Amber Archive Jan 2018 by thread
- [AMBER] AMBER intelmpi installation on cluster Simon Kit Sang Chu (Mon Jan 01 2018 - 22:31:51 PST)
- Re: [AMBER] DSSP CPPtraj Daniel Roe (Tue Jan 02 2018 - 10:12:51 PST)
- Re: [AMBER] CPPTRAJ HBOND Daniel Roe (Tue Jan 02 2018 - 10:21:00 PST)
- [AMBER] LIPID17 reference ? Marek Maly (Wed Jan 03 2018 - 05:37:01 PST)
- [AMBER] Trying to use AMBER parameters in GROMACS Crystal Vander Zanden (Wed Jan 03 2018 - 08:49:35 PST)
- Re: [AMBER] Binding energy of ligand with homology model Daniel Mermelstein (Wed Jan 03 2018 - 13:31:50 PST)
- [AMBER] Distance calculation between atoms from two different frames using CPPTRAJ anu chandra (Thu Jan 04 2018 - 03:41:56 PST)
- [AMBER] Which command to use for printing X Y Z coordinates of the given atom ? Marek Maly (Thu Jan 04 2018 - 17:54:07 PST)
- [AMBER] Problem regarding compiling in cpptraj with openmp Saikat Pal (Thu Jan 04 2018 - 22:54:54 PST)
- [AMBER] Density equilibration Thomas Exner (Fri Jan 05 2018 - 07:21:47 PST)
- [AMBER] qm2_extern_gau_module Thakur, Abhishek (Fri Jan 05 2018 - 11:46:50 PST)
- [AMBER] xmgr x-axis change to ns. Rana Rehan Khalid (Sat Jan 06 2018 - 08:30:31 PST)
- [AMBER] Minimization Problem(error shows "... RESTARTED DUE TO LINMIN FAILURE ..." ) Malay Raul (Sat Jan 06 2018 - 13:05:13 PST)
- [AMBER] Announcement: AMBER Molecular Dynamics Workshop 2018 Fabian Glaser (Sun Jan 07 2018 - 06:37:11 PST)
- [AMBER] resources for summer researches Mahendra B Thapa (Mon Jan 08 2018 - 10:35:33 PST)
- [AMBER] REMD job stops on loadleveler Andreas Tosstorff (Mon Jan 08 2018 - 11:56:21 PST)
- [AMBER] Error during the MMPBSA calculation -reg. Jeyaram R A (Mon Jan 08 2018 - 20:34:04 PST)
- [AMBER] Regarding error in preparation of HEME via MCPB.py Aashish Bhatt (Mon Jan 08 2018 - 20:47:34 PST)
- [AMBER] DNA melting temperature Marie Brut (Tue Jan 09 2018 - 01:16:13 PST)
- [AMBER] prmtop.pdf %FLAG SCREEN Johannes Kalliauer (Tue Jan 09 2018 - 04:53:21 PST)
- [AMBER] Hydrophobic interaction VS time in protein interfaces Jag Silwal (Tue Jan 09 2018 - 08:45:38 PST)
- [AMBER] Atom restraints in AMBER Nikolay N. Kuzmich (Tue Jan 09 2018 - 18:33:02 PST)
- [AMBER] AMBER workshop registration opened, 4-8 March, Technion, Israel Fabian Glaser (Wed Jan 10 2018 - 00:07:14 PST)
- [AMBER] cpptraj.OMP vs cpptraj Saikat Pal (Wed Jan 10 2018 - 03:06:25 PST)
- [AMBER] ligand outside the binding site - vmd visualisation problem M. Pyrka (Wed Jan 10 2018 - 03:47:50 PST)
- [AMBER] gnuplot x-axis represented the number of frames how to convert it in nano second time. Rana Rehan Khalid (Wed Jan 10 2018 - 05:44:48 PST)
- [AMBER] use_template = 0 Thakur, Abhishek (Wed Jan 10 2018 - 08:34:27 PST)
- [AMBER] pseudo-trajectory in pytraj Abdul-Rashid III Sampaco (Wed Jan 10 2018 - 09:04:17 PST)
- [AMBER] QM/MM MD B3LYP Thakur, Abhishek (Wed Jan 10 2018 - 09:25:05 PST)
- [AMBER] QM/MM MD B3LYP Thakur, Abhishek (Wed Jan 10 2018 - 09:35:29 PST)
- [AMBER] OS High Sierra Hallel Freedman (Wed Jan 10 2018 - 16:36:51 PST)
- [AMBER] error during MMPBSA calculation -reg. Jeyaram R A (Wed Jan 10 2018 - 23:06:16 PST)
- [AMBER] constant pH md Maciej Maciejczyk (Wed Jan 10 2018 - 23:44:21 PST)
- [AMBER] MMGBSA calculation gives very high positive free energy of binding!!! Sandip Mondal (Thu Jan 11 2018 - 01:41:12 PST)
- [AMBER] scaling of electrostatic interactions Antonija Tomić (Thu Jan 11 2018 - 02:18:00 PST)
- [AMBER] error 12-6-4 LJ with the last update (November 2017) Davide Sala (Thu Jan 11 2018 - 02:53:31 PST)
- [AMBER] AMBER GPU-TI implementation - paper? Hadházi Ádám (Thu Jan 11 2018 - 05:37:07 PST)
- [AMBER] Replica exchange thermodynamic integration in AMBER Roma Mukhopadhyay (Thu Jan 11 2018 - 15:45:55 PST)
- [AMBER] Amber 16.12 and 12-6-4 force field Problem Guanglin Kuang (Thu Jan 11 2018 - 18:49:22 PST)
- Re: [AMBER] pmemd.cuda and rigid CH2Cl2 Thomas Fox (Fri Jan 12 2018 - 00:38:48 PST)
- [AMBER] Amber mailing list Angela dos Reis (Fri Jan 12 2018 - 17:54:16 PST)
- [AMBER] going away for now Bill Ross (Fri Jan 12 2018 - 18:26:01 PST)
- [AMBER] RESP charges for capped C termimal glycine: NHCH2CONH2 ABEL Stephane (Sat Jan 13 2018 - 05:50:17 PST)
- Re: [AMBER] Fwd: Hydrophobic interaction VS time in protein interfaces Jag Silwal (Sun Jan 14 2018 - 09:06:44 PST)
- [AMBER] H-bond analysis in tetrameric protein complexes Jag Silwal (Mon Jan 15 2018 - 13:09:44 PST)
- [AMBER] distance to center of geometry Meng Wu (Mon Jan 15 2018 - 19:27:06 PST)
- [AMBER] email khair.bux.iccs.edu (Tue Jan 16 2018 - 01:58:45 PST)
- [AMBER] Reorienting the protein during simulation Ahmed Mashaly (Tue Jan 16 2018 - 02:52:20 PST)
- Re: [AMBER] more than 100% hydrogen bond population Daniel Roe (Tue Jan 16 2018 - 06:57:32 PST)
- [AMBER] leap Lara rajam (Tue Jan 16 2018 - 09:26:39 PST)
- [AMBER] MD run saving only 250 frames Paul Meister (Tue Jan 16 2018 - 11:58:00 PST)
- [AMBER] Errors in my installation Bhargava Sai M (Tue Jan 16 2018 - 20:52:23 PST)
- [AMBER] Error during MMPBSA calculation -reg. Jeyaram R A (Wed Jan 17 2018 - 03:40:01 PST)
- [AMBER] AMBER tools 17 installation problem maryam azimzadehirani (Wed Jan 17 2018 - 08:20:45 PST)
- [AMBER] umbrella sampling process krishna.2015.iitg.ernet.in (Wed Jan 17 2018 - 10:04:33 PST)
- [AMBER] Crystal water in Amber 16 Yuliana Bosken (Wed Jan 17 2018 - 21:12:45 PST)
- [AMBER] Change a residue in a protein David Sáez (Thu Jan 18 2018 - 00:45:47 PST)
- [AMBER] AMBER - QMMM with DFTB daniele selli (Thu Jan 18 2018 - 01:59:50 PST)
- [AMBER] AmberTools with Amber11 Jennifer L. Muzyka (Thu Jan 18 2018 - 11:35:22 PST)
- [AMBER] MMGBSA calculations with explicit water molecules Marawan Hussien (Thu Jan 18 2018 - 12:14:15 PST)
- [AMBER] MCPB Thakur, Abhishek (Thu Jan 18 2018 - 14:23:49 PST)
- [AMBER] Patent to solve floating point errors Kenneth McGuinness (Thu Jan 18 2018 - 14:41:33 PST)
- [AMBER] Ligand modifying softwares. Vatsal Purohit (Thu Jan 18 2018 - 20:23:21 PST)
- [AMBER] Mail from "Dr. MANAS MONDAL" <manas.pku.edu.cn>. Dr. MANAS MONDAL (Fri Jan 19 2018 - 01:48:01 PST)
- [AMBER] Parametrization of new amino acid in methanol solvent Chetna Tyagi (Fri Jan 19 2018 - 04:10:51 PST)
- [AMBER] Amber 18 Qinghua Liao (Fri Jan 19 2018 - 04:47:44 PST)
- [AMBER] error during MMPBSA-reg Jeyaram R A (Fri Jan 19 2018 - 06:47:34 PST)
- [AMBER] CPPTRAJ-Angle between two Helices Jag Silwal (Fri Jan 19 2018 - 10:23:06 PST)
- [AMBER] Installation - NetCDF C compile failed Jiří Dluhoš (Fri Jan 19 2018 - 10:23:31 PST)
- [AMBER] PB Bomb in pb_aaradi(): No radius assigned for atom 7 CB 3C Morrow,John Kenneth (Fri Jan 19 2018 - 15:14:12 PST)
- [AMBER] fatty acid ligand comes out of binding site during md. Saman Yousuf ali (Sat Jan 20 2018 - 05:43:11 PST)
- [AMBER] PROBLEM ENCOUNTERED WHILE UNDERGOING TUTUORIAL FOR ROOM TEMPERATURE IONIC LIQUID. Suman Bhaumik (Sun Jan 21 2018 - 01:46:05 PST)
- [AMBER] Non-PBC simulation in a droplet made of organic solvent Veronika Jurásková (Mon Jan 22 2018 - 02:13:49 PST)
- [AMBER] Writing mdcrd to inpcrd Simon Kit Sang Chu (Mon Jan 22 2018 - 03:29:09 PST)
- [AMBER] Best practices for lipid equilibration - Amber parameters in Gromacs Crystal Vander Zanden (Mon Jan 22 2018 - 08:13:30 PST)
- [AMBER] Transformation from cartesian to torsion space Siddhartha Jain (Mon Jan 22 2018 - 12:00:39 PST)
- [AMBER] Amber16 installation: Segmentation fault (core dumped) error when execute antechamber Yuan Hu (Mon Jan 22 2018 - 16:03:01 PST)
- [AMBER] How to perform Newton-Raphson minimization to protein 巩梦雪 (Mon Jan 22 2018 - 23:30:22 PST)
- [AMBER] Unreplicable AMBER tutorial 3 Audrius Laurynėnas (Tue Jan 23 2018 - 04:22:21 PST)
- [AMBER] Avoiding pdb4amber renumbering Sundar (Tue Jan 23 2018 - 10:04:22 PST)
- [AMBER] EVB xch_* values Stregone (Tue Jan 23 2018 - 11:44:07 PST)
- [AMBER] Amber16+AT17: Several checks failing w/Intel Parallel Studio XE 2018.1 Patrice Peterson (Tue Jan 23 2018 - 12:18:30 PST)
- [AMBER] cpptraj long writing queue Simon Kit Sang Chu (Wed Jan 24 2018 - 00:03:49 PST)
- [AMBER] Cannot match namelist object name 0 Núbia Prates (Wed Jan 24 2018 - 08:26:33 PST)
- [AMBER] Acpype and Gromacs Ahmed Mashaly (Wed Jan 24 2018 - 12:42:11 PST)
- [AMBER] KeyError: 'HIE-HD1' MCPB.py Thakur, Abhishek (Wed Jan 24 2018 - 12:43:10 PST)
- [AMBER] Extract Velocity (and Force) from Gromacs .trr trajectory using cpptraj Mohd Farid Ismail (Thu Jan 25 2018 - 02:19:19 PST)
- [AMBER] Metadynamics in pmemd Hannes Konegger (Thu Jan 25 2018 - 05:13:39 PST)
- [AMBER] Protonated cytosine and adenine: Parameter file was not saved Amen Shamim (Thu Jan 25 2018 - 05:15:28 PST)
- [AMBER] CPPTRAJ HBond analysis Segmentation fault (core dumped) 姚永霖 (Thu Jan 25 2018 - 06:54:00 PST)
- [AMBER] Problem to convert Alberto Bencomo (Thu Jan 25 2018 - 08:23:31 PST)
- [AMBER] CPPTRAJ HBond analysis Segmentation fault (core dumped) 姚永霖 (Thu Jan 25 2018 - 17:33:30 PST)
- [AMBER] QM/MM metadynamics with external QM code Qinghua Liao (Fri Jan 26 2018 - 01:42:22 PST)
- [AMBER] Compressing trajectory file Setyanto Md (Fri Jan 26 2018 - 04:16:07 PST)
- [AMBER] QM/MM SMD with 'external' theory and PBCs Ruth Helena Tichauer (Fri Jan 26 2018 - 06:33:05 PST)
- [AMBER] Can amber16 pmemd rigorously combine position restraints with pressure coupling on GPUs ? Chris Neale (Fri Jan 26 2018 - 11:48:09 PST)
- [AMBER] GBSA parameters Siddhartha Jain (Sat Jan 27 2018 - 17:11:57 PST)
- [AMBER] parmchk Yuliana Bosken (Sat Jan 27 2018 - 20:18:41 PST)
- [AMBER] box size and SMD simulation Ibrahim Said (Sun Jan 28 2018 - 10:18:46 PST)
- [AMBER] command problem SHALJA VERMA (Mon Jan 29 2018 - 02:27:46 PST)
- [AMBER] command not working SHALJA VERMA (Mon Jan 29 2018 - 02:28:34 PST)
- [AMBER] dftb_chg not working David Sáez (Mon Jan 29 2018 - 03:54:55 PST)
- [AMBER] hbond analysis on DNA-protein complex Kenneth Huang (Mon Jan 29 2018 - 07:26:47 PST)
- [AMBER] MCPB.py error with ion id Thakur, Abhishek (Mon Jan 29 2018 - 07:37:07 PST)
- [AMBER] Use amber output velocity for different system Khabiri, Morteza (Mon Jan 29 2018 - 08:48:11 PST)
- [AMBER] Empty .frcmod file roja rahmani (Tue Jan 30 2018 - 05:39:56 PST)
- [AMBER] Query regarding the ff99SB*ildn force field Leena Aggarwal (Tue Jan 30 2018 - 20:53:26 PST)
- [AMBER] Compiling AMBER16 with Open MPI 3.x Jonas Mansoor (Wed Jan 31 2018 - 01:15:09 PST)
- [AMBER] Query on thermodynamic integration of complexes involving metal ions Muthukumaran Rajagopalan (Wed Jan 31 2018 - 04:24:55 PST)
- [AMBER] Query on thermodynamic integration of complexes involving metal ions Muthukumaran Rajagopalan (Wed Jan 31 2018 - 05:16:02 PST)
- [AMBER] About rerun the same trajectory David Sáez (Wed Jan 31 2018 - 07:20:54 PST)
- [AMBER] Is there anyway to recover the potential energies obtained after running md Shamsi, Zahra (Wed Jan 31 2018 - 08:20:57 PST)
- Last message date: Wed Jan 31 2018 - 10:00:02 PST
- Archived on: Fri Nov 29 2024 - 05:55:37 PST
