Amber Archive Mar 2014 by thread
- [AMBER] error in running antechamber Arunima Shilpi (Sat Mar 01 2014 - 03:11:59 PST)
- [AMBER] amber trajectory to gromacs trajectory conversion Sohag Biswas (Sat Mar 01 2014 - 22:55:23 PST)
- [AMBER] extracting selected lipids from bilayer Vijay Manickam Achari (Mon Mar 03 2014 - 00:57:07 PST)
- Re: [AMBER] MMPBSA.py error almarques (Mon Mar 03 2014 - 03:06:13 PST)
- [AMBER] PairwiseDistance file after clustering analysis Elisa Frezza (Mon Mar 03 2014 - 04:15:16 PST)
- [AMBER] mass Zahra Khatti (Mon Mar 03 2014 - 06:13:13 PST)
- Re: [AMBER] Cpptraj bridge Daniel Roe (Mon Mar 03 2014 - 07:42:48 PST)
- [AMBER] pmemd.cuda segfaults pavel.banas.upol.cz (Mon Mar 03 2014 - 08:09:38 PST)
- [AMBER] format of FINAL_DECOMP_MMPBSA.dat Nitin Sharma (Mon Mar 03 2014 - 08:29:00 PST)
- [AMBER] MMPBSA TrajError Ahmed Ayoub (Mon Mar 03 2014 - 15:08:31 PST)
- [AMBER] question about mmpbsa result . mirage (Mon Mar 03 2014 - 22:47:55 PST)
- [AMBER] deprotonated histidine parameters Ahmet yıldırım (Tue Mar 04 2014 - 01:12:11 PST)
- [AMBER] calculate charge and spin multiplicity Arunima Shilpi (Tue Mar 04 2014 - 03:17:43 PST)
- [AMBER] Pmf-plane to plane restrain Rasha Alqus (Tue Mar 04 2014 - 09:03:19 PST)
- [AMBER] non-bonded parameters for ferric iron and ferrous iron Jean-Paul Becker (Tue Mar 04 2014 - 09:08:48 PST)
- Re: [AMBER] pmemd.CUDA.mpi micro-second long simulation psu4.uic.edu (Tue Mar 04 2014 - 10:40:14 PST)
- [AMBER] MMPBSA alanine scanning Maryam Azimzadeh Irani (Tue Mar 04 2014 - 17:56:40 PST)
- [AMBER] Amber settings in pymol Entomology Research Institute (Tue Mar 04 2014 - 22:54:40 PST)
- [AMBER] sander command Arunima Shilpi (Tue Mar 04 2014 - 23:09:54 PST)
- [AMBER] pmf-plane to plane restrain Rasha Alqus (Wed Mar 05 2014 - 00:02:13 PST)
- [AMBER] how to produce the prmtop of 'ch3cn' 闫玉娜 (Wed Mar 05 2014 - 00:16:25 PST)
- [AMBER] Unable to restrain A-DNA conformation DEBOSTUTI GHOSHDASTIDAR (Wed Mar 05 2014 - 02:23:56 PST)
- [AMBER] print molecular orbitals Florent Barbault (Wed Mar 05 2014 - 05:01:48 PST)
- [AMBER] Multiple vs Continuous MD opinion Soumendranath Bhakat (Wed Mar 05 2014 - 06:33:50 PST)
- [AMBER] Trouble obtaining force field parameters via Antechamber Hyun-seok Kim (Wed Mar 05 2014 - 10:43:49 PST)
- [AMBER] Error : while running force field modification files nalini chauhan (Wed Mar 05 2014 - 23:23:26 PST)
- [AMBER] ERROR in sidechain.bcl file in MCPB nalini chauhan (Thu Mar 06 2014 - 00:29:32 PST)
- Re: [AMBER] Including amino acid backbone into QM part during QM/MM Andreas Goetz (Thu Mar 06 2014 - 11:50:31 PST)
- [AMBER] Problem in using xleap 肖立 (Thu Mar 06 2014 - 21:07:53 PST)
- Re: [AMBER] PgP protein and amber14 lipid FF filip fratev (Thu Mar 06 2014 - 21:14:27 PST)
- [AMBER] Request for help in using Amberlite Robin Jain (Thu Mar 06 2014 - 23:02:33 PST)
- [AMBER] problem when performing the ired anaysis 肖立 (Fri Mar 07 2014 - 15:18:46 PST)
- [AMBER] FF10 Error Sorensen, Jesper (Fri Mar 07 2014 - 16:47:59 PST)
- [AMBER] Modified RNA frcmod error Sorensen, Jesper (Fri Mar 07 2014 - 16:51:49 PST)
- [AMBER] Mutating residues in an RNA Raviprasad Aduri (Fri Mar 07 2014 - 23:14:36 PST)
- [AMBER] Fwd: cpptraj -fixatomorder Saeed Nasiri (Sat Mar 08 2014 - 01:42:59 PST)
- [AMBER] modeling glucoside Vijay Manickam Achari (Sat Mar 08 2014 - 02:29:36 PST)
- [AMBER] Antechamber add new parameter Mengyuan Zhu (Sat Mar 08 2014 - 09:40:54 PST)
- [AMBER] how to get around "cudaDeviceEnablePeerAccess all CUDA-capable devices are busy or unavailable" Chris McClendon (Sat Mar 08 2014 - 17:52:45 PST)
- [AMBER] How can I create input for two molecule? Zahra Khatti (Sun Mar 09 2014 - 06:18:48 PDT)
- [AMBER] error in running Antechamber Arunima Shilpi (Sun Mar 09 2014 - 08:27:28 PDT)
- [AMBER] cpptraj -fixatomorder Saeed Nasiri (Mon Mar 10 2014 - 00:01:00 PDT)
- [AMBER] rism3d.snglpnt output in dx format Brian Radak (Mon Mar 10 2014 - 07:09:55 PDT)
- [AMBER] problem in "re-image" and "unwarp" Vijay Manickam Achari (Mon Mar 10 2014 - 07:18:49 PDT)
- [AMBER] Updater problems George Tzotzos (Mon Mar 10 2014 - 08:32:48 PDT)
- [AMBER] Call for participation: ISQBP Meeting, Telluride 15-19.06.2014 Thomas Cheatham (Mon Mar 10 2014 - 09:27:42 PDT)
- [AMBER] MMPBSA.py.MPI - Runtime error George Tzotzos (Mon Mar 10 2014 - 14:02:18 PDT)
- [AMBER] MMPBSA.py.MPI - Runtime error cont.d George Tzotzos (Mon Mar 10 2014 - 14:16:56 PDT)
- [AMBER] error in executing pmemd Arunima Shilpi (Mon Mar 10 2014 - 21:33:29 PDT)
- [AMBER] cpptraj -fixatomorder Saeed Nasiri (Tue Mar 11 2014 - 02:15:30 PDT)
- [AMBER] PM6-DH+ QM/MM-GBSA Kanin Wichapong (Tue Mar 11 2014 - 02:38:56 PDT)
- [AMBER] charges for QM/MM simulations Asaminew Haile (Tue Mar 11 2014 - 07:10:57 PDT)
- [AMBER] Help for system configuration Kshatresh Dutta Dubey (Tue Mar 11 2014 - 09:46:10 PDT)
- [AMBER] scale molecular dynamic / GPU available in Amber 12? psu4.uic.edu (Tue Mar 11 2014 - 12:57:18 PDT)
- [AMBER] MutateError: Mismatch in atom lnubbs2014 (Wed Mar 12 2014 - 01:43:11 PDT)
- [AMBER] MutateError: Mismatch in atom lnubbs2014 (Wed Mar 12 2014 - 03:07:27 PDT)
- [AMBER] MutateError: Mismatch in atom lnubbs2014 (Wed Mar 12 2014 - 04:06:27 PDT)
- [AMBER] MutateError: Mismatch in atom # in residue VAL lnubbs2014 (Wed Mar 12 2014 - 04:49:28 PDT)
- [AMBER] 3DRISM and orientationally averaged 3D pair distribution functions Brian Radak (Wed Mar 12 2014 - 11:34:46 PDT)
- Re: [AMBER] reg: the charges for methylated cytosine atoms Sidney Elmer (Wed Mar 12 2014 - 11:46:08 PDT)
- [AMBER] problem with -make-mdins mode in entropy MMPBSA.py.MPI calculations Marek Maly (Wed Mar 12 2014 - 17:40:12 PDT)
- [AMBER] AmberTools update 24 for CPPTRAJ Daniel Roe (Thu Mar 13 2014 - 07:35:58 PDT)
- [AMBER] Specifying a particular angle in ptraj when there is more than one residue with the same residue number Sajeewa Pemasinghe (Thu Mar 13 2014 - 18:00:42 PDT)
- [AMBER] Arsenic co-ordinates Sushi Shilpa (Thu Mar 13 2014 - 23:17:05 PDT)
- [AMBER] Problem in rst file Sushi Shilpa (Thu Mar 13 2014 - 23:33:35 PDT)
- [AMBER] unsubscribe mailing list John Chuang莊曜遠 (Fri Mar 14 2014 - 02:09:38 PDT)
- [AMBER] electric field Neha Gandhi (Fri Mar 14 2014 - 03:50:52 PDT)
- [AMBER] Parameters for a residue R R S Pissurlenkar (Fri Mar 14 2014 - 05:55:08 PDT)
- [AMBER] Water cap without MM-PBSA Antoine Marion (Fri Mar 14 2014 - 06:29:06 PDT)
- [AMBER] Compilation of amber12 on GRAY XE6 Stefan Richter (Fri Mar 14 2014 - 07:29:56 PDT)
- [AMBER] Question about Ambertools 1.5 installation Wook Lee (Fri Mar 14 2014 - 09:53:04 PDT)
- Re: [AMBER] AMBER Digest, Vol 793, Issue 1 R R S Pissurlenkar (Fri Mar 14 2014 - 20:40:09 PDT)
- [AMBER] linker error Ayesha Fatima (Fri Mar 14 2014 - 23:30:15 PDT)
- [AMBER] iRED: relaxation rates and NOEs with ptraj Ignacio Faustino (Sat Mar 15 2014 - 03:43:52 PDT)
- [AMBER] MMPBSA.py not generating specified frames for analysis manikanthan bhavaraju (Sat Mar 15 2014 - 19:34:44 PDT)
- Re: [AMBER] Ptraj's "NO ATOMS DETECTED" problem Vijay Singh (Sat Mar 15 2014 - 20:33:05 PDT)
- [AMBER] tleap lipid residue splitting warnings de Waal, Parker (Sun Mar 16 2014 - 09:35:19 PDT)
- [AMBER] qm/mm Jacopo Sgrignani (Sun Mar 16 2014 - 10:57:54 PDT)
- Re: [AMBER] (no subject) Rajiv Gandhi (Sun Mar 16 2014 - 23:43:40 PDT)
- [AMBER] MMPBSA Mary Varughese (Mon Mar 17 2014 - 03:51:51 PDT)
- [AMBER] pmf -Equilibration termination Rasha Alqus (Mon Mar 17 2014 - 05:25:04 PDT)
- [AMBER] calculating binding free energy using MM-GBSA FOR ZIF268-DNA complex Roza M (Mon Mar 17 2014 - 07:58:00 PDT)
- [AMBER] rdf around atom Jio M (Mon Mar 17 2014 - 12:18:24 PDT)
- [AMBER] error in running MMPBSA.py Arunima Shilpi (Mon Mar 17 2014 - 19:55:55 PDT)
- [AMBER] Energy unit in sqm Jacopo Sgrignani (Tue Mar 18 2014 - 02:12:33 PDT)
- [AMBER] Percentage of secondary structure determination Tanmoy Paul (Tue Mar 18 2014 - 04:23:19 PDT)
- [AMBER] tleap output of mol2 format incorrect bond order/atom types Browning, Nicholas (Tue Mar 18 2014 - 07:59:47 PDT)
- [AMBER] bugzilla searches Scott Brozell (Tue Mar 18 2014 - 08:52:47 PDT)
- [AMBER] Hbond Nitin Sharma (Tue Mar 18 2014 - 12:47:37 PDT)
- [AMBER] error in MMPBSA.py Arunima Shilpi (Tue Mar 18 2014 - 21:06:10 PDT)
- [AMBER] How to get the ESP on the grid point Kim TaeHwan (Wed Mar 19 2014 - 00:19:13 PDT)
- [AMBER] generating topology Vijay Manickam Achari (Wed Mar 19 2014 - 06:47:05 PDT)
- [AMBER] Error: Prmtop appears to contain modified off-diagonal elements for VDW A coef BERGY (Wed Mar 19 2014 - 08:55:06 PDT)
- [AMBER] strain/energy of backbone atoms Jio M (Wed Mar 19 2014 - 09:14:21 PDT)
- [AMBER] RESTRAINT FILE Sourav Purohit (Wed Mar 19 2014 - 16:16:32 PDT)
- [AMBER] problem in generating .prmtop and .inpcrd file using amber9 Vijayalaxmi Sahoo (Wed Mar 19 2014 - 20:08:47 PDT)
- [AMBER] Compilation error on Ubuntu 13.10 Weinzierl, Robert O J (Thu Mar 20 2014 - 00:57:50 PDT)
- [AMBER] trajectory concatenation using cpptraj Neha Gandhi (Thu Mar 20 2014 - 01:32:12 PDT)
- [AMBER] problem in generating .prmtop and .inpcrd file using amber9 Vijayalaxmi Sahoo (Thu Mar 20 2014 - 03:47:32 PDT)
- [AMBER] protein-ligand tutorial Arunima Shilpi (Thu Mar 20 2014 - 04:15:18 PDT)
- [AMBER] the combination ntb != 0, ntp != 0, ifbox == 0 is not supported! Saeed Nasiri (Thu Mar 20 2014 - 08:31:10 PDT)
- [AMBER] Lipid14 falling apart Ghulam Mustafa (Thu Mar 20 2014 - 08:50:28 PDT)
- [AMBER] Antechamber not converting HyperChem .hin files correctly CHRISTOPHER PATRICK MCNARY (Thu Mar 20 2014 - 10:50:56 PDT)
- [AMBER] AMOEBA force field in amber Geoffrey Gray (Thu Mar 20 2014 - 11:50:21 PDT)
- [AMBER] Cpptraj hbond bridgeout segmentation fault Juan.Aranda.uv.es (Thu Mar 20 2014 - 14:01:12 PDT)
- [AMBER] rescue amd.log psu4.uic.edu (Thu Mar 20 2014 - 16:49:41 PDT)
- [AMBER] strip_mask syntax error George Tzotzos (Fri Mar 21 2014 - 07:35:05 PDT)
- [AMBER] Cuda compilation problems with Ubuntu 13.10 Weinzierl, Robert O J (Fri Mar 21 2014 - 07:55:06 PDT)
- [AMBER] Incomplete frcmod from parmchk Prema Mallipeddi (Fri Mar 21 2014 - 11:11:43 PDT)
- [AMBER] Error: EOF when searching for tprmtop Nelson Max (Fri Mar 21 2014 - 17:32:04 PDT)
- [AMBER] cpptraj grid function Jio M (Sat Mar 22 2014 - 11:43:02 PDT)
- [AMBER] cpptraj h-bond: error George Tzotzos (Sat Mar 22 2014 - 13:13:00 PDT)
- [AMBER] delta G calculation in MMPBSA Arunima Shilpi (Sat Mar 22 2014 - 23:01:26 PDT)
- [AMBER] MMPBSA.py: decomposition error Kshatresh Dutta Dubey (Sun Mar 23 2014 - 10:57:46 PDT)
- [AMBER] aMD error for the coordinates file maryam azimzadehirani (Sun Mar 23 2014 - 19:24:23 PDT)
- [AMBER] Problem with Decomposition of Binding Free Energy loue chen (Sun Mar 23 2014 - 20:31:25 PDT)
- [AMBER] Positive value of delta G Arunima Shilpi (Sun Mar 23 2014 - 20:58:51 PDT)
- Re: [AMBER] tleap cannot handle dummies in the middle? Hannes Loeffler (Mon Mar 24 2014 - 05:10:11 PDT)
- [AMBER] Open Source Drug Design and In Silico Molecules Pledge to AMBER developers Soumendranath Bhakat (Mon Mar 24 2014 - 06:35:19 PDT)
- [AMBER] Generalized Born subroutines Debayan Chakraborty (Mon Mar 24 2014 - 06:41:19 PDT)
- [AMBER] Adenine parameters and topology files Valentina Romano (Mon Mar 24 2014 - 08:20:29 PDT)
- [AMBER] QM/MM John Smith (Mon Mar 24 2014 - 09:17:32 PDT)
- [AMBER] Adenine without ribose ring and/or phosphate groups Valentina Romano (Mon Mar 24 2014 - 09:46:20 PDT)
- [AMBER] using chamber with vmd-generated psf (after reformatting to extended format) Pete Kekenes-Huskey (Mon Mar 24 2014 - 11:42:18 PDT)
- [AMBER] libgfortran.2.dylib Fabian Glaser (Tue Mar 25 2014 - 00:54:05 PDT)
- [AMBER] Generating frc and prep files DEBOSTUTI GHOSHDASTIDAR (Tue Mar 25 2014 - 07:38:52 PDT)
- [AMBER] Problem in configuring the amber Akashdeep Biswas (Tue Mar 25 2014 - 23:55:59 PDT)
- [AMBER] How to update cpptraj and setting donor/acceptormask Setyanto Md (Wed Mar 26 2014 - 01:34:38 PDT)
- [AMBER] Fwd: MMGBSA of protein DNA complex Aditya Sarkar (Wed Mar 26 2014 - 03:40:01 PDT)
- [AMBER] combining trajectories with diff. number of residues for same protein Nitin Sharma (Wed Mar 26 2014 - 06:29:37 PDT)
- [AMBER] running amber on multigpu Neha Gandhi (Wed Mar 26 2014 - 07:17:52 PDT)
- [AMBER] setangle in parmed API hannes.loeffler.stfc.ac.uk (Wed Mar 26 2014 - 08:01:11 PDT)
- [AMBER] Possible bug in xleap Ilias Patmanidis (Wed Mar 26 2014 - 08:10:11 PDT)
- [AMBER] Regarding SPC/E water model MOHD HOMAIDUR RAHMAN (Wed Mar 26 2014 - 11:07:01 PDT)
- [AMBER] why the 1-4 electric and vdw scaling factor are 0.0 in my .prmtop file? Dongshan Wei (Wed Mar 26 2014 - 20:04:58 PDT)
- [AMBER] error in running density coomand Arunima Shilpi (Wed Mar 26 2014 - 23:33:11 PDT)
- [AMBER] antechamber for two ligands Fabian Glaser (Thu Mar 27 2014 - 05:40:15 PDT)
- [AMBER] Problem with REMD simulation Gargi Borgohai (Thu Mar 27 2014 - 08:03:15 PDT)
- [AMBER] repulsive restraints Thomas Evangelidis (Thu Mar 27 2014 - 08:34:12 PDT)
- [AMBER] How is ZN treated in AMBER14 R R S Pissurlenkar (Thu Mar 27 2014 - 08:46:17 PDT)
- [AMBER] non-protonated and protonated phosphate Thomas Exner (Thu Mar 27 2014 - 08:47:14 PDT)
- [AMBER] data overflow in dx output from rism3d Brian Radak (Thu Mar 27 2014 - 14:02:03 PDT)
- [AMBER] small box changes still fail with 'Nonbond cells need to be recalculated' Pete Kekenes-Huskey (Thu Mar 27 2014 - 21:46:34 PDT)
- [AMBER] MMPBSA calculation with entropy Arun Kumar Somavarapu (Thu Mar 27 2014 - 22:02:02 PDT)
- [AMBER] Replica exchange restart file Mele N. (Fri Mar 28 2014 - 05:15:17 PDT)
- [AMBER] anybody knows how Langevin dynamics affects time-correlation functions? Jose Borreguero (Fri Mar 28 2014 - 12:27:41 PDT)
- [AMBER] cpptraj hbond analysis cutoff angle DEBOSTUTI GHOSHDASTIDAR (Fri Mar 28 2014 - 22:37:22 PDT)
- [AMBER] Problem regarding running job in AMBER 12 Souvik Sur (Sat Mar 29 2014 - 04:16:29 PDT)
- [AMBER] restart MD from arbitrary snapshot Milo Westler (Sun Mar 30 2014 - 13:29:35 PDT)
- [AMBER] GPU not being recognised Ayesha Fatima (Mon Mar 31 2014 - 03:38:58 PDT)
- [AMBER] central atom always 3rd in improper Hannes Loeffler (Mon Mar 31 2014 - 07:45:21 PDT)
- [AMBER] AMBER on GTX-Titan Black Ross Walker (Mon Mar 31 2014 - 09:51:09 PDT)
- Last message date: Mon Mar 31 2014 - 14:00:04 PDT
- Archived on: Wed Dec 25 2024 - 05:54:56 PST
