Amber Archive Oct 2013 by thread
- [AMBER] RED-VIII.52 Problem--cannot find scratch file and punch file Dongshan Wei (Mon Sep 30 2013 - 10:56:42 PDT)
- [AMBER] MMPBSA.py MPI problem on TACC Stampede Sorensen, Jesper (Mon Sep 30 2013 - 17:55:49 PDT)
- Re: [AMBER] Erro in the Thermodynamic Intergration using soft core potentials" 冉挺 (Tue Oct 01 2013 - 02:17:00 PDT)
- [AMBER] Ambiguity in PMF calculated from umbrella sampling of a dihedral angle Mohan Pradhan (Tue Oct 01 2013 - 04:11:32 PDT)
- Re: [AMBER] Use of Langevin Thermostat with Amoeba force field David A Case (Tue Oct 01 2013 - 04:34:24 PDT)
- [AMBER] Modified Cysteine Devlina Chakravarty (Tue Oct 01 2013 - 04:36:09 PDT)
- Re: [AMBER] Generating topology files for two proteins in a single input pdb David A Case (Tue Oct 01 2013 - 04:43:07 PDT)
- Re: [AMBER] problem with addIons in tleap David A Case (Tue Oct 01 2013 - 04:44:03 PDT)
- [AMBER] Problem in antechamber execution Problem in antechamber execution problem in antechamber execution Tanmoy Paul (Tue Oct 01 2013 - 08:15:21 PDT)
- [AMBER] about error with "Must have more residues than processors!" Biao Ma (Tue Oct 01 2013 - 09:00:20 PDT)
- Re: [AMBER] Fwd: DMPC GAFF lipid membrane is freezing at 303 K. Ross Walker (Tue Oct 01 2013 - 09:04:27 PDT)
- Re: [AMBER] rotational diffusion error Vijay Manickam Achari (Tue Oct 01 2013 - 19:49:18 PDT)
- Re: [AMBER] Temperature based trajectory in REMD Gargi Borgohai (Wed Oct 02 2013 - 02:05:13 PDT)
- [AMBER] Predicting druggable hotspots anu chandra (Wed Oct 02 2013 - 03:36:15 PDT)
- [AMBER] PROBLEM USING ANTECHAMBER Tanmoy Paul (Wed Oct 02 2013 - 05:36:47 PDT)
- [AMBER] About INP in case of MS=1 Hiromasa WATANABE (Wed Oct 02 2013 - 22:55:00 PDT)
- [AMBER] The Error when I run MdoutAnalysizer.py Biao Ma (Wed Oct 02 2013 - 23:41:37 PDT)
- [AMBER] Questions about VDW process of thermodynamic integration method 袁丹丹 (Thu Oct 03 2013 - 05:57:43 PDT)
- [AMBER] Questions about VDW process of thermodynamic integration method 袁丹丹 (Thu Oct 03 2013 - 06:06:54 PDT)
- [AMBER] Replica exchange umbrella sampling Fabrício Bracht (Fri Oct 04 2013 - 00:00:52 PDT)
- [AMBER] QM/MM MMPBSA Jacopo Sgrignani (Fri Oct 04 2013 - 01:18:10 PDT)
- [AMBER] ITN Marie Curie positions available for early-stage researchers Paolo Ruggerone (Fri Oct 04 2013 - 02:25:08 PDT)
- [AMBER] About the Mg charge in AMBER FF George Patargias (Fri Oct 04 2013 - 02:28:36 PDT)
- [AMBER] changeLJ14Pair CHAMI F. (Fri Oct 04 2013 - 04:52:24 PDT)
- [AMBER] Regarding addition of DL_Poly Inversion potential in Amber MOHD HOMAIDUR RAHMAN (Fri Oct 04 2013 - 05:17:33 PDT)
- [AMBER] Reading NetCDF file Uday Midya (Fri Oct 04 2013 - 05:46:46 PDT)
- [AMBER] Regarding addition of DL_Poly Inversion and three body potential in Amber MOHD HOMAIDUR RAHMAN (Fri Oct 04 2013 - 10:09:02 PDT)
- [AMBER] A problem with a specific input in pmemd.cuda.MPI. 4 GPU fails, 2 GPU works fine. Jeremy Hallum (Fri Oct 04 2013 - 11:26:52 PDT)
- [AMBER] NAB : Orienting a molecule HIMANSHU JOSHI (Fri Oct 04 2013 - 11:33:48 PDT)
- [AMBER] Generating reservoirs for non-Boltzmann T-RREMD Eugene Yedvabny (Fri Oct 04 2013 - 12:50:42 PDT)
- [AMBER] MPI install with openmpi Makoto Chikira (Sat Oct 05 2013 - 00:33:21 PDT)
- [AMBER] sumit.saurav.jain.gmail.com has indicated you're a friend. Accept? sumit.saurav.jain.gmail.com (Sat Oct 05 2013 - 16:31:25 PDT)
- [AMBER] Error in antechamber Installation Vijayalaxmi Sahoo (Sat Oct 05 2013 - 22:27:27 PDT)
- [AMBER] Hydrogen Bond Term in Amber ff99SB forcefield Asmit Bhowmick (Sun Oct 06 2013 - 18:48:52 PDT)
- [AMBER] Phenyl-boronic acid derivatives lacking of parameter in Mol2 file 陈发生 (Sun Oct 06 2013 - 20:48:07 PDT)
- [AMBER] Generation of melting curves Gargi Borgohai (Sun Oct 06 2013 - 20:59:11 PDT)
- [AMBER] Soft-core questions for TI method yuandandan (Mon Oct 07 2013 - 00:26:16 PDT)
- [AMBER] problem in creating .mol2 and .frcmod files Vijayalaxmi Sahoo (Mon Oct 07 2013 - 06:48:50 PDT)
- [AMBER] ambertools patch 19 fails Matthew Wampole (Mon Oct 07 2013 - 07:57:46 PDT)
- [AMBER] Parameter Discrepancy in Walker Tutorial B1? Robert Molt (Mon Oct 07 2013 - 18:58:12 PDT)
- [AMBER] Block Averaging of Trajectory Mathias Gruber (Tue Oct 08 2013 - 06:03:23 PDT)
- [AMBER] GAFF angle term constants with phosphor or sulphur Igor Marques (Tue Oct 08 2013 - 06:30:49 PDT)
- [AMBER] ERROR in DISTANCE RESTRAINT Sourav Purohit (Tue Oct 08 2013 - 10:21:26 PDT)
- [AMBER] Scaling of multi GPU runs peter.stauffert.boehringer-ingelheim.com (Tue Oct 08 2013 - 10:55:29 PDT)
- [AMBER] Amber99SB force field Shomesankar Bhunia (Tue Oct 08 2013 - 11:13:52 PDT)
- Re: [AMBER] Problem in creating .mol2 and .frcmod files Vijayalaxmi Sahoo (Wed Oct 09 2013 - 06:38:28 PDT)
- [AMBER] AMBER ff99Sbildn Shomesankar Bhunia (Wed Oct 09 2013 - 07:20:48 PDT)
- [AMBER] Shifting molecules by a box length Heribert Reis (Wed Oct 09 2013 - 07:53:29 PDT)
- [AMBER] Distributions of the phi and psi torsion angles during MD simulations Baptiste Legrand (Thu Oct 10 2013 - 00:51:54 PDT)
- [AMBER] Questions about softcore part yuandandan (Thu Oct 10 2013 - 02:22:14 PDT)
- [AMBER] High energy in per-residue MMPBSA calculation anu chandra (Thu Oct 10 2013 - 05:22:50 PDT)
- [AMBER] How to run npt simulation if IFBOX=0 in .prmtop file? Dongshan Wei (Thu Oct 10 2013 - 05:43:30 PDT)
- [AMBER] Fwd: Shifting molecules by a box length Heribert Reis (Thu Oct 10 2013 - 07:41:11 PDT)
- [AMBER] solvate box Rasha Alqus (Thu Oct 10 2013 - 08:35:50 PDT)
- [AMBER] SHAKE flucatuation Zhiye Tang (Thu Oct 10 2013 - 11:54:30 PDT)
- [AMBER] MMPBSA error Symon Gathiaka (Thu Oct 10 2013 - 12:36:02 PDT)
- [AMBER] Stuck on AmberTools bugfix.23 Terry M. Gray (Thu Oct 10 2013 - 14:52:14 PDT)
- [AMBER] I/O errors while using CHARMM psf with CHAMBER Debayan Chakraborty (Thu Oct 10 2013 - 16:23:01 PDT)
- [AMBER] Segmentation fault in tleap mmalett.nmt.edu (Thu Oct 10 2013 - 16:53:58 PDT)
- [AMBER] Protein-DNA covalent bond John Gehman (Thu Oct 10 2013 - 17:51:55 PDT)
- [AMBER] Stuck on AmberTools12 bug fix.23 Terry M. Gray (Thu Oct 10 2013 - 20:25:48 PDT)
- [AMBER] How to calculate the free energy change of a chemical reaction by the thermodynamic integration approach? cwt (Thu Oct 10 2013 - 23:18:00 PDT)
- Re: [AMBER] [Amber]Question about softcore yuandandan (Fri Oct 11 2013 - 06:48:50 PDT)
- [AMBER] AmberTools13 and Amber11 Alan (Fri Oct 11 2013 - 08:07:10 PDT)
- [AMBER] tleap cannot handle dummies in the middle? Hannes Loeffler (Fri Oct 11 2013 - 09:18:43 PDT)
- Re: [AMBER] MMPSA: PB Bomb in pb_aaradi(): ... psu4.uic.edu (Fri Oct 11 2013 - 10:39:56 PDT)
- [AMBER] running MMPBSA.py on an NMR ensemble Thomas Evangelidis (Sat Oct 12 2013 - 06:50:54 PDT)
- [AMBER] Questions regarding AMBER Kamali Sripathi (Sat Oct 12 2013 - 07:22:10 PDT)
- Re: [AMBER] How do I use MMPBSA.py for namd .dcd file? sudipta (Sat Oct 12 2013 - 10:31:35 PDT)
- [AMBER] Iron(III)Hydroxide complexing with Enterobactin (quantum chemistry calculations?) Jonathan Saboury (Sat Oct 12 2013 - 21:43:07 PDT)
- [AMBER] Problem in deriving RESP charges with RED-3.52 tools Sajeewa Pemasinghe (Sat Oct 12 2013 - 23:12:39 PDT)
- [AMBER] Problem about water Cap with igb=10 Tong ZHU (Sun Oct 13 2013 - 07:11:39 PDT)
- [AMBER] DNA with NAB Jio M (Sun Oct 13 2013 - 15:47:52 PDT)
- [AMBER] PMEMD trajectory and MMPBSA Sangita Kachhap (Sun Oct 13 2013 - 22:46:51 PDT)
- Re: [AMBER] inquiry Vaibhav Dixit (Mon Oct 14 2013 - 02:43:03 PDT)
- [AMBER] about rms atomic fluctuation for protein crystal .thank you very much! Yongxiu Li (Mon Oct 14 2013 - 04:36:06 PDT)
- [AMBER] Exceed character limit in bellyrestraint mask selection Mike Limb (Tue Oct 15 2013 - 08:29:18 PDT)
- [AMBER] Constant pH with ligand Nicole Ippolito (Tue Oct 15 2013 - 14:55:52 PDT)
- [AMBER] PMF for 2 Arginines Nihal Korkmaz (Tue Oct 15 2013 - 20:44:52 PDT)
- [AMBER] PTRAJ - Problem with inserting TER card anu chandra (Wed Oct 16 2013 - 00:56:09 PDT)
- [AMBER] RESP charge calculation problem for SO4 -2 group Bajarang Kumbhar (Wed Oct 16 2013 - 05:00:00 PDT)
- [AMBER] strange behavior of MCPB houcemeddine (Wed Oct 16 2013 - 08:50:03 PDT)
- [AMBER] Error message from pmemd.cuda Brian Radak (Wed Oct 16 2013 - 13:30:00 PDT)
- [AMBER] ratio between frames for MM/PBSA and frames for normal mode calculations Thomas Evangelidis (Wed Oct 16 2013 - 16:10:54 PDT)
- [AMBER] Python script to reweight aMD simulations filip fratev (Wed Oct 16 2013 - 21:02:59 PDT)
- [AMBER] unique atoms in TI softcore Hannes Loeffler (Thu Oct 17 2013 - 03:01:11 PDT)
- [AMBER] Doubt regarding the metadynamics simulation Ravi Tripathi (Thu Oct 17 2013 - 07:59:31 PDT)
- [AMBER] CYM residue problem(MCPB) houcemeddine (Thu Oct 17 2013 - 08:29:17 PDT)
- [AMBER] problem for prmtop and inpcrd file generation Bajarang Kumbhar (Thu Oct 17 2013 - 22:44:42 PDT)
- [AMBER] How to deal with duplicate frames during MD? rohitarora10.gmail.com (Fri Oct 18 2013 - 01:34:38 PDT)
- [AMBER] problem with heme parameters bound to HIS moitrayee.mbu.iisc.ernet.in (Fri Oct 18 2013 - 02:05:48 PDT)
- [AMBER] Running simultaneously AMBER jobs in CPU and GPU Muthukumaran R (Fri Oct 18 2013 - 04:24:54 PDT)
- [AMBER] parmchk doesn't recognize the changes made in leaprc.ff99SB and parm.99 Sajeewa Pemasinghe (Fri Oct 18 2013 - 06:06:36 PDT)
- [AMBER] Fwd: FW: Fwd: DMPC GAFF lipid membrane is freezing at 303 K. Subbarao Kanchi (Fri Oct 18 2013 - 07:21:36 PDT)
- [AMBER] PROBLEM IN QM/MM RUN Tanmoy Paul (Sat Oct 19 2013 - 00:17:48 PDT)
- [AMBER] output of diffusion data doesn't show two columns for big number values Vijay Manickam Achari (Sat Oct 19 2013 - 04:01:58 PDT)
- [AMBER] problem using the R.E.D server output Bajarang Kumbhar (Mon Oct 21 2013 - 01:58:30 PDT)
- [AMBER] optimization using gaussian and RESP using antechamber Bajarang Kumbhar (Mon Oct 21 2013 - 04:29:16 PDT)
- [AMBER] example of MTKpp on Ambertools 13 setyanto md (Mon Oct 21 2013 - 07:18:30 PDT)
- [AMBER] MMPBSA problem with CHAMBER generated topology file Uday Midya (Mon Oct 21 2013 - 20:15:06 PDT)
- [AMBER] Fwd: requesting in executing CHAMBER Soumya Lipsa Rath (Mon Oct 21 2013 - 22:57:30 PDT)
- [AMBER] PCA analysis and amber prmtop file Neha Gandhi (Tue Oct 22 2013 - 01:29:37 PDT)
- [AMBER] namelist input > 80 columns thomas.fox.boehringer-ingelheim.com (Tue Oct 22 2013 - 02:41:32 PDT)
- [AMBER] High Temperature at NSTEP = 0 Alessandra Lacetera (Tue Oct 22 2013 - 08:41:12 PDT)
- [AMBER] Script? Beale, John (Tue Oct 22 2013 - 10:30:30 PDT)
- [AMBER] Update 21 for Amber 12: EXTERN QM/MM interface Andreas Goetz (Tue Oct 22 2013 - 15:44:03 PDT)
- [AMBER] MMPBSA calculation Mary Varughese (Tue Oct 22 2013 - 15:57:59 PDT)
- [AMBER] Terachem tests with trial version Fabrício Bracht (Wed Oct 23 2013 - 00:21:47 PDT)
- [AMBER] MMPBSA.py error Rasha Alqus (Wed Oct 23 2013 - 03:11:53 PDT)
- [AMBER] Leap ff10 and Sodium ion Johannes Zuegg (Wed Oct 23 2013 - 17:05:56 PDT)
- [AMBER] AMBERTOOLS13 test error: 01_Generalized_Born and 03_Alanine_Scanning marco.molinari (Thu Oct 24 2013 - 03:55:11 PDT)
- [AMBER] Regarding radial distribution function MOHD HOMAIDUR RAHMAN (Thu Oct 24 2013 - 04:46:48 PDT)
- [AMBER] MMPBSA.py problem Indrajit Deb (Thu Oct 24 2013 - 05:31:01 PDT)
- [AMBER] MMGBSA, Generalized Born, protein-nucleic acid complex Vlad Cojocaru (Thu Oct 24 2013 - 05:53:45 PDT)
- Re: [AMBER] igb=7, 8 incompatible with the ILDN modifications of ff99SB Vlad Cojocaru (Thu Oct 24 2013 - 07:35:17 PDT)
- [AMBER] parmed.py bug when using the "parmout" command ? Vlad Cojocaru (Thu Oct 24 2013 - 07:55:12 PDT)
- [AMBER] MMPBSA, ligand sequence maghtar (Fri Oct 25 2013 - 03:29:28 PDT)
- Re: [AMBER] AMBERTOOLS13 test error: 01_Generalized_Born and, 03_Alanine_Scanning (Jason Swails) marco.molinari (Fri Oct 25 2013 - 05:42:27 PDT)
- [AMBER] ionic strength conversion between MMPBSA.py and PBSA Vlad Cojocaru (Fri Oct 25 2013 - 07:21:12 PDT)
- [AMBER] About foundations of T-REMD Francesco Pietra (Fri Oct 25 2013 - 07:28:51 PDT)
- [AMBER] Making Au surface using xleap Hoshin Kim (Fri Oct 25 2013 - 08:39:30 PDT)
- [AMBER] why are pres_X, pres_Y, and pres_Z different? Jose Borreguero (Fri Oct 25 2013 - 08:42:02 PDT)
- [AMBER] mmpbsa_py_energy and PBSA options Vlad Cojocaru (Fri Oct 25 2013 - 09:02:39 PDT)
- [AMBER] Constant pH with enzyme and substrate Nicole Ippolito (Fri Oct 25 2013 - 11:00:28 PDT)
- [AMBER] Single quotes in AMBER manual Jonathan Sheehan (Fri Oct 25 2013 - 12:40:34 PDT)
- [AMBER] How to use TIP4P/2005 water model Deborah Howe (Fri Oct 25 2013 - 19:57:22 PDT)
- [AMBER] Difference between the .crd file format in AMBER-7 and AMBER-12 anu chandra (Sat Oct 26 2013 - 00:40:19 PDT)
- [AMBER] QM/MM interfacing Gaussian Ahmed Ayoub (Sat Oct 26 2013 - 04:21:45 PDT)
- [AMBER] ptraj - loading list of frames Mark Healey (Sat Oct 26 2013 - 13:24:06 PDT)
- [AMBER] idecomp does not work for canonical-residues kurisaki (Sat Oct 26 2013 - 23:43:00 PDT)
- Re: [AMBER] FW: Fwd: DMPC GAFF lipid membrane is freezing at 303 K. Subbarao Kanchi (Sun Oct 27 2013 - 17:39:15 PDT)
- [AMBER] problem after minimization of pure DMF Sohag Biswas (Sun Oct 27 2013 - 21:09:31 PDT)
- [AMBER] Error - PMEMD.MPI cannot understand line in rst file rohitarora10.gmail.com (Mon Oct 28 2013 - 04:34:22 PDT)
- [AMBER] problem in saving prmtop file in ff12SB force field Subrata Paul (Mon Oct 28 2013 - 06:58:09 PDT)
- [AMBER] huge values for the vibrational entropy from ptraj Vlad Cojocaru (Tue Oct 29 2013 - 01:56:31 PDT)
- [AMBER] acclerated molecular dynamics alphaP Nicole Ippolito (Tue Oct 29 2013 - 07:59:22 PDT)
- [AMBER] calculatie the energy between two groups of atoms from an MD trajectory, is it possible? Jose Borreguero (Tue Oct 29 2013 - 13:37:07 PDT)
- [AMBER] Installation error Dhananjay (Wed Oct 30 2013 - 01:41:49 PDT)
- Re: [AMBER] Trajectory determination and directionality in TI with softcore potentials Ying-Chieh Sun (Wed Oct 30 2013 - 01:43:06 PDT)
- [AMBER] Free binding energy calculations for Zinc dependent ligands Tivani Mashamba (Wed Oct 30 2013 - 02:09:05 PDT)
- [AMBER] Amber 12 Updater error on Arch linux M. Reza Ganjalikhany (Wed Oct 30 2013 - 02:52:16 PDT)
- [AMBER] Hbond analysis Fabrício Bracht (Wed Oct 30 2013 - 11:34:26 PDT)
- Re: [AMBER] AMBER Digest, Vol 659, Issue 1 Sohag Biswas (Wed Oct 30 2013 - 23:23:10 PDT)
- [AMBER] Monte Carlo Method/Simulation in AMBER 12 Emmanuel Oluwatobi SALAWU (Thu Oct 31 2013 - 03:38:15 PDT)
- [AMBER] About calculating entropy Olayide Arodola (Thu Oct 31 2013 - 04:26:52 PDT)
- [AMBER] mdcrd to dcd 石坪江梨花 (Thu Oct 31 2013 - 04:36:18 PDT)
- [AMBER] TI soft-core parameters Hamed S. Hayatshahi (Thu Oct 31 2013 - 13:13:54 PDT)
- Last message date: Thu Oct 31 2013 - 15:00:03 PDT
- Archived on: Fri Nov 22 2024 - 05:54:49 PST
