Amber Archive Feb 2016 by thread
- [AMBER] Wrong or no center in RdPar. Fatemeh Sadat Alavi (Sun Jan 31 2016 - 22:25:38 PST)
- [AMBER] Replacement for xmgrace Jean-Patrick Francoia (Mon Feb 01 2016 - 01:48:31 PST)
- Re: [AMBER] 3DRISM: erratic values for partial molar volume Josh Berryman (Mon Feb 01 2016 - 05:16:01 PST)
- [AMBER] Value of ntrx=7 Krantzman, Kristin D (Mon Feb 01 2016 - 11:50:21 PST)
- [AMBER] Segmentation fault when converting charmm to amber toppar using chamber Gary Zhang (Mon Feb 01 2016 - 13:09:27 PST)
- [AMBER] amber14 update Carlos Romero (Mon Feb 01 2016 - 16:50:14 PST)
- [AMBER] SP3 Nitrogen planarity issue with ff14SB Prayagraj Fandilolu (Mon Feb 01 2016 - 20:15:17 PST)
- [AMBER] Regaridng FIle preparation in AMBERTOOLS14 Sivanandam M (Tue Feb 02 2016 - 01:24:26 PST)
- [AMBER] Question about mask command A kS (Tue Feb 02 2016 - 01:28:24 PST)
- [AMBER] Dear All ankita mehta (Tue Feb 02 2016 - 03:18:52 PST)
- [AMBER] Amber/tutorial/advanced/tutorial16/ zoran matovic (Tue Feb 02 2016 - 06:10:42 PST)
- [AMBER] MMPBSA ImportError Joseph Baker (Tue Feb 02 2016 - 18:25:51 PST)
- [AMBER] standard deviation of rmsd values Atila Petrosian (Tue Feb 02 2016 - 23:39:04 PST)
- [AMBER] Dihedral angles restraints from x-ray to NMR Vasantha Kumar (Wed Feb 03 2016 - 02:52:59 PST)
- Re: [AMBER] free energy calculation of folding Josh Berryman (Wed Feb 03 2016 - 04:06:21 PST)
- Re: [AMBER] Help to choose best-fit ion model Pengfei Li (Wed Feb 03 2016 - 08:17:48 PST)
- [AMBER] Size of solvent box Krantzman, Kristin D (Wed Feb 03 2016 - 09:27:20 PST)
- [AMBER] Problems with when using DFTB halorg .skf files in sqm Marc van der Kamp (Thu Feb 04 2016 - 04:37:42 PST)
- [AMBER] REMD tutorial abdennour braka (Thu Feb 04 2016 - 09:51:23 PST)
- Re: [AMBER] Size of solvent box, RDF Krantzman, Kristin D (Thu Feb 04 2016 - 10:42:50 PST)
- [AMBER] Regarding MMGBSA calculation neha chaudhary (Thu Feb 04 2016 - 23:48:24 PST)
- [AMBER] Zero pressure with pmemd.cuda Batuhan Kav (Fri Feb 05 2016 - 08:10:57 PST)
- [AMBER] accelerated MD - frequency of conformational change Weinzierl, Robert O J (Fri Feb 05 2016 - 09:54:33 PST)
- Re: [AMBER] Wrong or no center in RdPar Fatemeh Sadat Alavi (Sat Feb 06 2016 - 01:05:38 PST)
- [AMBER] Z-constraint PMF method zoran matovic (Sat Feb 06 2016 - 05:32:26 PST)
- [AMBER] aMD Secondary Structure Weinzierl, Robert O J (Sun Feb 07 2016 - 03:12:57 PST)
- [AMBER] error in minimization whole system Fatemeh Sadat Alavi (Sun Feb 07 2016 - 04:26:32 PST)
- [AMBER] Question about AmberTools14/15 installation A kS (Mon Feb 08 2016 - 00:15:28 PST)
- [AMBER] Steered MD of membrane proteins Ofir Tal (Mon Feb 08 2016 - 01:14:04 PST)
- [AMBER] Error atommask selectElemMask Ruth Helena Tichauer (Mon Feb 08 2016 - 05:36:38 PST)
- Re: [AMBER] Problem with saving parameters for a complex having Heme group Emilio Lence (Mon Feb 08 2016 - 08:46:43 PST)
- [AMBER] Getting and keeping ACPYPE updated Alan (Tue Feb 09 2016 - 03:33:03 PST)
- [AMBER] Is the Force Constant in the Parm**.dat file derived from a mass-weighted Hessian Thomas Collier (Tue Feb 09 2016 - 03:56:15 PST)
- [AMBER] Parameter for Aspartic Acid-Lysine Cyclic peptide Mohammed Khaled Tumbi (Tue Feb 09 2016 - 06:44:18 PST)
- [AMBER] Parameter for Aspartic Acid-Lysine Cyclic peptide Mohammed Khaled Tumbi (Tue Feb 09 2016 - 07:05:26 PST)
- [AMBER] problem with energy minimization (sander) Maryam Hamzehee (Wed Feb 10 2016 - 04:26:06 PST)
- [AMBER] citrulline parameters Marie Brut (Wed Feb 10 2016 - 06:13:46 PST)
- [AMBER] MMPB (GB) SA cpptraj failed with prmtop Arati Paudyal (Wed Feb 10 2016 - 06:39:53 PST)
- [AMBER] PDB to distance in AMBER Vasantha Kumar (Wed Feb 10 2016 - 07:39:57 PST)
- [AMBER] Normalizing histogram with CPPTRAJ anu chandra (Wed Feb 10 2016 - 09:05:25 PST)
- [AMBER] Gist Installation in Amber12 Mongam Riba (Wed Feb 10 2016 - 22:39:15 PST)
- [AMBER] minimization error : segmentation fault Saman Yousuf ali (Wed Feb 10 2016 - 23:34:09 PST)
- [AMBER] Is there a way to compare trajectories? Karolina Markowska (Thu Feb 11 2016 - 01:07:01 PST)
- [AMBER] Restarting a heating simulation Elisa Pieri (Thu Feb 11 2016 - 02:43:50 PST)
- [AMBER] Amber 14 w/ CUDA - unclear "make test"-errors Falko Jähnert (Thu Feb 11 2016 - 04:36:50 PST)
- [AMBER] Unable to run QM/MM with RNA and sodium ion kaushik chakraborty (Thu Feb 11 2016 - 08:57:39 PST)
- [AMBER] interpret results Carlos Romero (Thu Feb 11 2016 - 09:27:08 PST)
- [AMBER] Error: Bad > topology file. Batuhan Kav (Thu Feb 11 2016 - 11:56:50 PST)
- [AMBER] cpptraj nativecontacts. George Tzotzos (Thu Feb 11 2016 - 13:49:58 PST)
- [AMBER] Paramfit, negative bond parameters David Poole (Thu Feb 11 2016 - 15:53:41 PST)
- Re: [AMBER] minimization error : segmentation fault (AMBER Digest, Vol 1483, Issue 1) Saman Yousuf ali (Thu Feb 11 2016 - 21:14:54 PST)
- [AMBER] Downloading of Ambertools15 Mongam Riba (Fri Feb 12 2016 - 01:23:22 PST)
- [AMBER] Dear all ankita mehta (Fri Feb 12 2016 - 03:03:33 PST)
- [AMBER] Li & Mertz ion parameters Vlad Cojocaru (Fri Feb 12 2016 - 09:51:06 PST)
- [AMBER] gpu_allreduce cudaDeviceSynchronize failed an illegal memory access was encountered Sarah Anderson (Fri Feb 12 2016 - 10:42:09 PST)
- [AMBER] MMPBSA.py.MPI won't recognise mpy4pi Wesley Michael Botello-Smith (Fri Feb 12 2016 - 16:45:14 PST)
- [AMBER] Regarding minimization in AMBER neha chaudhary (Fri Feb 12 2016 - 22:26:18 PST)
- [AMBER] broken iodine bond problem in NEWPDB.PDB file. Saman Yousuf ali (Fri Feb 12 2016 - 22:30:41 PST)
- [AMBER] summary.ETOT analysis Michael Shokhen (Sun Feb 14 2016 - 01:47:03 PST)
- [AMBER] Fwd: PC square fluctuations Rajeswari A. (Mon Feb 15 2016 - 01:02:24 PST)
- [AMBER] delta G computation (MMPBSA.py) Карлов Дмитрий (Mon Feb 15 2016 - 04:29:11 PST)
- [AMBER] average 3D structure with condition Michael Shokhen (Mon Feb 15 2016 - 08:42:05 PST)
- [AMBER] Fw: Hg parameterization nida baig (Mon Feb 15 2016 - 08:43:35 PST)
- [AMBER] want to ask you about PCA plotting Ayesha Kanwal (Tue Feb 16 2016 - 01:58:58 PST)
- [AMBER] Reg: problem in generating prmtop and crd files by using ff12SB of magnesium ions Yogeeshwar Ajjugal (Tue Feb 16 2016 - 04:35:32 PST)
- [AMBER] parmed/chamber problem recognizing atom types Amy Rice (Tue Feb 16 2016 - 10:02:42 PST)
- [AMBER] [AMBER} nonpolar term for MMPBSA decomp showing up as 0 Kalenkiewicz, Andrew (NIH/NICHD) [F] (Tue Feb 16 2016 - 11:55:29 PST)
- [AMBER] how to check protonation state Ayesha Kanwal (Tue Feb 16 2016 - 12:46:13 PST)
- [AMBER] unable to generate Mercury parameter file Sehrish Naz Aijaz (Tue Feb 16 2016 - 21:06:51 PST)
- [AMBER] Technical problem running pH-REMD Elisa Pieri (Wed Feb 17 2016 - 06:22:06 PST)
- [AMBER] cationic-pi interactions Jose luis Borioni (Wed Feb 17 2016 - 19:56:48 PST)
- [AMBER] A question about cpptraj autoimage 肖立 (Thu Feb 18 2016 - 17:02:17 PST)
- [AMBER] membrane potential Balaji Selvam (Thu Feb 18 2016 - 17:22:04 PST)
- [AMBER] antechamber run for FAD 홍종희 (Fri Feb 19 2016 - 02:12:20 PST)
- [AMBER] Relabeling Atoms after a Run Trajectory Robert Molt (Fri Feb 19 2016 - 06:54:59 PST)
- [AMBER] charge derivation Abelak, Kavin (Fri Feb 19 2016 - 07:48:18 PST)
- [AMBER] Energy decomposition error Renato Freitas (Fri Feb 19 2016 - 13:17:20 PST)
- [AMBER] Covariance Matrix in CPPTRAJ Joel Lapin (Sat Feb 20 2016 - 15:10:46 PST)
- [AMBER] lmod & xmin in sander Jérémie KNOOPS [531802] (Sun Feb 21 2016 - 06:09:47 PST)
- [AMBER] Defining Units in nastruct Robert Molt (Sun Feb 21 2016 - 15:45:16 PST)
- [AMBER] KeyError - MCPB.py Taylor, Cooper (Sun Feb 21 2016 - 18:58:44 PST)
- [AMBER] velocity auto correlation function Vertika Gautam (Sun Feb 21 2016 - 21:27:16 PST)
- [AMBER] Fwd: Error with disulphide bonds in tleap maryam azimzadehirani (Mon Feb 22 2016 - 01:10:54 PST)
- [AMBER] parameter file for isoaspartate acid Jesmita Dhar (Mon Feb 22 2016 - 01:15:20 PST)
- [AMBER] want script for plotting graph on entropy Ayesha Kanwal (Mon Feb 22 2016 - 03:40:15 PST)
- [AMBER] charmmlipid2amber.py Batuhan Kav (Mon Feb 22 2016 - 04:44:57 PST)
- [AMBER] Paradynamics with Amber Ulf Ryde (Mon Feb 22 2016 - 06:56:43 PST)
- [AMBER] calculate ligand RMSD for MD simulations; nofit or not? Marc Zhang (Mon Feb 22 2016 - 07:52:23 PST)
- [AMBER] CPPtraj & ParmEd - delete atoms Balaji Selvam (Mon Feb 22 2016 - 10:41:20 PST)
- [AMBER] No exe file in Amberhome Mahdieh Hadi (Mon Feb 22 2016 - 10:53:15 PST)
- [AMBER] Ligand Molecules Being Rejected in SHIFTS 5.0.1 Dan Morris (Mon Feb 22 2016 - 12:01:11 PST)
- [AMBER] cpptraj command for pi-stacking or hydrophobic interactions. Saman Yousuf ali (Mon Feb 22 2016 - 20:34:58 PST)
- [AMBER] tMD with ligand Jean-Marc Billod (Tue Feb 23 2016 - 01:45:45 PST)
- [AMBER] Post-doctoral position in Computational Physics Andrea Spitaleri (Tue Feb 23 2016 - 02:08:26 PST)
- [AMBER] parameter file for graphene oxide Jesmita Dhar (Tue Feb 23 2016 - 03:34:23 PST)
- [AMBER] Fwd: cpinutil.py problem Elisa Pieri (Tue Feb 23 2016 - 07:39:38 PST)
- [AMBER] Dihedral parameters Jungho Yang (Tue Feb 23 2016 - 07:54:36 PST)
- [AMBER] Nucleic acid builder yhzahsc (Tue Feb 23 2016 - 18:04:39 PST)
- [AMBER] manually addition of parameters in frcmod file Mongam Riba (Tue Feb 23 2016 - 22:22:55 PST)
- [AMBER] Query regarding extracting protons from coordinate/trajectory file Madhura De (Wed Feb 24 2016 - 00:42:16 PST)
- [AMBER] Typing {} in Xleap Mahdieh Hadi (Wed Feb 24 2016 - 01:48:28 PST)
- Re: [AMBER] How to transfer amino acid sequence to Xleap. Mahdieh Hadi (Wed Feb 24 2016 - 02:54:20 PST)
- [AMBER] Query: extracting protons from trajectory/coordinate file Madhura De (Wed Feb 24 2016 - 03:52:00 PST)
- [AMBER] error in running rmsf command cpptraj Saman Yousuf ali (Wed Feb 24 2016 - 06:01:16 PST)
- [AMBER] Thermodynamic Integration Vertika Gautam (Wed Feb 24 2016 - 22:44:05 PST)
- [AMBER] Ph.D. position, Nancy, France Gerald Monard (Thu Feb 25 2016 - 00:39:31 PST)
- [AMBER] problem running MD for diphosphoric acid anion necmettin pirinccioglu (Thu Feb 25 2016 - 00:48:45 PST)
- [AMBER] Minimization error using Sander Anna Cebrian Prats (Thu Feb 25 2016 - 02:17:15 PST)
- [AMBER] Maximum input value for the isothermal compressibility in AMBER BLEY Michael (Thu Feb 25 2016 - 05:25:55 PST)
- [AMBER] Question regarding protein-Dna binding free energy Mahdieh Hadi (Thu Feb 25 2016 - 06:25:54 PST)
- [AMBER] MMGBSA error Indrajit Deb (Thu Feb 25 2016 - 09:24:38 PST)
- [AMBER] the angle between two axis maryam azimzadehirani (Thu Feb 25 2016 - 23:20:57 PST)
- [AMBER] error in sqm.out file Jesmita Dhar (Fri Feb 26 2016 - 00:15:31 PST)
- [AMBER] Problem with HIS/HIE residue and ff14SB force field Casalini Tommaso (Fri Feb 26 2016 - 02:20:02 PST)
- [AMBER] Regarding trajectory analysis using CPPTRAJ Sivanandam M (Fri Feb 26 2016 - 02:38:17 PST)
- [AMBER] Gaussian error with MCPB ion modeling calculation anu chandra (Fri Feb 26 2016 - 03:20:22 PST)
- [AMBER] Regarding caution message in the out file with pmemd.cuda.MPI anu chandra (Fri Feb 26 2016 - 03:28:45 PST)
- [AMBER] Pdb file to Mol2 Mahdieh Hadi (Fri Feb 26 2016 - 04:03:47 PST)
- [AMBER] Duration parmchk Stefano Sarao S215563 (Fri Feb 26 2016 - 04:41:54 PST)
- [AMBER] External library for leap Anna Cebrian Prats (Fri Feb 26 2016 - 05:14:28 PST)
- Re: [AMBER] AMBER Digest, Vol 1497, Issue 1 necmettin pirinccioglu (Fri Feb 26 2016 - 05:21:53 PST)
- [AMBER] waters inside cavity Elisa Pieri (Fri Feb 26 2016 - 07:00:54 PST)
- [AMBER] How to analyze mutational free energy difference? Mijiddorj Batsaikhan (Fri Feb 26 2016 - 23:34:20 PST)
- [AMBER] gzip -9 heat.mdcrd Error Mahdieh Hadi (Sat Feb 27 2016 - 06:27:03 PST)
- [AMBER] draw vector along axis of an alpha helix Emilio Angelina (Sat Feb 27 2016 - 07:50:28 PST)
- [AMBER] How to separate a protein complex to its components Mahdieh Hadi (Sat Feb 27 2016 - 23:39:00 PST)
- [AMBER] Bounds command with GIst peter.schmidtke.discngine.servier.com (Mon Feb 29 2016 - 02:35:04 PST)
- [AMBER] Preparing needed input files for TI Mahdieh Hadi (Mon Feb 29 2016 - 03:26:02 PST)
- [AMBER] Need Amber entropy calculated values Ayesha Kanwal (Mon Feb 29 2016 - 06:48:41 PST)
- Re: [AMBER] reading Amber trajectory files with chamber topology file Daniel Roe (Mon Feb 29 2016 - 07:42:01 PST)
- [AMBER] more extra points needed Ivanov, Maxim (Mon Feb 29 2016 - 09:15:17 PST)
- [AMBER] EPtot, Angle, Bond, Dihed Starovoytov, Oleg (Mon Feb 29 2016 - 18:02:26 PST)
- Re: [AMBER] Inquiry regarding amber installation Nhai (Mon Feb 29 2016 - 23:25:04 PST)
- Last message date: Mon Feb 29 2016 - 23:30:07 PST
- Archived on: Wed Dec 25 2024 - 05:55:19 PST
