing instability Neville Bethel (Tue Apr 20 2021 - 10:34:53 PDT)
- [AMBER] running sander.MPI :forrtl: severe (174): SIGSEGV, segmentation fault occurred 周丽萍 (Wed Apr 21 2021 - 01:32:23 PDT)
- [AMBER] Error when using 1DRISM to generate .xvv organic solvent files Daniel Fowles (Wed Apr 21 2021 - 01:33:29 PDT)
- [AMBER] Error in using ambpdb to convert rst to pdb Suchetana Gupta (Wed Apr 21 2021 - 07:41:23 PDT)
- [AMBER] PatchingError: .patches/AmberTools20_Unapplied_Patches/update.13 failed to apply. No changes made from this patch David Ricardo Figueroa Blanco (Wed Apr 21 2021 - 15:20:47 PDT)
- [AMBER] Max relative errors questions in parallel and cuda.serial test 石谷沁 (Wed Apr 21 2021 - 19:50:16 PDT)
- [AMBER] serial amber installation on wsl Ayesha Fatima (Thu Apr 22 2021 - 01:05:02 PDT)
- [AMBER] error installing parallel amber Ayesha Fatima (Thu Apr 22 2021 - 01:51:29 PDT)
- [AMBER] Problem with incomplete solvation with tleap Cato, Lee (Thu Apr 22 2021 - 07:43:46 PDT)
- [AMBER] parmchk2 Alesadi, Amirhadi (Thu Apr 22 2021 - 20:26:23 PDT)
- [AMBER] Make the two ligands independent in one simulation 李明玉 (Fri Apr 23 2021 - 07:18:35 PDT)
- [AMBER] mmgbsa issue Ayesha Fatima (Fri Apr 23 2021 - 08:45:12 PDT)
- [AMBER] mmgbsa error Ayesha Fatima (Fri Apr 23 2021 - 09:07:11 PDT)
- [AMBER] Forcefield File and Adding My Own Polymer Unit Swisher, Justin S (Fri Apr 23 2021 - 12:00:47 PDT)
- [AMBER] Questions about REMD extracting temperature trajectory Ojet (Fri Apr 23 2021 - 18:07:20 PDT)
- [AMBER] WARNING: INCONSISTENCIES EXIST WITHIN INTERNAL POTENTIAL TERMS. THE VALIDITY OF THESE RESULTS ARE HIGHLY QUESTIONABLE 周丽萍 (Fri Apr 23 2021 - 20:28:24 PDT)
- Re: [AMBER] [ambermd.org代发]Re: Max relative errors questions in parallel and cuda.serial test 石谷沁 (Sat Apr 24 2021 - 17:37:12 PDT)
- [AMBER] Regarding the forcefield parameters for cytochrome P450 heme group Patil Pranita Uttamrao (Sun Apr 25 2021 - 03:53:50 PDT)
- Re: [AMBER] [ambermd.org代发]Re: [ambermd.org代发]Re: Max relative errors questions in parallel and cuda.serial test 石谷沁 (Sun Apr 25 2021 - 17:37:13 PDT)
- [AMBER] TI free energy calculation issue after applying smoothstep in Amber20 zz sheng (Sun Apr 25 2021 - 20:32:38 PDT)
- [AMBER] AMBER installation on multiple computers Ravi Abrol (Mon Apr 26 2021 - 01:12:22 PDT)
- [AMBER] AMBER/EVB Dusanka Golo (Mon Apr 26 2021 - 06:10:41 PDT)
- [AMBER] MD Simulation of Ribosome including Protein & RNA Shirin Jamshidi (Mon Apr 26 2021 - 11:16:44 PDT)
- [AMBER] Covalent bonded inhibitors and mm-pb(gb)sa analys Hector A. Baldoni (Mon Apr 26 2021 - 12:58:23 PDT)
- [AMBER] Compile Amber20 with SGI/MPT 2.20 Gabriel Cretin (Tue Apr 27 2021 - 03:56:53 PDT)
- [AMBER] Citation for LEaP Robert Molt (Tue Apr 27 2021 - 16:52:43 PDT)
- [AMBER] 答复: [ambermd.org代发]Re: Max relative errors questions in parallel and cuda.serial test 石谷沁 (Tue Apr 27 2021 - 17:54:26 PDT)
- [AMBER] Gaussian derived RESP charges and antechamber Gustaf Olsson (Wed Apr 28 2021 - 03:30:13 PDT)
- [AMBER] Problems to install AmberTools20 Miguel Garavís (Wed Apr 28 2021 - 04:33:42 PDT)
- [AMBER] Heating stages ntx = 1 or ntx=5 Jenny 148 (Wed Apr 28 2021 - 06:23:26 PDT)
- [AMBER] CPPTRAJ configuration is failing Markus Metz (Wed Apr 28 2021 - 12:04:56 PDT)
- [AMBER] Trouble Creating a pdb File Khong, Megan (Wed Apr 28 2021 - 14:14:36 PDT)
- [AMBER] Questions about REMD extracting temperature trajectory Ojet (Wed Apr 28 2021 - 23:26:12 PDT)
- [AMBER] Adventures installing AMBER 20 in Centos 7 Azurmendi, Hugo (Thu Apr 29 2021 - 08:59:40 PDT)
- [AMBER] cpptraj energy using 2 masks German P. Barletta (Thu Apr 29 2021 - 11:01:07 PDT)
- [AMBER] FW: AMBER Digest, Vol 3348, Issue 1 Markus Metz (Thu Apr 29 2021 - 12:09:23 PDT)
- [AMBER] trpcage benchmark: reduce 32x or dimerize ? Scott Brozell (Thu Apr 29 2021 - 18:26:12 PDT)
- [AMBER] Release of AmberTools21 David A Case (Thu Apr 29 2021 - 18:29:34 PDT)
- [AMBER] Troubleshooting long idle times in pmemd.MPI Kevin Keane (Thu Apr 29 2021 - 20:39:00 PDT)
- [AMBER] About cpptraj (v18) extracting temperature trajectory from REMD trajectory Ojet (Thu Apr 29 2021 - 21:02:49 PDT)
- Re: [AMBER] polarizable FF in amber18 or 20 Vaibhav Dixit (Thu Apr 29 2021 - 21:03:38 PDT)
- [AMBER] installation of AmberTools 21 Qinghua Liao (Fri Apr 30 2021 - 07:54:17 PDT)
- Last message date: Fri Apr 30 2021 - 14:00:02 PDT
- Archived on: Wed Dec 25 2024 - 05:56:06 PST
