Amber Archive Sep 2017 by thread
- Re: [AMBER] An equilibration of the membrane protein prepared by charmm-gui James Starlight (Fri Sep 01 2017 - 00:52:56 PDT)
- [AMBER] Pressure tensor Sonata Kvedaravičiūtė (Fri Sep 01 2017 - 01:43:48 PDT)
- [AMBER] ACE and NME capping protein is essential for protein simulation jacky zhao (Fri Sep 01 2017 - 03:30:57 PDT)
- [AMBER] significance of iwrap Saikat Pal (Fri Sep 01 2017 - 04:59:28 PDT)
- [AMBER] H++ salinity Andreas Tosstorff (Fri Sep 01 2017 - 05:38:46 PDT)
- Re: [AMBER] Calculation the Area per lipids using cpptraj Daniel Roe (Fri Sep 01 2017 - 06:13:58 PDT)
- [AMBER] Missing amino acids preparation for long-term simulation jacky zhao (Fri Sep 01 2017 - 09:31:43 PDT)
- [AMBER] Cpptraj and parmwrite and strip Khabiri, Morteza (Fri Sep 01 2017 - 11:16:16 PDT)
- Re: [AMBER] How to add the charged sphere (ion) with arbitrary charge to my PDB file. Parviz Seifpanahi Shabane (Fri Sep 01 2017 - 16:57:38 PDT)
- [AMBER] Explicit solvent CpHMD: seeking clarifications George Tzotzos (Sat Sep 02 2017 - 10:07:21 PDT)
- [AMBER] amberlite p38 tutorial: Failure of final step of "pymdpbsa" in amberlite Bartberger, Michael (Sun Sep 03 2017 - 09:25:31 PDT)
- [AMBER] Error bad atom Br Fábio Jorge (Sun Sep 03 2017 - 12:43:58 PDT)
- [AMBER] Binding Free Energy Calculation in Ionic Liquid Debasish Mandal (Sun Sep 03 2017 - 21:57:09 PDT)
- [AMBER] Moldeling with MCPB.py Lê Ngọc Chính (Mon Sep 04 2017 - 04:09:45 PDT)
- [AMBER] Question about MM/PBSA idecomp=1: Eelec from receptor and ligand don't add up Guqin Shi (Mon Sep 04 2017 - 17:13:25 PDT)
- [AMBER] Residue wise energy decomposition via MM-PBSA Rajarshi Roy (Mon Sep 04 2017 - 21:06:49 PDT)
- [AMBER] Rebuilt missing amino acid gap is critical for long-time MD simulation by Amber jacky zhao (Mon Sep 04 2017 - 22:00:53 PDT)
- [AMBER] .crd file format error Thakur, Abhishek (Tue Sep 05 2017 - 08:37:15 PDT)
- Re: [AMBER] Question about MM/PBSA idecomp=1: decomposed Eelec stays the same when internal dielec constant increases. Is this a bug? Guqin Shi (Tue Sep 05 2017 - 08:54:40 PDT)
- [AMBER] Zinc dummy atom error in MMPBSA calculation Sharon D. Morris (Tue Sep 05 2017 - 22:26:13 PDT)
- [AMBER] MD terminate in HPC Garima Singh (Wed Sep 06 2017 - 03:49:05 PDT)
- [AMBER] Oct 2 deadline for awards applications, Computers in Chemistry Division of ACS Carlos Simmerling (Wed Sep 06 2017 - 05:27:12 PDT)
- [AMBER] Error in MM-PBSA -- BondError: Cannot exclude an atom from itself 康宁 (Thu Sep 07 2017 - 00:47:07 PDT)
- [AMBER] Error after using Parmed: A residue defined as "fast 3-point water"... David Sáez (Thu Sep 07 2017 - 16:07:32 PDT)
- [AMBER] Fixed links and files: Error in parmed: A residue defined as "fast 3-point water"... David Adrian Saez San Martin (Thu Sep 07 2017 - 17:14:24 PDT)
- [AMBER] umbrella sampling - restraint problem Nisha Amarnath Jonniya (Fri Sep 08 2017 - 04:37:14 PDT)
- [AMBER] Problem in restarting pH-REMD CpHMD Elisa Pieri (Fri Sep 08 2017 - 05:43:56 PDT)
- [AMBER] Frcmod file for ionic liquids guptashilpa_91.yahoo.com (Fri Sep 08 2017 - 07:42:13 PDT)
- [AMBER] I only receive a digest, but not specific answers to my posts David Adrian Saez San Martin (Fri Sep 08 2017 - 12:36:40 PDT)
- [AMBER] Frcmod file for ionic liquids Shilpa Gupta (Fri Sep 08 2017 - 21:43:05 PDT)
- [AMBER] Regarding Glucose naming Aashish Bhatt (Sat Sep 09 2017 - 08:02:12 PDT)
- [AMBER] Error in quasiharmonic calculation: prmtop file? Nada Afiva (Sat Sep 09 2017 - 19:50:48 PDT)
- [AMBER] Obtaining AM1-BCC charges in Antechamber Zachary Smithline (Sat Sep 09 2017 - 23:33:14 PDT)
- [AMBER] index error -reg Jeyaram R A (Sun Sep 10 2017 - 04:54:00 PDT)
- [AMBER] tleap atom numbering Neha Gandhi (Sun Sep 10 2017 - 18:38:03 PDT)
- [AMBER] CNT hongping zhang (Sun Sep 10 2017 - 18:58:34 PDT)
- [AMBER] rmsf < 5A colvin (Mon Sep 11 2017 - 01:11:46 PDT)
- [AMBER] MMPBSA.py failing with topologies Sebastian Franco Ulloa (Mon Sep 11 2017 - 01:46:18 PDT)
- [AMBER] MMPBSA error Sebastian Franco Ulloa (Mon Sep 11 2017 - 02:10:18 PDT)
- [AMBER] gamd.log for multiple runs Battocchio, Giovanni (Mon Sep 11 2017 - 02:37:35 PDT)
- [AMBER] TLEAP generation of ionized amino acid residue? Michael Shokhen (Mon Sep 11 2017 - 03:38:55 PDT)
- Re: [AMBER] Minimization error due to modified residue Bill Ross (Mon Sep 11 2017 - 06:09:40 PDT)
- [AMBER] How to use two different force fields for a molecule? Anhui Wang (Mon Sep 11 2017 - 07:09:05 PDT)
- [AMBER] Atom does not have file type -reg. Jeyaram R A (Mon Sep 11 2017 - 08:04:39 PDT)
- Re: [AMBER] TIP3p lennard jones parameters Pengfei Li (Mon Sep 11 2017 - 09:28:01 PDT)
- [AMBER] pmemd and sander simulations different - sander equilibration crashes Chayya Bhargac (Mon Sep 11 2017 - 09:34:14 PDT)
- [AMBER] Can we specify the length and width of the water box in LEaP ? Xing (Mon Sep 11 2017 - 16:27:45 PDT)
- [AMBER] NEW machine need help with GPU choice. Mohit Mazumder (Mon Sep 11 2017 - 18:46:02 PDT)
- [AMBER] Could not import Amber Python modules when using mdout_analyzer.py jacky zhao (Mon Sep 11 2017 - 21:31:50 PDT)
- [AMBER] GPU-accelerated thermodynamic integration available in Amber Darrin York (Tue Sep 12 2017 - 06:01:40 PDT)
- [AMBER] Etot and TEMP become NaN during a simulation on commodity GPUs Chris Neale (Tue Sep 12 2017 - 09:28:30 PDT)
- [AMBER] Creation of unusual bonding via pdb4amber. Rajarshi Roy (Tue Sep 12 2017 - 11:18:18 PDT)
- [AMBER] How to calculate RDF with 'radial' 杨满意 (Tue Sep 12 2017 - 20:58:06 PDT)
- [AMBER] tleap error jacky zhao (Wed Sep 13 2017 - 03:28:24 PDT)
- [AMBER] Amber16 archive corrupted? Casalini Tommaso (Wed Sep 13 2017 - 03:30:01 PDT)
- [AMBER] REMD one long or many short runs? Andreas Tosstorff (Wed Sep 13 2017 - 06:18:02 PDT)
- [AMBER] Deprotonated SER side residue by AMBER? Michael Shokhen (Wed Sep 13 2017 - 10:18:07 PDT)
- [AMBER] Total energy of peptide simulation is positive Chetna Tyagi (Thu Sep 14 2017 - 05:51:00 PDT)
- [AMBER] cpptraj SPAM error George Tzotzos (Thu Sep 14 2017 - 08:13:50 PDT)
- [AMBER] Installing Compiling Errors Timothy Schutt (Thu Sep 14 2017 - 13:30:10 PDT)
- [AMBER] New Phospho Amino Acids Parameters? martin.lepsik.uochb.cas.cz (Fri Sep 15 2017 - 01:32:46 PDT)
- [AMBER] cpptraj volmap: some questions George Tzotzos (Fri Sep 15 2017 - 06:54:25 PDT)
- [AMBER] Is geometric center of atoms same as center of mass ? Saikat Pal (Sat Sep 16 2017 - 00:28:39 PDT)
- [AMBER] simulation time Rana Rehan Khalid (Sat Sep 16 2017 - 09:52:51 PDT)
- [AMBER] Mcpb.py for bay60 compound Rana Rehan Khalid (Sat Sep 16 2017 - 10:43:17 PDT)
- [AMBER] MCPB.py hbay.in input (system does not have metal ion) Rana Rehan Khalid (Sat Sep 16 2017 - 12:19:05 PDT)
- [AMBER] cpptraj: modification of topologies/trajectories George Tzotzos (Sun Sep 17 2017 - 08:02:43 PDT)
- [AMBER] Manually set residues Protonation states for HIS and CYS Rana Rehan Khalid (Sun Sep 17 2017 - 12:27:46 PDT)
- [AMBER] How to specify the liquid-liquid interface 鲁俊波 (Mon Sep 18 2017 - 01:45:49 PDT)
- [AMBER] CpHMD and cys residues Angus Voice (Mon Sep 18 2017 - 03:55:42 PDT)
- [AMBER] AmberTools 17 incomplete compilation D L S Dinuka (Mon Sep 18 2017 - 05:31:04 PDT)
- [AMBER] improper torsion terms Lizelle Lubbe (Mon Sep 18 2017 - 09:07:08 PDT)
- [AMBER] Problem with parallel install Maria Clelia Milletti (Mon Sep 18 2017 - 09:18:47 PDT)
- [AMBER] cpptraj: usage of strip and parmstrip George Tzotzos (Mon Sep 18 2017 - 11:15:45 PDT)
- [AMBER] How tleap read a Ruthenium complex solvent box generated by packmol? Sanaa ALAbbad (Mon Sep 18 2017 - 15:18:03 PDT)
- [AMBER] Hoogsteen base pair using "useboundsfrom" Mandar Kulkarni (Tue Sep 19 2017 - 02:42:05 PDT)
- [AMBER] Pytraj Gyration Tensor Domenico Marson (Tue Sep 19 2017 - 03:18:19 PDT)
- [AMBER] angle between two subdomains Sowmya Indrakumar (Tue Sep 19 2017 - 06:44:11 PDT)
- [AMBER] reduce command warnings Rana Rehan Khalid (Tue Sep 19 2017 - 08:13:30 PDT)
- [AMBER] converting crd to pdb Rana Rehan Khalid (Tue Sep 19 2017 - 10:05:21 PDT)
- [AMBER] ambertools install issue Eric Smoll (Tue Sep 19 2017 - 10:50:30 PDT)
- [AMBER] Restart Simulation Rana Rehan Khalid (Tue Sep 19 2017 - 11:29:44 PDT)
- Re: [AMBER] ambertools install issue (Eric Smoll) Eric Smoll (Tue Sep 19 2017 - 12:38:21 PDT)
- [AMBER] .com file creation Rana Rehan Khalid (Tue Sep 19 2017 - 13:21:41 PDT)
- [AMBER] Error in pmemd.cuda David Sáez (Tue Sep 19 2017 - 22:58:39 PDT)
- [AMBER] Protein drifts out of the periodic cell Michael Shokhen (Wed Sep 20 2017 - 02:21:07 PDT)
- [AMBER] Distance restraint Lizelle Lubbe (Wed Sep 20 2017 - 07:26:44 PDT)
- [AMBER] protein-membrane visualize in VMD Kanin Wichapong (Wed Sep 20 2017 - 09:00:05 PDT)
- [AMBER] simulation of docked domains of protein Rana Rehan Khalid (Wed Sep 20 2017 - 09:26:30 PDT)
- [AMBER] Antechamber Rana Rehan Khalid (Wed Sep 20 2017 - 09:46:19 PDT)
- [AMBER] Inverting a selection in NAB atom expression? Istvan Kolossvary (Wed Sep 20 2017 - 13:47:52 PDT)
- [AMBER] Question about MCPB.py Lê Ngọc Chính (Thu Sep 21 2017 - 00:07:33 PDT)
- [AMBER] Amber16 electric field parameters Alessandro Mariani (Thu Sep 21 2017 - 02:22:33 PDT)
- [AMBER] simulation stop due to size limit exceed Rana Rehan Khalid (Thu Sep 21 2017 - 05:36:43 PDT)
- [AMBER] Antechamber error Rana Rehan Khalid (Thu Sep 21 2017 - 07:34:08 PDT)
- [AMBER] Quasi-Harmonic Analysis and Entropy Calculations in cpptraj - Help Requested Mo Rahman (Thu Sep 21 2017 - 08:36:55 PDT)
- [AMBER] Setting water box with fix dimension Ashutosh Shandilya (Thu Sep 21 2017 - 09:13:45 PDT)
- [AMBER] Question about MCPB.py Lê Ngọc Chính (Thu Sep 21 2017 - 09:26:05 PDT)
- [AMBER] MCPB.py AmberTools17 Amani Eshtiwi (Thu Sep 21 2017 - 09:36:18 PDT)
- [AMBER] Reduce command warnings Skipped hydrogen Rana Rehan Khalid (Thu Sep 21 2017 - 10:55:00 PDT)
- [AMBER] Is it possible to compile without linking C++ and fortran? Timothy Schutt (Thu Sep 21 2017 - 10:56:19 PDT)
- [AMBER] cpinutil.py Pacheco, Sayuri (Thu Sep 21 2017 - 12:45:40 PDT)
- [AMBER] Split the image to run in the string method Chunli Yan (Thu Sep 21 2017 - 12:50:50 PDT)
- Re: [AMBER] Problem regarding Chamber and psf file David Sáez (Thu Sep 21 2017 - 13:45:09 PDT)
- [AMBER] [david.case.rutgers.edu: Re: Is it possible to compile without linking C++ and fortran?] David A Case (Thu Sep 21 2017 - 13:46:29 PDT)
- [AMBER] simulations crash Ana Luisa Novo de Oliveira (Fri Sep 22 2017 - 04:50:07 PDT)
- [AMBER] SHAKE failure Lizelle Lubbe (Fri Sep 22 2017 - 05:30:13 PDT)
- [AMBER] PMEMD TERMINATED ABNORMALLY (But simulation run with sander command) Rana Rehan Khalid (Fri Sep 22 2017 - 08:04:55 PDT)
- [AMBER] cluster analysis of protein complex simulation jacky zhao (Fri Sep 22 2017 - 08:10:09 PDT)
- [AMBER] mdcrd file not open in vmd Rana Rehan Khalid (Fri Sep 22 2017 - 10:47:51 PDT)
- [AMBER] How to compare the difference between two trajectories with two very similar parm files jacky zhao (Fri Sep 22 2017 - 18:32:12 PDT)
- [AMBER] Antechamber RESP calculation error Rana Rehan Khalid (Sat Sep 23 2017 - 10:05:26 PDT)
- [AMBER] Different production speeds at different pHs when doing explicit constant pH simulations Andrew Schaub (Sat Sep 23 2017 - 23:47:36 PDT)
- [AMBER] CpHMD: seeking clarification George Tzotzos (Sun Sep 24 2017 - 10:41:05 PDT)
- [AMBER] cluster analysis using cpptraj Sowmya Indrakumar (Mon Sep 25 2017 - 02:22:33 PDT)
- [AMBER] Using FEW with a transmembrane protein Tarsis (Mon Sep 25 2017 - 10:34:32 PDT)
- [AMBER] water bridge analysis Thakur, Abhishek (Mon Sep 25 2017 - 15:17:00 PDT)
- [AMBER] analysizing the trajectory for water interaction Thakur, Abhishek (Mon Sep 25 2017 - 15:31:00 PDT)
- [AMBER] PyRed Steven M. Graham (Mon Sep 25 2017 - 18:42:18 PDT)
- [AMBER] How to save reimaged trajectory file during MD? Ravi Abrol (Mon Sep 25 2017 - 22:51:57 PDT)
- [AMBER] Problem with MM-GBSA decomposition Sergey Samsonov (Tue Sep 26 2017 - 00:13:59 PDT)
- [AMBER] A query about coordinate saving frequency for solvation entropy calculation using GIST SHAILESH KUMAR (Tue Sep 26 2017 - 00:37:13 PDT)
- [AMBER] Problem in analysing radius of gyration value in CPPTRAJ krishna.2015.iitg.ernet.in (Tue Sep 26 2017 - 09:07:04 PDT)
- [AMBER] cpptraj distance: error George Tzotzos (Tue Sep 26 2017 - 09:41:37 PDT)
- [AMBER] Air-water interface jesus berlanga (Tue Sep 26 2017 - 22:58:12 PDT)
- [AMBER] Error with MMGBSA/PBSA jacob wick (Wed Sep 27 2017 - 08:38:17 PDT)
- [AMBER] [Fwd: Re: Problem in analysing radius of gyration value in CPPTRAJ] krishna.2015.iitg.ernet.in (Wed Sep 27 2017 - 11:35:23 PDT)
- [AMBER] Avoid pH Titration of LYS and TYR R zu (Wed Sep 27 2017 - 12:17:21 PDT)
- [AMBER] Dr. Nick Riviera Eric Pettersen (Wed Sep 27 2017 - 12:43:21 PDT)
- [AMBER] moveanchor waleed zalloum (Thu Sep 28 2017 - 04:41:55 PDT)
- [AMBER] RAC_analysis jacky zhao (Thu Sep 28 2017 - 06:53:27 PDT)
- [AMBER] leaprc.constph and ff14sb R zu (Thu Sep 28 2017 - 08:06:18 PDT)
- [AMBER] Cpptraj Sayuri Pacheco (Thu Sep 28 2017 - 09:01:42 PDT)
- [AMBER] trajout last x frames cpptraj Hughes, Travis (Thu Sep 28 2017 - 11:23:06 PDT)
- [AMBER] identiy the step of interaction from an entire trajectory Thakur, Abhishek (Thu Sep 28 2017 - 12:10:47 PDT)
- [AMBER] barostat with large coupling constant R zu (Thu Sep 28 2017 - 18:14:57 PDT)
- [AMBER] identifying the step of hbond interaction from trajectories Thakur, Abhishek (Fri Sep 29 2017 - 11:20:24 PDT)
- [AMBER] Multiple Simulations on One GPU R zu (Fri Sep 29 2017 - 14:58:43 PDT)
- Last message date: Sat Sep 30 2017 - 06:00:03 PDT
- Archived on: Fri Nov 22 2024 - 05:55:31 PST
