Amber Archive Jan 2017 by thread
- [AMBER] failed to visualize trajectories in vmd. Saman Yousuf ali (Mon Jan 02 2017 - 02:02:25 PST)
- [AMBER] partial replica exchange molecular dynamics Johannes Loeffler (Mon Jan 02 2017 - 06:09:30 PST)
- Re: [AMBER] Problem in not defining the hybridization of a atomtype A kS (Mon Jan 02 2017 - 08:33:24 PST)
- [AMBER] how to use depreciated cpptraj code Chris Neale (Mon Jan 02 2017 - 11:21:24 PST)
- [AMBER] Error in reordering pH-REMD trajectories Elisa Pieri (Mon Jan 02 2017 - 12:31:16 PST)
- Re: [AMBER] cpptraj LIE on a ghost-atom Elisa Pieri (Tue Jan 03 2017 - 03:36:25 PST)
- Re: [AMBER] Remove motion of center of mass after obtaining trajectory Daniel Roe (Tue Jan 03 2017 - 06:06:17 PST)
- [AMBER] Amber16 on K80 GPUs --poor performance on multiple GPUs Susan Chacko (Tue Jan 03 2017 - 08:00:09 PST)
- Re: [AMBER] Water density near the protein suspiciously low I Lőrincz (Tue Jan 03 2017 - 15:46:04 PST)
- [AMBER] Question about Empirical Valence Bond(EVB) simulation 没关系 (Tue Jan 03 2017 - 18:21:21 PST)
- [AMBER] Zinc +2 SMD pulling Fabian gmail (Wed Jan 04 2017 - 01:33:29 PST)
- [AMBER] tLeap adding non-library hydrogens David Poole (Wed Jan 04 2017 - 02:07:31 PST)
- [AMBER] tLeap and acetonitrile/chloroform solvation Luka Bilić (Wed Jan 04 2017 - 06:12:51 PST)
- [AMBER] mmCIF from amber Thomas Pochapsky (Wed Jan 04 2017 - 06:34:22 PST)
- [AMBER] Problems about membrane protein simulation Shanghaitech University WuMeng (Wed Jan 04 2017 - 06:44:22 PST)
- [AMBER] compatibility issues erik rp zuiderweg (Wed Jan 04 2017 - 09:54:18 PST)
- [AMBER] antechamber: why the net charge does not sum up to zero? Azade Yazdan Yar (Thu Jan 05 2017 - 02:52:34 PST)
- [AMBER] cpptraj clustering doubt Mary Varughese (Thu Jan 05 2017 - 02:59:52 PST)
- [AMBER] 'Diffusion' calculation in Ptraj - could not understand a description of Ptraj code in Amber14 wei (Thu Jan 05 2017 - 04:39:40 PST)
- [AMBER] VMD/netcdf Adrian Roitberg (Thu Jan 05 2017 - 07:09:50 PST)
- [AMBER] cpptraj PCA of crystal structure anu chandra (Thu Jan 05 2017 - 08:25:48 PST)
- [AMBER] /dev/hfi1_0 device failed to appear after 15 seconds: Connection timed out jacky zhao (Thu Jan 05 2017 - 08:34:46 PST)
- [AMBER] Ion Parameters for tip4pfb Samaneh Ghassabi Kondalaji (Thu Jan 05 2017 - 09:44:25 PST)
- [AMBER] Amber16 benchmark suite error jacky zhao (Thu Jan 05 2017 - 22:51:31 PST)
- [AMBER] xmin and QM/MM Åsmund Kjendseth Røhr (Fri Jan 06 2017 - 01:19:33 PST)
- Re: [AMBER] Force field modifications Jonathan Huihui (Fri Jan 06 2017 - 13:09:26 PST)
- [AMBER] 回复：AMBER Digest, Vol 1806, Issue 1 wei (Fri Jan 06 2017 - 21:42:38 PST)
- [AMBER] Simple normal mode analysis in amber Ella Gale (Sat Jan 07 2017 - 09:15:45 PST)
- [AMBER] autoimage colvin (Mon Jan 09 2017 - 00:10:57 PST)
- [AMBER] 2nd eChemInfo Training and Innovation Course in Drug Design 2017 in Milano Thomas Exner (Mon Jan 09 2017 - 01:17:00 PST)
- [AMBER] Split trajectory by atom The Cromicus Productions (Mon Jan 09 2017 - 02:22:41 PST)
- Re: [AMBER] Fw: Problems with imaging Daniel Roe (Mon Jan 09 2017 - 06:25:41 PST)
- [AMBER] Python Programs Chase Zagorec-Marks (Mon Jan 09 2017 - 12:53:28 PST)
- [AMBER] Error in leaprc.ff14SB (Amber14) Subashini .K (Mon Jan 09 2017 - 21:29:03 PST)
- [AMBER] ACPYPE ERROR Subashini .K (Tue Jan 10 2017 - 00:28:51 PST)
- [AMBER] restrain protein with two different force constant Khabiri, Morteza (Tue Jan 10 2017 - 06:58:47 PST)
- [AMBER] QMMM with MOPAC2016 Carlos SOTO GARZA (Tue Jan 10 2017 - 15:06:10 PST)
- [AMBER] verification of ligand rmsd script. Saman Yousuf ali (Wed Jan 11 2017 - 03:11:53 PST)
- [AMBER] All working now, except some trajectories erik rp zuiderweg (Wed Jan 11 2017 - 07:48:22 PST)
- [AMBER] /tmp/sh24281: Permission denied. Thakur, Abhishek (Wed Jan 11 2017 - 07:48:18 PST)
- [AMBER] minimum distance between two sets of atoms anu chandra (Wed Jan 11 2017 - 08:55:03 PST)
- [AMBER] Sander input into Gaussian Aseel Bala (Wed Jan 11 2017 - 13:55:58 PST)
- [AMBER] New user needs help imam siswanto (Wed Jan 11 2017 - 20:23:26 PST)
- [AMBER] TLEAP error Subashini .K (Thu Jan 12 2017 - 00:15:54 PST)
- [AMBER] RDF between centers of mass/geometry Lorenzo Gontrani (Thu Jan 12 2017 - 02:36:43 PST)
- [AMBER] Issues for updating AmberTools 16 - update.14 Kihoon.Yoon.dell.com (Thu Jan 12 2017 - 09:03:59 PST)
- [AMBER] csh to bash Thakur, Abhishek (Thu Jan 12 2017 - 09:11:12 PST)
- [AMBER] LJ parameters in frcmod files Jacob Monroe (Thu Jan 12 2017 - 10:34:37 PST)
- [AMBER] MD for covalent inhibitors Ren Jinhong (Thu Jan 12 2017 - 14:23:58 PST)
- [AMBER] Radius of gyration for the hydrophobic core Aishani Prem (Thu Jan 12 2017 - 15:51:38 PST)
- [AMBER] potential energy Albert (Fri Jan 13 2017 - 00:42:08 PST)
- Re: [AMBER] How to have a certain number of water molecules? Azade Yazdan Yar (Fri Jan 13 2017 - 02:57:49 PST)
- [AMBER] amber14 parallel build problems Ada Sedova (Fri Jan 13 2017 - 09:52:40 PST)
- [AMBER] Handling modified residues asdda asa (Sat Jan 14 2017 - 01:12:46 PST)
- [AMBER] Single-Point MM-PBSA/GBSA Energy Calculations Naiem Issa (Sat Jan 14 2017 - 08:20:10 PST)
- [AMBER] Continue running an incomplete MD with NMR restraints Kat G (Sat Jan 14 2017 - 22:43:04 PST)
- [AMBER] CpHREMD (explicit solvent) parameter settings inquiry Andrew Schaub (Sun Jan 15 2017 - 01:39:41 PST)
- [AMBER] alpha helical content as reaction coordinate Bin Sun (Sun Jan 15 2017 - 09:28:15 PST)
- [AMBER] intermolecular hydrogen bonding. Saman Yousuf ali (Mon Jan 16 2017 - 02:50:55 PST)
- [AMBER] lipid membrane tleap problem amber16 Sofia Vasilakaki (Mon Jan 16 2017 - 12:32:21 PST)
- [AMBER] ambmask issue Aseel Bala (Mon Jan 16 2017 - 13:50:20 PST)
- [AMBER] Modified residue separated in leap module asdda asa (Mon Jan 16 2017 - 17:16:10 PST)
- [AMBER] Fwd: [AMBER-Developers] non-neutral ethane from antechamber FyD (Mon Jan 16 2017 - 21:40:17 PST)
- [AMBER] pmemd.cuda.MPI not running well with SGE Wang, Yin (Tue Jan 17 2017 - 03:22:54 PST)
- [AMBER] TIP4P-Ew vs TIP3 vs TIP5 DmitryASuplatov (Tue Jan 17 2017 - 07:21:30 PST)
- [AMBER] matching times from .out with frames from .mdcrd Chris Neale (Tue Jan 17 2017 - 10:00:30 PST)
- [AMBER] ACPYPE now works with GAFF2 Alan (Tue Jan 17 2017 - 10:42:26 PST)
- [AMBER] Reference for GAFF2? Alan (Tue Jan 17 2017 - 14:36:34 PST)
- [AMBER] rmsf value for 2 chains Hirdesh Kumar (Tue Jan 17 2017 - 15:08:59 PST)
- [AMBER] amber16 Centos 7 Coleman, Marcus [JRDUS Non-J&J] (Tue Jan 17 2017 - 15:50:54 PST)
- [AMBER] antechamber syntax error Aseel Bala Ahmed (Tue Jan 17 2017 - 17:38:03 PST)
- [AMBER] Model Folding Wong Li Zhe (Tue Jan 17 2017 - 18:49:02 PST)
- [AMBER] Installing Amber Karla Galdamez (Tue Jan 17 2017 - 22:24:50 PST)
- [AMBER] Kmeans-clustering : AvgDist query Bala subramanian (Wed Jan 18 2017 - 02:51:04 PST)
- [AMBER] Error while creation topology and coordinate files in tleap Manjula Saravanan (Wed Jan 18 2017 - 02:53:24 PST)
- [AMBER] REMD_suggestion Thakur, Abhishek (Wed Jan 18 2017 - 07:03:26 PST)
- [AMBER] Center atoms (translate & rotate reference) abdennour braka (Wed Jan 18 2017 - 08:40:07 PST)
- [AMBER] Fwd: some clues about yacc errors on OLCF rhea Ada Sedova (Wed Jan 18 2017 - 10:19:24 PST)
- [AMBER] Fwd: amber14 parallel build problems Ada Sedova (Wed Jan 18 2017 - 11:44:38 PST)
- [AMBER] constrain nitrate as bound and neutral Liyang Zhu (Wed Jan 18 2017 - 12:22:03 PST)
- [AMBER] About constraints on QM system of QM/MM simulation Pengfei Li (Wed Jan 18 2017 - 14:04:07 PST)
- [AMBER] REGARDING ACPYPE GENERATED TOPOLOGY FILE Subashini .K (Wed Jan 18 2017 - 21:24:05 PST)
- [AMBER] Regarding trajectory analysis Debodyuti Dutta (Wed Jan 18 2017 - 21:24:48 PST)
- [AMBER] cpptraj: list command throws seqfault Thomas Fox (Thu Jan 19 2017 - 04:58:36 PST)
- [AMBER] valiine chirality inversion Thomas Pochapsky (Thu Jan 19 2017 - 05:52:10 PST)
- [AMBER] REMD_Multiple_GPU Thakur, Abhishek (Thu Jan 19 2017 - 08:29:57 PST)
- [AMBER] Amber tutorial of APR(attach-pull-release) approach Jian Yin (Thu Jan 19 2017 - 10:58:52 PST)
- [AMBER] Distance between the center of gravities of tow molecules-CPPTRAJ konda003 . (Thu Jan 19 2017 - 11:01:06 PST)
- [AMBER] setup_equilibrate_input.x Thakur, Abhishek (Thu Jan 19 2017 - 11:40:09 PST)
- [AMBER] cpptraj: segfault after list command Thomas Fox (Fri Jan 20 2017 - 05:07:53 PST)
- [AMBER] adqmmm with PM6 for copper complex M_Chikira (Fri Jan 20 2017 - 05:13:46 PST)
- [AMBER] Interpreting energy decomposition in Amber thermodynamic integration Stefan Ivanov (Fri Jan 20 2017 - 07:28:00 PST)
- [AMBER] Ntt value for Nose-hoover chain thermostat Samaneh Ghassabi Kondalaji (Fri Jan 20 2017 - 12:46:39 PST)
- [AMBER] Pure POPC Membrane Tilts during MD simulation Rodriguez, Yoel (Sat Jan 21 2017 - 16:21:52 PST)
- [AMBER] [david.case.rutgers.edu: Re: Modified residue separated in leap module] David Case (Mon Jan 23 2017 - 04:52:52 PST)
- [AMBER] INCREASING BOX SIZE Subashini .K (Mon Jan 23 2017 - 08:05:51 PST)
- [AMBER] REMD_suggestion Thakur, Abhishek (Mon Jan 23 2017 - 08:46:51 PST)
- [AMBER] From PMF to free energy of binding Andreas Tosstorff (Mon Jan 23 2017 - 09:03:17 PST)
- [AMBER] In REMD there is two irest=0 in amber tut Thakur, Abhishek (Mon Jan 23 2017 - 09:18:38 PST)
- [AMBER] Simulating lipid bilayer below phase transition temperature Casalini Tommaso (Mon Jan 23 2017 - 14:12:24 PST)
- [AMBER] Error opening unit 15: File "remd.groupfile" is missing or unreadable Thakur, Abhishek (Mon Jan 23 2017 - 14:25:19 PST)
- [AMBER] Molecular Modelling Workshop: March 27-29, 2017 in Erlangen, Germany Dr. Anselm Horn (Tue Jan 24 2017 - 00:20:22 PST)
- [AMBER] Regarding forcefields for Z-DNA Yogeeshwar Ajjugal (Tue Jan 24 2017 - 01:53:24 PST)
- [AMBER] error in finding vdW (or other) parameters for type Fatemeh Fatemi (Tue Jan 24 2017 - 03:42:54 PST)
- [AMBER] paramfit stephanie.essafi.ens.fr (Tue Jan 24 2017 - 05:23:03 PST)
- [AMBER] QM method used for force constants derivation in GAFF2 ? Marek Maly (Tue Jan 24 2017 - 09:47:19 PST)
- [AMBER] REMD_just_1.10ns/day Thakur, Abhishek (Tue Jan 24 2017 - 10:53:26 PST)
- [AMBER] Reproduce tetraalanine Phi and Psi amplitudes ff99SB with Paramfit BOSISIO Stefano (Tue Jan 24 2017 - 11:07:29 PST)
- [AMBER] Issue with solvateOct for a large system benedikt.diewald.fau.de (Wed Jan 25 2017 - 07:03:34 PST)
- [AMBER] distance restraints failed Qinghua Liao (Wed Jan 25 2017 - 07:44:55 PST)
- [AMBER] Give the correct charge to heme using antechamber Matteo Uggeri (Thu Jan 26 2017 - 06:15:44 PST)
- [AMBER] Split a trajectory into frames Elisa Pieri (Thu Jan 26 2017 - 06:35:11 PST)
- [AMBER] 5' Terminal Phosphate Parameters Paul Meister (Thu Jan 26 2017 - 06:54:30 PST)
- [AMBER] How to make restrt file for specific step Thakur, Abhishek (Thu Jan 26 2017 - 11:52:58 PST)
- [AMBER] Implicit Solvent CpHMD Chase Zagorec-Marks (Thu Jan 26 2017 - 12:29:21 PST)
- [AMBER] Thermodynamic Integration on GPU in AMBER16? Hadházi Ádám (Thu Jan 26 2017 - 13:30:12 PST)
- [AMBER] Fw: Process exclusive mode and GPU peer-to-peer communication Matthew Harrigan (Thu Jan 26 2017 - 14:12:39 PST)
- [AMBER] the formatting of the CPPTRAJ-generated restart files Vlad Cojocaru (Fri Jan 27 2017 - 01:56:54 PST)
- [AMBER] how to Neutralize system automatically? Albert (Fri Jan 27 2017 - 02:00:37 PST)
- [AMBER] Free energy techniques for conformational changes and alchemical mutations Hadházi Ádám (Fri Jan 27 2017 - 02:25:20 PST)
- [AMBER] Peptide with non-standard residues Andreas Tosstorff (Fri Jan 27 2017 - 03:03:36 PST)
- [AMBER] TI simulations blowing up with clambda = 1 with pmemd Stefan Ivanov (Fri Jan 27 2017 - 03:15:02 PST)
- [AMBER] Is there any command in tleap by which I can change Met to Leu Thakur, Abhishek (Fri Jan 27 2017 - 08:04:41 PST)
- [AMBER] Parameters Anna Cebrian Prats (Fri Jan 27 2017 - 09:00:24 PST)
- [AMBER] is there any way by which I can use tleap to do mutation? Thakur, Abhishek (Fri Jan 27 2017 - 10:00:10 PST)
- [AMBER] amber installation test failure Hirdesh Kumar (Fri Jan 27 2017 - 10:20:41 PST)
- [AMBER] amber16 on parallel GPUs Hirdesh Kumar (Fri Jan 27 2017 - 13:06:23 PST)
- [AMBER] amber installation test question James Kress (Fri Jan 27 2017 - 20:11:04 PST)
- [AMBER] problems with input file preparation sunyeping (Sat Jan 28 2017 - 12:23:56 PST)
- [AMBER] hbond Backbone CPPTRAJ. Saman Yousuf ali (Sun Jan 29 2017 - 08:19:38 PST)
- [AMBER] pH-REMD explicit solvent Sowmya Indrakumar (Sun Jan 29 2017 - 12:59:57 PST)
- [AMBER] VMD not working after parmed Andreas Tosstorff (Mon Jan 30 2017 - 02:33:56 PST)
- [AMBER] CpHMD – Effect of explicit ions when calculating the pKa of model compounds Eric Lang (Mon Jan 30 2017 - 04:33:37 PST)
- [AMBER] script to run background job? Michael Shokhen (Mon Jan 30 2017 - 08:31:50 PST)
- [AMBER] mpi error in Amber16 Hirdesh Kumar (Mon Jan 30 2017 - 12:26:34 PST)
- [AMBER] MMPBSA failed Albert (Mon Jan 30 2017 - 23:28:55 PST)
- [AMBER] strip inpcrd Saman Yousuf ali (Tue Jan 31 2017 - 00:58:53 PST)
- [AMBER] cpptraj: autoimage DCD trajectories (with Amber topology) Vlad Cojocaru (Tue Jan 31 2017 - 01:10:02 PST)
- [AMBER] lj1264 pmemd.cuda Andreas Tosstorff (Tue Jan 31 2017 - 01:40:32 PST)
- [AMBER] Fwd: Error during installation process Danu Fajar (Tue Jan 31 2017 - 06:25:07 PST)
- [AMBER] Radical Carbon Anna Cebrian Prats (Tue Jan 31 2017 - 06:54:58 PST)
- [AMBER] clustering Sowmya Indrakumar (Tue Jan 31 2017 - 07:03:32 PST)
- [AMBER] DFTB3 in Amber is not there, but it may be in gromacs. Markus Kaukonen (Tue Jan 31 2017 - 08:06:54 PST)
- [AMBER] visualization problem Albert (Tue Jan 31 2017 - 08:09:13 PST)
- [AMBER] Multiple ligands in MMGBSA Abhilash J (Tue Jan 31 2017 - 08:20:05 PST)
- [AMBER] Methods to count the different species Liyang Zhu (Tue Jan 31 2017 - 12:32:23 PST)
- [AMBER] Differences using leaprc.ff14SB from AmberTools15 and oldff/leaprc.ff14SB from AmberTools16 Joao Damas (Tue Jan 31 2017 - 12:33:16 PST)
- Last message date: Tue Jan 31 2017 - 20:30:03 PST
- Archived on: Fri Dec 20 2024 - 05:55:29 PST
