Amber Archive Sep 2013 by thread
- Re: [AMBER] problem installin amber9 in ubuntu 12.04 Jason Swails (Sat Aug 31 2013 - 22:01:54 PDT)
- [AMBER] Constraint failure in RATTLE algorithm occurs during NAMD simulation with amber force field sunyeping (Sun Sep 01 2013 - 07:31:07 PDT)
- [AMBER] compile ambertools with -nofftw3 sunyeping (Sun Sep 01 2013 - 20:37:44 PDT)
- [AMBER] deltaG binding obtained from AmberTools 12 and 13 are different Xioling Chuang (Mon Sep 02 2013 - 06:18:58 PDT)
- [AMBER] Problem passing cuda tests. Szymon Murawski (Mon Sep 02 2013 - 06:36:06 PDT)
- [AMBER] Distance restraint using com keyword Sun (Mon Sep 02 2013 - 07:27:50 PDT)
- [AMBER] issues with MMPBSA and explicit waters Alfredo Quevedo (Mon Sep 02 2013 - 07:39:19 PDT)
- [AMBER] best Generalized Born solvation model for intrinsically disordered peptides Thomas Evangelidis (Mon Sep 02 2013 - 13:48:12 PDT)
- [AMBER] Minimization terminates with unknown reason Xiaoquan Sun (Mon Sep 02 2013 - 13:59:18 PDT)
- [AMBER] RED-vIII.52 problems Julio Dominguez (Mon Sep 02 2013 - 18:58:41 PDT)
- [AMBER] some questions about PCA qiao xue (Mon Sep 02 2013 - 19:55:35 PDT)
- [AMBER] Sander aborted during the minimization of the whole system. X Sun (Mon Sep 02 2013 - 21:42:17 PDT)
- [AMBER] problem in installing AmberTools13 Vijay Manickam Achari (Mon Sep 02 2013 - 23:36:50 PDT)
- [AMBER] NaN problem with GTX680 JAVAD MAHMOUDZADEH (Tue Sep 03 2013 - 00:12:05 PDT)
- [AMBER] updates for amber12 bugfix18 & 19 fail Vijay Manickam Achari (Tue Sep 03 2013 - 01:08:15 PDT)
- [AMBER] NaN problem with GTX680 JAVAD MAHMOUDZADEH (Tue Sep 03 2013 - 05:18:20 PDT)
- [AMBER] missing loop Fabian Glaser (Tue Sep 03 2013 - 07:05:53 PDT)
- [AMBER] problem in running AMBER12 in GPU Sanjib Paul (Tue Sep 03 2013 - 08:01:24 PDT)
- Re: [AMBER] CHAMBER VDW energy in PBC Jun Feng (Tue Sep 03 2013 - 10:54:03 PDT)
- Re: [AMBER] CHAMBER: dihe energy in c36 vs c22 Jun Feng (Tue Sep 03 2013 - 14:32:19 PDT)
- [AMBER] problem with antechamber in ambertools 13 Rodrigo Salazar (Tue Sep 03 2013 - 18:01:44 PDT)
- Re: [AMBER] RED-vIII52 problems... Julio Dominguez (Wed Sep 04 2013 - 07:06:22 PDT)
- [AMBER] Amber Install Lindsay Morrison (Wed Sep 04 2013 - 10:45:27 PDT)
- [AMBER] Force constant in umbrella sampling Fabrício Bracht (Wed Sep 04 2013 - 13:02:59 PDT)
- [AMBER] Convert DCD to MDCRD, lose PBC. X Sun (Wed Sep 04 2013 - 14:54:18 PDT)
- Re: [AMBER] TI input files in A9 tutorial and Amber12 manual Hamed S. Hayatshahi (Wed Sep 04 2013 - 15:02:32 PDT)
- [AMBER] Questions about TI calculation yuandandan05 (Wed Sep 04 2013 - 18:24:30 PDT)
- [AMBER] make error in installing sander.APBS Asmita Gupta (Wed Sep 04 2013 - 23:35:34 PDT)
- [AMBER] hbond in Ambertools Neha Gandhi (Thu Sep 05 2013 - 00:31:47 PDT)
- [AMBER] Average Conformations from trajectory Covington, Cody Lance (Thu Sep 05 2013 - 06:33:39 PDT)
- [AMBER] Question about MMPBSA.py rohitarora10.gmail.com (Thu Sep 05 2013 - 08:16:51 PDT)
- Re: [AMBER] cpptraj removes velocities upon imaging Daniel Roe (Thu Sep 05 2013 - 10:45:23 PDT)
- Re: [AMBER] mmP(G)BSA correlation time psu4.uic.edu (Thu Sep 05 2013 - 12:13:16 PDT)
- [AMBER] update_amber script confuses Amber versions Robyn Ayscue (Thu Sep 05 2013 - 12:30:40 PDT)
- [AMBER] MMPBSA.py EPB problem with idecomp=3 Ryan Pavlovicz (Thu Sep 05 2013 - 16:17:02 PDT)
- [AMBER] For format correction after generating solvent file. Krati Sharma (Thu Sep 05 2013 - 20:25:19 PDT)
- [AMBER] How to get the prmtop and inpcrd files of melamine in Amber? 张明焜 (Thu Sep 05 2013 - 20:52:05 PDT)
- [AMBER] to generate a Glycine(NH2-CH2-COOH) complete prmtop file? 张明焜 (Fri Sep 06 2013 - 02:23:27 PDT)
- [AMBER] REMD jobs crashing repeatedly on GPUs Joe Passman (Fri Sep 06 2013 - 10:57:42 PDT)
- [AMBER] Xleap Lindsay Morrison (Fri Sep 06 2013 - 11:37:05 PDT)
- [AMBER] Are Amber able to analyze the feature of certain bond? X Sun (Fri Sep 06 2013 - 20:09:24 PDT)
- Re: [AMBER] rmsd 김준기 (Fri Sep 06 2013 - 19:57:20 PDT)
- [AMBER] hbond analysis Mary Varughese (Sat Sep 07 2013 - 00:19:29 PDT)
- [AMBER] Unable to run decomposition analysis using mmpbsa.py of amber12 Manikanthan Bhavaraju (Sat Sep 07 2013 - 16:21:48 PDT)
- [AMBER] GTX 600/700 benchmarks Parker de Waal (Sun Sep 08 2013 - 17:03:35 PDT)
- [AMBER] Question about QM/MM? X Sun (Sun Sep 08 2013 - 22:39:26 PDT)
- [AMBER] Issue with intramolecular pairwise-residue energy decomposition rohitarora10.gmail.com (Mon Sep 09 2013 - 00:33:23 PDT)
- [AMBER] Forcefield for lipopeptides Prasanna Venkatesh D (Mon Sep 09 2013 - 01:28:00 PDT)
- [AMBER] rmsd and hbond Mary Varughese (Mon Sep 09 2013 - 02:20:39 PDT)
- [AMBER] Different MMPBSA results in the use of sander and pmemd 千语千寻 (Mon Sep 09 2013 - 02:49:35 PDT)
- [AMBER] question of analyze matrix command of ptraj 张明焜 (Mon Sep 09 2013 - 03:52:12 PDT)
- [AMBER] Amber Tools cpptraj woes Geoffrey Gray (Mon Sep 09 2013 - 11:42:54 PDT)
- [AMBER] Unable to run decomposition analysis using mmpbsa.py of amber12 Manikanthan Bhavaraju (Mon Sep 09 2013 - 12:27:12 PDT)
- [AMBER] Error with NVT and NPT Simulations Kyler L Cook (Mon Sep 09 2013 - 13:28:29 PDT)
- [AMBER] atomic fluctuation and average structure Mary Varughese (Mon Sep 09 2013 - 17:55:54 PDT)
- [AMBER] Difference between atomtype s6 and sy? X Sun (Mon Sep 09 2013 - 21:16:08 PDT)
- [AMBER] REMD exchange Francesco Pietra (Tue Sep 10 2013 - 00:38:25 PDT)
- [AMBER] error in leap -- Glycam residue building lara lara (Tue Sep 10 2013 - 12:29:47 PDT)
- [AMBER] Question: MM/PBSA and MM/GBSA Hiromasa WATANABE (Tue Sep 10 2013 - 22:56:06 PDT)
- [AMBER] error in installing ambertools 1.5 Kumud Agarwal (Wed Sep 11 2013 - 00:08:08 PDT)
- [AMBER] Query on Alanine scanning Mannan (Wed Sep 11 2013 - 02:29:55 PDT)
- [AMBER] Fwd: DMPC GAFF lipid membrane is freezing at 303 K. Subbarao Kanchi (Wed Sep 11 2013 - 03:23:14 PDT)
- [AMBER] Path Setting arundhati dutta (Wed Sep 11 2013 - 12:27:47 PDT)
- [AMBER] query reg ptraj RMSD calculation Asmita Gupta (Thu Sep 12 2013 - 06:45:18 PDT)
- [AMBER] glycam - leap error lara lara (Thu Sep 12 2013 - 10:31:16 PDT)
- [AMBER] antechamber no convergence Jianhui Tian (Thu Sep 12 2013 - 12:05:18 PDT)
- [AMBER] Antechamber Jasim, Mahmood (Student) (Fri Sep 13 2013 - 06:15:48 PDT)
- [AMBER] Setting forcefield parameters Tanmoy Paul (Fri Sep 13 2013 - 06:44:28 PDT)
- [AMBER] Assigning atom type. Sanjib Paul (Fri Sep 13 2013 - 06:52:35 PDT)
- [AMBER] How do I use MMPBSA.py for namd .dcd file? sudipta (Fri Sep 13 2013 - 07:45:50 PDT)
- [AMBER] Three body potential MOHD HOMAIDUR RAHMAN (Fri Sep 13 2013 - 11:47:50 PDT)
- [AMBER] running simulation using increased number of cores onetwo (Fri Sep 13 2013 - 21:13:50 PDT)
- [AMBER] mmpbsa number of atoms issues Ayesha Fatima (Sat Sep 14 2013 - 03:44:31 PDT)
- [AMBER] How to choose ntc value? X Sun (Sat Sep 14 2013 - 10:55:08 PDT)
- Re: [AMBER] mpi4py building error during AmberTools 13 install sunyeping (Sat Sep 14 2013 - 10:18:23 PDT)
- [AMBER] compile ambertools 13 with -nofftw3 sunyeping (Sat Sep 14 2013 - 10:23:21 PDT)
- [AMBER] significance of 3-10 helixes in Secstruct Chinthaka Ratnaweera (Sat Sep 14 2013 - 14:51:30 PDT)
- Re: [AMBER] namd-l: MMPBSA calculation using NAMD sunyeping (Sun Sep 15 2013 - 21:56:31 PDT)
- [AMBER] Cpptraj bug - low priority Sorensen, Jesper (Mon Sep 16 2013 - 00:23:07 PDT)
- [AMBER] MMPBSA.py: energy decomposition Kshatresh Dutta Dubey (Mon Sep 16 2013 - 01:01:11 PDT)
- [AMBER] About T-REMD convergence Francesco Pietra (Mon Sep 16 2013 - 02:17:24 PDT)
- [AMBER] radial distribution function results Vijay Manickam Achari (Mon Sep 16 2013 - 02:25:15 PDT)
- [AMBER] rem.log file generated in REMD simulation Gargi Borgohai (Mon Sep 16 2013 - 06:00:46 PDT)
- [AMBER] issue running AMBER on double sockets hexa cores Pascal Bonnet (Mon Sep 16 2013 - 11:42:12 PDT)
- [AMBER] How to do clustering analysis by ptraj? Biao Ma (Tue Sep 17 2013 - 00:43:33 PDT)
- [AMBER] Calculate average property Gargi Borgohai (Tue Sep 17 2013 - 04:03:42 PDT)
- [AMBER] Trajectory determination and directionality in TI with softcore potentials Ryan Muraglia (Tue Sep 17 2013 - 12:39:22 PDT)
- [AMBER] MMPBSA/GBSA error Sumra Wajid Abbasi 30-FBAS/MSBI/F09 (Wed Sep 18 2013 - 00:27:47 PDT)
- [AMBER] problems with reimage cmd Chiara Pallara (Wed Sep 18 2013 - 01:11:50 PDT)
- [AMBER] Hydrogen bond analysis problem Sumra Wajid Abbasi 30-FBAS/MSBI/F09 (Wed Sep 18 2013 - 02:50:06 PDT)
- [AMBER] CPPtraj not producing outputs Neha Sikka (Wed Sep 18 2013 - 08:51:29 PDT)
- [AMBER] Ti problem - system must be very inhomogeneous Fabrício Bracht (Wed Sep 18 2013 - 13:02:25 PDT)
- [AMBER] RESP_ A1-charge failed Shomesankar Bhunia (Wed Sep 18 2013 - 23:16:30 PDT)
- [AMBER] PCA analysis and porcupine plots Soma Ghosh (Thu Sep 19 2013 - 22:58:54 PDT)
- [AMBER] Adding an extra non-bonded pair list jfloresc.andrew.cmu.edu (Fri Sep 20 2013 - 11:40:11 PDT)
- [AMBER] Word of caution for Xcode 5, Mac OS X Julio Dominguez (Fri Sep 20 2013 - 18:58:27 PDT)
- Re: [AMBER] DMPC GAFF lipid membrane is freezing at 303 K. Subbarao Kanchi (Sat Sep 21 2013 - 00:16:02 PDT)
- [AMBER] problem in installation esther nehu (Sat Sep 21 2013 - 02:58:42 PDT)
- [AMBER] AMBER: the units of the physical quantities hustgt08 (Sat Sep 21 2013 - 05:08:34 PDT)
- [AMBER] DMPC GAFF lipid membrane is freezing at 303 K. Subbarao Kanchi (Sun Sep 22 2013 - 02:48:28 PDT)
- [AMBER] water cluster analysis Subrata Paul (Sun Sep 22 2013 - 06:46:45 PDT)
- [AMBER] help with RESP tutorial using antechamber and gaussian Fengxue Li (Sun Sep 22 2013 - 19:29:59 PDT)
- [AMBER] AMBER version Mary Varughese (Mon Sep 23 2013 - 01:27:28 PDT)
- [AMBER] Jobs hanging on parallel CUDA without producing output Nils Oberhauser (Mon Sep 23 2013 - 03:12:59 PDT)
- [AMBER] AmberTools update 17 for CPPTRAJ Daniel Roe (Mon Sep 23 2013 - 08:03:06 PDT)
- [AMBER] How to use makeDIST_RST without MAPping? Jan-Philip Gehrcke (Mon Sep 23 2013 - 08:43:36 PDT)
- [AMBER] Coordinate of excess charge (proton) Fabrício Bracht (Mon Sep 23 2013 - 14:48:04 PDT)
- [AMBER] REGARDING UMBRELLA SAMPLING TUTORIAL Sourav Purohit (Mon Sep 23 2013 - 20:03:26 PDT)
- [AMBER] energetics of displacing water molecules from protein binding sites Changqing Yan (Mon Sep 23 2013 - 21:09:51 PDT)
- [AMBER] how to use commands “sequence”, “set”, “add”, “bond”, “ impose” or someothers necessary to add a –H and a –OH to the GLY 张明焜 (Mon Sep 23 2013 - 23:53:36 PDT)
- [AMBER] help with RESP tutorial using antechambe Fengxue Li (Tue Sep 24 2013 - 00:44:19 PDT)
- [AMBER] Temperature based trajectory in REMD Gargi Borgohai (Tue Sep 24 2013 - 05:44:43 PDT)
- [AMBER] Help on MMPBSA script R R S Pissurlenkar (Tue Sep 24 2013 - 05:59:21 PDT)
- [AMBER] Protonated Histidine (HIP) charges in Amber03 (AMBERFF03) Adam (Tue Sep 24 2013 - 12:07:25 PDT)
- [AMBER] Norleucine Parameters Adam (Tue Sep 24 2013 - 12:16:46 PDT)
- [AMBER] AmberTools 1.5.2 compilation Error: Return type mismatch of function 'cgalf' at (1) (REAL(8)/REAL(4)) harry mangalam (Tue Sep 24 2013 - 12:19:37 PDT)
- [AMBER] HEATING run using SANDER Sourav Purohit (Tue Sep 24 2013 - 12:30:12 PDT)
- [AMBER] Running Amber on a SGI cluster George Tzotzos (Tue Sep 24 2013 - 12:32:25 PDT)
- [AMBER] Superposition of 3D structures for wid type and mutants with VMD Yanyan ZHU (Tue Sep 24 2013 - 18:46:57 PDT)
- [AMBER] Probelm with antechamber for resp charge derivation Fengxue Li (Tue Sep 24 2013 - 20:23:37 PDT)
- [AMBER] Sodium Ion Citation Lars Holte (Tue Sep 24 2013 - 21:27:07 PDT)
- [AMBER] Problem in antechamber execution Tanmoy Paul (Tue Sep 24 2013 - 22:55:34 PDT)
- [AMBER] problem running antechamber - amber Version 10 Concha, Monica (Wed Sep 25 2013 - 07:17:03 PDT)
- [AMBER] the difference between proper torsion and improper torsion Ming Huang (Wed Sep 25 2013 - 08:43:02 PDT)
- [AMBER] Problems with sander.MPI Moacyr Comar (Wed Sep 25 2013 - 10:12:35 PDT)
- [AMBER] R.E.D. double bond revisit psu4.uic.edu (Wed Sep 25 2013 - 10:51:09 PDT)
- [AMBER] November 11 deadline for ACS COMP Division Awards for Spring 2014 meeting Carlos Simmerling (Wed Sep 25 2013 - 10:17:35 PDT)
- [AMBER] openmp on 64core/AMD vs MPI over IB on multiple nodes harry mangalam (Wed Sep 25 2013 - 12:42:06 PDT)
- [AMBER] CORRECTION: Oct 22 deadline for ACS COMP Division Awards for Spring 2014 meeting Carlos Simmerling (Wed Sep 25 2013 - 12:34:32 PDT)
- [AMBER] AMBER on AWS - Beta testers wanted. Ross Walker (Wed Sep 25 2013 - 13:14:11 PDT)
- [AMBER] protein in popc bilayer simulation Wang Chern Hoe (Dr) (Wed Sep 25 2013 - 19:46:43 PDT)
- [AMBER] Generating periodic box parameters for a pdb file already solvated Sajeewa Pemasinghe (Wed Sep 25 2013 - 22:54:22 PDT)
- [AMBER] No torsion terms for N-Cg-Cg-Ng sunita gupta (Thu Sep 26 2013 - 00:08:32 PDT)
- [AMBER] Fwd: Re: R.E.D. double bond revisit FyD (Thu Sep 26 2013 - 00:10:02 PDT)
- [AMBER] How do I read a trail file in the format of NetCDF with VMD ? Yanyan ZHU (Thu Sep 26 2013 - 02:00:40 PDT)
- [AMBER] Number of residues in a solvent box Chinthaka Ratnaweera (Thu Sep 26 2013 - 09:53:27 PDT)
- [AMBER] cytidine triphosphate Hallel Freedman (Thu Sep 26 2013 - 11:46:32 PDT)
- [AMBER] Using NMODE with NAMD trajectories Valeria Marquez (Thu Sep 26 2013 - 11:50:38 PDT)
- [AMBER] shortest distance Norah Schlacter (Thu Sep 26 2013 - 14:19:20 PDT)
- [AMBER] Error in QM/MM calculations Cuiyl (Thu Sep 26 2013 - 19:00:00 PDT)
- [AMBER] Superposition of 3D structures for wid type and mutants with VMD Yanyan ZHU (Thu Sep 26 2013 - 19:16:36 PDT)
- [AMBER] histidine_residue Shomesankar Bhunia (Fri Sep 27 2013 - 02:24:07 PDT)
- [AMBER] Oct 22nd deadline for ACS COMP division awards for Spring national meeting Carlos Simmerling (Fri Sep 27 2013 - 06:41:27 PDT)
- [AMBER] problem with addIons in tleap Fengxue Li (Fri Sep 27 2013 - 06:50:22 PDT)
- [AMBER] NAMD_AMBER_MD Shomesankar Bhunia (Fri Sep 27 2013 - 08:42:49 PDT)
- [AMBER] Changing the Lennard Jones potential Pengzhi Zhang (Sat Sep 28 2013 - 15:44:25 PDT)
- [AMBER] Generating topology files for two proteins in a single input pdb George Green (Sun Sep 29 2013 - 14:26:37 PDT)
- [AMBER] entropy kirtana S (Sun Sep 29 2013 - 17:17:07 PDT)
- [AMBER] Erro in the Thermodynamic Intergration using soft core potentials" 冉挺 (Sun Sep 29 2013 - 19:02:28 PDT)
- [AMBER] Predicting druggable hotspots anu chandra (Sun Sep 29 2013 - 22:54:36 PDT)
- [AMBER] rotational diffusion error Vijay Manickam Achari (Mon Sep 30 2013 - 00:15:46 PDT)
- [AMBER] help to run restricted MD Fengxue Li (Mon Sep 30 2013 - 07:17:23 PDT)
- [AMBER] MMPBSA.py PB error Aronica, Pietro (Mon Sep 30 2013 - 07:27:38 PDT)
- [AMBER] passing a new argument to sander on command line Kepa K. Burusco (Mon Sep 30 2013 - 08:56:10 PDT)
- Re: [AMBER] RED-VIII.52 Problem--cannot find scratch file and punch file FyD (Mon Sep 30 2013 - 13:07:01 PDT)
- [AMBER] Use of Langevin Thermostat with Amoeba force field Karl Debiec (Mon Sep 30 2013 - 19:40:13 PDT)
- Last message date: Mon Sep 30 2013 - 20:00:04 PDT
- Archived on: Fri Nov 22 2024 - 05:54:48 PST
