Amber Archive Jul 2012 by thread
- [AMBER] failure about pmemd.cuda caobb0214 (Sat Jun 30 2012 - 20:27:10 PDT)
- Re: [AMBER] How to call up ptraj in supercomputer facilities? should I use mpi? Ben Roberts (Sat Jun 30 2012 - 22:43:03 PDT)
- Re: [AMBER] Amber: mm_pbsa.pl rajeevy.iitk.ac.in (Sun Jul 01 2012 - 00:10:01 PDT)
- Re: [AMBER] Problem while running MMPBSA Jason Swails (Sun Jul 01 2012 - 19:18:11 PDT)
- [AMBER] complex of protein dimer and two ligands simulated MMPBSA.py error kamlesh sahu (Mon Jul 02 2012 - 01:19:28 PDT)
- Re: [AMBER] TI calculation Amber 12 Anna Bauß (Mon Jul 02 2012 - 02:36:30 PDT)
- [AMBER] Error on REMD trajectory analysis Dilraj LAMA (Mon Jul 02 2012 - 05:11:17 PDT)
- [AMBER] Error in post-processing REMD trajectory Dilraj LAMA (Mon Jul 02 2012 - 05:13:00 PDT)
- Re: [AMBER] trajectory imaging results in structural clashes in protein-ligand complexes Fredrick Devadoss (Mon Jul 02 2012 - 06:40:22 PDT)
- [AMBER] error to run pmemd.MPI on Opteron CPU Yubo Fan (Mon Jul 02 2012 - 22:52:30 PDT)
- [AMBER] Script to restore resid numbering Francesco Pietra (Tue Jul 03 2012 - 00:49:03 PDT)
- [AMBER] Constraint simulations Rajendra Sharma (Wed Jul 04 2012 - 00:21:24 PDT)
- Re: [AMBER] all_prot_nucleic10.lib file in amber12 FyD (Wed Jul 04 2012 - 01:16:10 PDT)
- [AMBER] Thermodynamic integration with polarizable force field VAN DAMME Steven (Wed Jul 04 2012 - 05:56:27 PDT)
- [AMBER] velocities and irest=0 in Amber 11/12 Jan-Philip Gehrcke (Wed Jul 04 2012 - 08:33:46 PDT)
- Re: [AMBER] NaN with GTX580 pmemd.cuda simulation with and without iwrap = 1 Fabrício Bracht (Wed Jul 04 2012 - 11:20:16 PDT)
- [AMBER] ff12SB manikanthan bhavaraju (Wed Jul 04 2012 - 12:04:44 PDT)
- Re: [AMBER] Looping over a trajectory Lee-Ping Wang (Wed Jul 04 2012 - 12:48:01 PDT)
- [AMBER] MMPBSA calculation problem 刘金峰 (Wed Jul 04 2012 - 22:17:46 PDT)
- [AMBER] AMBER 12 benchmarks Hannes Loeffler (Thu Jul 05 2012 - 05:54:37 PDT)
- Re: [AMBER] Ion clumping in large protein-RNA systems Kamali Sripathi (Thu Jul 05 2012 - 07:41:49 PDT)
- [AMBER] CUDA MPI failed in Ubuntu Albert (Thu Jul 05 2012 - 08:38:26 PDT)
- [AMBER] entropy calculations bmartini (Thu Jul 05 2012 - 09:50:49 PDT)
- [AMBER] Difficulty using ptraj to generate pdb frames from .mdcrd trajectory Gordon S Freeman (Thu Jul 05 2012 - 12:23:42 PDT)
- [AMBER] Force field for bend DNA sudipta (Thu Jul 05 2012 - 17:07:00 PDT)
- [AMBER] Polarizable vs Fixed Charge FF Nikolay Igorovich Rodionov (Fri Jul 06 2012 - 07:11:28 PDT)
- [AMBER] different RMSF between CPU and GPU Massimiliano Porrini (Fri Jul 06 2012 - 12:37:17 PDT)
- [AMBER] protonated nucleic acid residues Timothy Robbins (trobbins) (Fri Jul 06 2012 - 14:13:32 PDT)
- [AMBER] Fwd: Protein aggregation energy calculation Binwu Zhao (Sat Jul 07 2012 - 14:54:32 PDT)
- [AMBER] I can prepare Na+ parameter files under LEAPRC.CONSTPH. kurisaki (Sun Jul 08 2012 - 01:22:39 PDT)
- [AMBER] MMPBSA: dubious results George Tzotzos (Mon Jul 09 2012 - 04:18:49 PDT)
- Re: [AMBER] MMPBSA results and huge SD Massimiliano Porrini (Mon Jul 09 2012 - 06:35:51 PDT)
- Re: [AMBER] Fwd: AmberTools 12 pbsa: missing newline character in OpenDX output (patched gen_dx_file.F90 attached) Jan-Philip Gehrcke (Mon Jul 09 2012 - 11:57:21 PDT)
- [AMBER] Compiling Amber12 on the Cray XK6 (Jaguar) Gustavo Seabra (Mon Jul 09 2012 - 12:43:37 PDT)
- [AMBER] amd.log file Milo Westler (Mon Jul 09 2012 - 12:48:06 PDT)
- [AMBER] Updated free GPU test drives for AMBER Ross Walker (Mon Jul 09 2012 - 21:56:17 PDT)
- Re: [AMBER] cpptraj-secstruct N-terminal proline colvin (Tue Jul 10 2012 - 01:06:16 PDT)
- [AMBER] Installation Amber 12 using cygwin on windows 7 64 bit Mohammad Jane Alam (Tue Jul 10 2012 - 07:54:36 PDT)
- [AMBER] MMPBSA.py decomposition option Damodaran, Komath (Tue Jul 10 2012 - 09:06:31 PDT)
- [AMBER] Aqueous Ionic Grouping Problems Eckler, Logan, H (Tue Jul 10 2012 - 14:23:59 PDT)
- [AMBER] installing amber12 huseyin istanbullu (Wed Jul 11 2012 - 01:57:42 PDT)
- [AMBER] Met92 not bound to Cu atom in TUTORIAL-A1(simple version) Mahendra B Thapa (Wed Jul 11 2012 - 13:50:55 PDT)
- [AMBER] Bug? tleap of AmberTools12 cannot deal with branch carbohydrates contain sialic acid Tomoshi Kameda (Wed Jul 11 2012 - 16:21:46 PDT)
- [AMBER] Error: Error in box coord line of trajectory (AMBER 12.0) - MM/PBSA per residue decomposition Ashley Ferraro (Wed Jul 11 2012 - 17:25:56 PDT)
- [AMBER] Bug? tleap of AmberTools12 cannot deal with branch carbohydrates contain sialic acid Tomoshi Kameda (Wed Jul 11 2012 - 23:58:49 PDT)
- [AMBER] Ptraj discrepancy C.M.Sampson (Thu Jul 12 2012 - 02:56:49 PDT)
- Re: [AMBER] installing Amber12 Jason Swails (Thu Jul 12 2012 - 05:03:30 PDT)
- Re: [AMBER] Error in writing of coordinate file after simulation Ashutosh Shandilya (Thu Jul 12 2012 - 11:17:08 PDT)
- Re: [AMBER] Protein aggregation energy calculation(Binwu Zhao) Binwu Zhao (Thu Jul 12 2012 - 11:28:21 PDT)
- [AMBER] frcmod file to include Urey Bradley angle terms Scott Pendley (Thu Jul 12 2012 - 11:44:49 PDT)
- [AMBER] Sulfotyrosine force field Pedro Swagger (Thu Jul 12 2012 - 12:56:45 PDT)
- [AMBER] atoms on phosphonic acid groups collapse during minimization Maria Minakova (Thu Jul 12 2012 - 15:23:28 PDT)
- [AMBER] AMBER11_CUDA issue with binary restart HIMANSHU JOSHI (Thu Jul 12 2012 - 22:47:03 PDT)
- [AMBER] system out of pbc box Albert (Fri Jul 13 2012 - 00:57:42 PDT)
- [AMBER] lipid params Jio M (Fri Jul 13 2012 - 01:35:31 PDT)
- [AMBER] PB with inp=2 doesn't recognize ff10 atom types? (Amber Archive Mar 2012) Miguel Ortiz Lombardia (Fri Jul 13 2012 - 05:21:40 PDT)
- [AMBER] benzene-sulfonate (atom type for Sulfur) Jio M (Fri Jul 13 2012 - 05:37:56 PDT)
- [AMBER] no restart file from pmemd.cuda in Amber 11 Seren Soner (Fri Jul 13 2012 - 06:44:02 PDT)
- [AMBER] Amber12 qm_ewald DJH71.pitt.edu (Fri Jul 13 2012 - 09:01:39 PDT)
- [AMBER] http://archive.ambermd.org/201206/0014.html Osman, Roman (Fri Jul 13 2012 - 09:42:35 PDT)
- [AMBER] can Amber run in Anton? Albert (Fri Jul 13 2012 - 11:01:10 PDT)
- [AMBER] npt stacked with CUDA running Albert (Fri Jul 13 2012 - 13:15:03 PDT)
- [AMBER] Amber10 and AmberTools12 compatibility vaibhav dixit (Fri Jul 13 2012 - 22:32:23 PDT)
- [AMBER] ambertool12 installation in Cygwin 钟舜 (Sat Jul 14 2012 - 19:22:33 PDT)
- [AMBER] problem to attach n terminal residue to protein Sanjib Paul (Sun Jul 15 2012 - 00:21:38 PDT)
- [AMBER] Global Minimum? jit mukherjee (Sun Jul 15 2012 - 02:56:29 PDT)
- [AMBER] parameters reading Yun Shi (Sun Jul 15 2012 - 15:42:38 PDT)
- [AMBER] what do the preceding "E" and "B" mean in rdparm dihedral prints Yun Shi (Sun Jul 15 2012 - 19:38:51 PDT)
- [AMBER] installing on ubuntu 12.04 LTS 64 bit huseyin istanbullu (Mon Jul 16 2012 - 01:31:53 PDT)
- [AMBER] AMBER12 - ninterface for double bilayer system James Murdock (Mon Jul 16 2012 - 03:30:52 PDT)
- [AMBER] Quantification of fraction of Helicity. Rajendra Sharma (Mon Jul 16 2012 - 04:08:51 PDT)
- [AMBER] AMBER GPU Bench mark procedure Ravi Teja (Mon Jul 16 2012 - 04:41:52 PDT)
- [AMBER] problem in minimization jit mukherjee (Mon Jul 16 2012 - 08:23:21 PDT)
- [AMBER] pi-pi stacking interaction and hydrogen bonding with amber jit mukherjee (Mon Jul 16 2012 - 09:37:31 PDT)
- [AMBER] GPU bugs for Amber 12? Albert (Mon Jul 16 2012 - 09:42:42 PDT)
- [AMBER] Dihedral parameters assignment by tleap Yun Shi (Mon Jul 16 2012 - 09:59:48 PDT)
- [AMBER] Parmtop files for TI Softcore Potentials Kepa K. Burusco (Mon Jul 16 2012 - 11:30:24 PDT)
- [AMBER] Continuation of thread regarding problems with Zinc parameterization with MCPB (Apparently solved) Fabrício Bracht (Mon Jul 16 2012 - 13:24:48 PDT)
- [AMBER] Langevin Dynamics Qian Wang (Mon Jul 16 2012 - 15:55:53 PDT)
- [AMBER] Polarization Nikolay Igorovich Rodionov (Mon Jul 16 2012 - 17:10:09 PDT)
- [AMBER] Problem with MMPBSA using a solvated structure topology Osman, Roman (Mon Jul 16 2012 - 18:57:12 PDT)
- [AMBER] MMPBSA.py Delwar Hossain (Mon Jul 16 2012 - 19:55:46 PDT)
- [AMBER] Two md.in files in manual and tutorials when running SMD 崔颖璐 (Tue Jul 17 2012 - 00:35:51 PDT)
- [AMBER] Defining bonds between calcium and protein Zalikha Ibrahim (Tue Jul 17 2012 - 01:02:16 PDT)
- [AMBER] MMPBSA Entropies: N-mode and Quasi Harmonic calculations George Tzotzos (Tue Jul 17 2012 - 04:38:16 PDT)
- [AMBER] Amber 11: iwrap=1 separates two RNA chains Kasprzak, Wojciech (NIH/NCI) [C] (Tue Jul 17 2012 - 07:30:44 PDT)
- [AMBER] How to convert AMBER atom type to CYANA Rahul Banerjee (Tue Jul 17 2012 - 15:18:19 PDT)
- [AMBER] RNA chi torsion corrections Asmita Gupta (Wed Jul 18 2012 - 03:06:21 PDT)
- [AMBER] Help with amber12 at ORNL Foertter, Fernanda S. (Wed Jul 18 2012 - 08:31:19 PDT)
- Re: [AMBER] Installation of Amber in Cygwin Jason Swails (Wed Jul 18 2012 - 12:35:04 PDT)
- [AMBER] Difference between "jar=1" and "ncsu_smd" when running SMD simulations 崔颖璐 (Wed Jul 18 2012 - 19:11:55 PDT)
- [AMBER] ZAFF parameters Siavoush Dastmalchi (Wed Jul 18 2012 - 22:33:26 PDT)
- [AMBER] error with ambertools12 and amber10 installation vaibhav dixit (Thu Jul 19 2012 - 04:39:06 PDT)
- [AMBER] Question concerning TI using soft core potential Wook Lee (Thu Jul 19 2012 - 07:04:21 PDT)
- [AMBER] Interaction energy between residue pairs Fabrício Bracht (Thu Jul 19 2012 - 14:47:25 PDT)
- [AMBER] GBIS and SASA Aron Broom (Thu Jul 19 2012 - 15:03:29 PDT)
- [AMBER] how to make statistics of solvent molecules? Albert (Fri Jul 20 2012 - 00:52:31 PDT)
- [AMBER] Amber Error hclengineer niper (Fri Jul 20 2012 - 04:26:37 PDT)
- [AMBER] LEaP problems with non-standard residue Francesco Pietra (Fri Jul 20 2012 - 06:57:25 PDT)
- [AMBER] Iwrap=1 and imaging revisited Kasprzak, Wojciech (NIH/NCI) [C] (Fri Jul 20 2012 - 08:05:01 PDT)
- [AMBER] TI calculation with amber and finite size correction for PME manikanthan bhavaraju (Fri Jul 20 2012 - 14:02:54 PDT)
- [AMBER] Restrained minimization pancham lal gupta (Sat Jul 21 2012 - 10:31:00 PDT)
- [AMBER] stripping number of residues (>20K) problem Jio M (Sun Jul 22 2012 - 02:48:44 PDT)
- [AMBER] Question about corrections to the quasi-harmonic approximation zhouhaibin2008.ok (Sun Jul 22 2012 - 08:39:26 PDT)
- [AMBER] problem with testing water movement during md simulation Danny Blue (Sun Jul 22 2012 - 09:44:27 PDT)
- [AMBER] PMF of a salt bridge. Rajendra Sharma (Sun Jul 22 2012 - 12:03:08 PDT)
- Re: [AMBER] qmmm_EXTERN/ tests failing Andreas Goetz (Sun Jul 22 2012 - 14:18:50 PDT)
- [AMBER] KeyError: 'Total' at parsing MMPBSA results Miguel Ortiz Lombardía (Mon Jul 23 2012 - 01:01:45 PDT)
- [AMBER] problem in installing sander.MPI devawati dutta (Mon Jul 23 2012 - 02:12:50 PDT)
- [AMBER] Regarding creating a leap input file aneesh cna (Mon Jul 23 2012 - 05:25:32 PDT)
- [AMBER] pbsa: unit of the electrostatic potential values written to DX file Jan-Philip Gehrcke (Mon Jul 23 2012 - 08:43:20 PDT)
- [AMBER] Problem with MMPBSA.py.MPI sudipta (Mon Jul 23 2012 - 13:03:06 PDT)
- [AMBER] the meaning of variables used in source file force.f Xin Geng (Mon Jul 23 2012 - 15:22:24 PDT)
- [AMBER] Error: periodicity of dihedral is zero Francesco Pietra (Tue Jul 24 2012 - 01:26:01 PDT)
- [AMBER] problem in parallel testing devawati dutta (Tue Jul 24 2012 - 03:51:30 PDT)
- [AMBER] pbsa: how to increase the sampling volume (grid dimensions)? Jan-Philip Gehrcke (Tue Jul 24 2012 - 10:13:00 PDT)
- [AMBER] xLeap and Windows questions Mickey Richards (Tue Jul 24 2012 - 11:56:33 PDT)
- Re: [AMBER] How to Calculate SASA with Amber? Shafinaz Chowdhury (Tue Jul 24 2012 - 13:40:56 PDT)
- [AMBER] install amber10 error onfiguring netcdf; (may be time-consuming) ./configure: line 22350: type: mpic++: not found NETCDF configure succeeded. Jorgen Simonsen (Tue Jul 24 2012 - 14:34:32 PDT)
- [AMBER] internal dielectric constant in MMPBSA Qiong Zhang (Tue Jul 24 2012 - 18:12:11 PDT)
- [AMBER] RDF calculation Bhanita Sharma (Tue Jul 24 2012 - 23:40:27 PDT)
- [AMBER] "Error: unknown flag: -rismmpi" Daniel Sindhikara (Wed Jul 25 2012 - 00:07:09 PDT)
- [AMBER] MMPBSA per-residue decomposition: how is the polar solvation contribution calculated? Jan-Philip Gehrcke (Wed Jul 25 2012 - 03:07:12 PDT)
- [AMBER] Bending force constant in kcal/mol/rad2 from bending frequency(cm-1) arup pathak (Wed Jul 25 2012 - 04:56:19 PDT)
- [AMBER] FW: Re: How to Calculate SASA with Amber? Shafinaz Chowdhury (Wed Jul 25 2012 - 09:09:40 PDT)
- [AMBER] installation of amber10 Jorgen Simonsen (Wed Jul 25 2012 - 09:18:18 PDT)
- [AMBER] Bfactor for binding site waters Senthil Natesan (Wed Jul 25 2012 - 09:26:36 PDT)
- [AMBER] internal dielectric constant in MMPBSA Qiong Zhang (Wed Jul 25 2012 - 09:58:22 PDT)
- [AMBER] Molecular Surface from MMPBSA Damodaran, Komath (Wed Jul 25 2012 - 10:58:41 PDT)
- [AMBER] TI with softcore at lambda=0 or 1? Liu Denis (Wed Jul 25 2012 - 19:58:18 PDT)
- [AMBER] RDF considering center of mass Bhanita Sharma (Wed Jul 25 2012 - 21:47:31 PDT)
- [AMBER] Amber12 issue with SMD protocol Agostino Bruno (Thu Jul 26 2012 - 03:05:25 PDT)
- [AMBER] Bugfix 16: New cpptraj action, AutoImage Daniel Roe (Thu Jul 26 2012 - 07:36:42 PDT)
- [AMBER] radgyr command ? Marek Maly (Thu Jul 26 2012 - 09:30:13 PDT)
- [AMBER] aMD issues: sander vs. pmemd vs. pmemd.cuda Niel Henriksen (Thu Jul 26 2012 - 13:24:36 PDT)
- [AMBER] Diverging sander.MPI results according to core allocation Bashford, Donald (Thu Jul 26 2012 - 15:25:11 PDT)
- [AMBER] Bug in PM6: Halogens (?) DJH71.pitt.edu (Wed Jul 25 2012 - 12:31:09 PDT)
- [AMBER] compilation aborted for pme_setup.f90 (code 1) Jorgen Simonsen (Thu Jul 26 2012 - 20:11:17 PDT)
- [AMBER] iAPBS huseyin istanbullu (Fri Jul 27 2012 - 05:53:53 PDT)
- [AMBER] trajin lastframe keyword problem Marek Maly (Fri Jul 27 2012 - 09:01:19 PDT)
- [AMBER] GAFF c2-c data lacking? Francesco Pietra (Sun Jul 29 2012 - 07:31:26 PDT)
- [AMBER] mm_pbsa (.pl) calculations for a complex composed of 11 chains and 6 ligand molecules Naeem Attari (Mon Jul 30 2012 - 04:58:31 PDT)
- [AMBER] problem in converting rst-file to pdb using cpptraj Mahendra B Thapa (Mon Jul 30 2012 - 09:32:24 PDT)
- [AMBER] NPT equilibration error: ASSERTion 'e' failed in nonbond_list.F90 at line 849 Maria Minakova (Mon Jul 30 2012 - 12:32:34 PDT)
- [AMBER] compiling amber on Ranger/Teragrid Pawel (Mon Jul 30 2012 - 13:36:09 PDT)
- [AMBER] Using CHAMBER with implicit solvent CHARMM force field Anna Tarakanova (Mon Jul 30 2012 - 14:36:05 PDT)
- [AMBER] mobility of protein from MD trajectories kamlesh sahu (Mon Jul 30 2012 - 19:42:32 PDT)
- [AMBER] Bug in AmberTools12 cpptraj? 'trajout onlyframes' doesn't work Marc van der Kamp (Tue Jul 31 2012 - 06:24:01 PDT)
- [AMBER] Creating AMBER files from implicit solvent CHARMM19 force field Anna Tarakanova (Tue Jul 31 2012 - 08:52:41 PDT)
- [AMBER] Problems parameterizing water/ZN active site with MKT++ Fabrício Bracht (Tue Jul 31 2012 - 12:36:56 PDT)
- Last message date: Tue Jul 31 2012 - 15:00:03 PDT
- Archived on: Mon Dec 23 2024 - 05:54:32 PST
