Amber Archive Apr 2014 by thread
- Re: [AMBER] GPU not being recognised Ayesha Fatima (Mon Mar 31 2014 - 09:52:05 PDT)
- [AMBER] SHAWKTRAJ, a new trajectory analysis tool Jason Swails (Tue Apr 01 2014 - 04:03:25 PDT)
- Re: [AMBER] Possible bug in xleap Bill Ross (Tue Apr 01 2014 - 16:44:23 PDT)
- Re: [AMBER] How to update cpptraj and setting donor/acceptormask Setyanto Md (Tue Apr 01 2014 - 20:03:00 PDT)
- [AMBER] WHAM Analysis Histograms amr hamed (Tue Apr 01 2014 - 21:33:50 PDT)
- Re: [AMBER] MMPBSA calculation with entropy Arun Kumar Somavarapu (Wed Apr 02 2014 - 02:11:07 PDT)
- Re: [AMBER] reg: the charges for methylated cytosine atoms Filip Lankas (Wed Apr 02 2014 - 02:25:24 PDT)
- [AMBER] loading multiple prepin file in xleap - gives warning Vijay Manickam Achari (Wed Apr 02 2014 - 02:57:31 PDT)
- [AMBER] truncatiing water molecules Nitin Sharma (Wed Apr 02 2014 - 04:36:27 PDT)
- [AMBER] Distance constraints Urszula Uciechowska (Wed Apr 02 2014 - 06:33:23 PDT)
- [AMBER] Normal mode for truncated system Ahmed Ayoub (Wed Apr 02 2014 - 11:45:19 PDT)
- [AMBER] coordinates for replicating truncated octahedron Jio M (Wed Apr 02 2014 - 13:51:45 PDT)
- [AMBER] Asking about using Vector Analysis: Thermo Setyanto Md (Wed Apr 02 2014 - 20:10:26 PDT)
- [AMBER] Asking about using Vector Analysis: Thermo Setyanto Md (Wed Apr 02 2014 - 22:35:44 PDT)
- [AMBER] antechamber Lara rajam (Thu Apr 03 2014 - 08:29:13 PDT)
- [AMBER] antechamber_error Lara rajam (Thu Apr 03 2014 - 08:38:19 PDT)
- [AMBER] leap error sammia khatak (Thu Apr 03 2014 - 08:49:09 PDT)
- [AMBER] pmemd.cuda.mpi installation Cenk \(Jenk\) Andac (Thu Apr 03 2014 - 09:03:27 PDT)
- [AMBER] pmemd.cuda.mpi installation Cenk \(Jenk\) Andac (Thu Apr 03 2014 - 09:29:01 PDT)
- [AMBER] Parameters for Ca+2 ion for the decomposition analysis Manikanthan Bhavaraju (Thu Apr 03 2014 - 12:22:01 PDT)
- [AMBER] distance in one plane Jio M (Thu Apr 03 2014 - 12:35:37 PDT)
- [AMBER] Error: Could not parse mask [(:1]: radial calculation Jio M (Thu Apr 03 2014 - 14:57:31 PDT)
- [AMBER] query regarding simulation! Pallavi Mohanty (Thu Apr 03 2014 - 23:40:49 PDT)
- [AMBER] Query regrading simulation Pallavi Mohanty (Fri Apr 04 2014 - 00:00:27 PDT)
- [AMBER] Regarding Interaction energy calculation MOHD HOMAIDUR RAHMAN (Fri Apr 04 2014 - 01:57:49 PDT)
- [AMBER] Query regrading simulation Pallavi Mohanty (Fri Apr 04 2014 - 02:02:20 PDT)
- [AMBER] Error using MMPBSA.py Souvik Sur (Fri Apr 04 2014 - 03:00:04 PDT)
- [AMBER] new error sammia khatak (Fri Apr 04 2014 - 05:21:33 PDT)
- [AMBER] Bad atom type: C0 Manikanthan Bhavaraju (Fri Apr 04 2014 - 07:32:21 PDT)
- [AMBER] Inconsistent results of MMPBSA.py with option inp=1 and inp=2 tong (Fri Apr 04 2014 - 07:57:04 PDT)
- [AMBER] Bad atom type: C0 Mani Bhavaraju (Fri Apr 04 2014 - 09:04:54 PDT)
- [AMBER] Why do I get an error in antechamber when a metal is involved? CHRISTOPHER PATRICK MCNARY (Fri Apr 04 2014 - 12:01:43 PDT)
- [AMBER] Why do I get an error in antechamber when a metal is involved? CHRISTOPHER PATRICK MCNARY (Fri Apr 04 2014 - 12:24:10 PDT)
- [AMBER] Principal component analysis Ibrahim Said (Fri Apr 04 2014 - 13:19:45 PDT)
- [AMBER] Regarding Interaction energy calculation MOHD HOMAIDUR RAHMAN (Fri Apr 04 2014 - 21:05:35 PDT)
- [AMBER] Ligand-residue interaction plot Arunima Shilpi (Sat Apr 05 2014 - 00:08:37 PDT)
- [AMBER] Ligand-residue interaction plot Arunima Shilpi (Sat Apr 05 2014 - 04:39:54 PDT)
- Re: [AMBER] ATOMIC NUMBER section in prmtop file - Sustiva example ye renlo (Sat Apr 05 2014 - 07:39:38 PDT)
- Re: [AMBER] ATOMIC NUMBER section in prmtop file - Sustiva example:potential bug ye renlo (Sat Apr 05 2014 - 08:56:32 PDT)
- [AMBER] ligand residue interaction Arunima Shilpi (Sat Apr 05 2014 - 20:00:39 PDT)
- [AMBER] ligand residue interaction Arunima Shilpi (Sat Apr 05 2014 - 20:37:53 PDT)
- [AMBER] protein-ligand interaction Arunima Shilpi (Sat Apr 05 2014 - 21:07:04 PDT)
- [AMBER] Protein-ligand interaction Arunima Shilpi (Sun Apr 06 2014 - 09:05:28 PDT)
- [AMBER] averaged NMR distance Neha Gandhi (Sun Apr 06 2014 - 20:00:01 PDT)
- [AMBER] US+QM/MM enzyme + substrate - howto Tamara Meirelles (Mon Apr 07 2014 - 00:26:05 PDT)
- [AMBER] entropy calculation mmpbsa_nm Arunima Shilpi (Mon Apr 07 2014 - 04:35:15 PDT)
- [AMBER] simulating small molecules systems Fabian Glaser (Mon Apr 07 2014 - 05:10:59 PDT)
- [AMBER] small molecules Fabian Glaser (Mon Apr 07 2014 - 05:14:14 PDT)
- [AMBER] Really Weird Problem with Replica Exchange Christopher A Thiebaut (Mon Apr 07 2014 - 11:58:26 PDT)
- [AMBER] REMD with pmemd.cuda Milo Westler (Mon Apr 07 2014 - 18:04:52 PDT)
- [AMBER] number of ions (integral) too much in RDF plot Jio M (Mon Apr 07 2014 - 19:33:01 PDT)
- [AMBER] About the error "Unable to correctly identify element CU" in QMMM simulation Yeng-Tseng Wang (Mon Apr 07 2014 - 20:43:54 PDT)
- [AMBER] When I run the pmemd.cuda, sometimes computer will be rebooted. KangMooseok (Mon Apr 07 2014 - 22:34:26 PDT)
- [AMBER] error in reading protein file Arunima Shilpi (Mon Apr 07 2014 - 22:58:18 PDT)
- [AMBER] When I run the pmemd.cuda, sometimes computer will be rebooted. KangMooseok (Mon Apr 07 2014 - 23:01:45 PDT)
- [AMBER] error in loading protein Arunima Shilpi (Mon Apr 07 2014 - 23:05:11 PDT)
- [AMBER] Karplus J-coupling Neha Gandhi (Tue Apr 08 2014 - 02:32:39 PDT)
- [AMBER] Questions about the energy of H3O+ jinfenghuang (Tue Apr 08 2014 - 07:26:22 PDT)
- [AMBER] comparing RDF plots Jio M (Tue Apr 08 2014 - 19:12:17 PDT)
- [AMBER] Fwd: MMPBSA.py PrmtopError: Complex natom != receptor natom + ligand natom Javier Alejandro Rendon Carrillo (Tue Apr 08 2014 - 20:47:14 PDT)
- [AMBER] MMPBSA.py PrmtopError: Complex natom != receptor natom + ligand natom Javier Alejandro Rendon Carrillo (Tue Apr 08 2014 - 21:54:12 PDT)
- [AMBER] error in input file /nmropt=1 Urszula Uciechowska (Wed Apr 09 2014 - 01:22:57 PDT)
- [AMBER] I make box with solvatebox complex TIP3PBOX 15.0 and unfilled gap remains near wall Vytautas Rakeviius (Wed Apr 09 2014 - 05:39:12 PDT)
- [AMBER] KShake problem with GPU Lorenzo Gontrani (Wed Apr 09 2014 - 07:05:33 PDT)
- [AMBER] antechamber Lara rajam (Thu Apr 10 2014 - 06:39:41 PDT)
- [AMBER] rdf averaging problem newamber list (Thu Apr 10 2014 - 15:08:49 PDT)
- Re: [AMBER] AMBER Digest, Vol 818, Issue 1 jinfenghuang (Thu Apr 10 2014 - 19:18:48 PDT)
- [AMBER] Fw:Problems with the gas energy of H3O+ and H2O jinfenghuang (Thu Apr 10 2014 - 20:06:53 PDT)
- [AMBER] Error when runing sietraj for AMBER trajectory Shulin Zhuang (Thu Apr 10 2014 - 22:34:14 PDT)
- [AMBER] Problems with the gas energy of H3O+ and H2O 黄 (Fri Apr 11 2014 - 07:46:09 PDT)
- [AMBER] Mailing list problems David A Case (Fri Apr 11 2014 - 08:02:26 PDT)
- [AMBER] rism1d error Brian Radak (Fri Apr 11 2014 - 17:19:08 PDT)
- [AMBER] MMPBSA Sourav Purohit (Sun Apr 13 2014 - 02:39:17 PDT)
- [AMBER] MMPBSA Sourav Purohit (Sun Apr 13 2014 - 07:09:44 PDT)
- [AMBER] MMPBSA Sourav Purohit (Sun Apr 13 2014 - 12:04:53 PDT)
- [AMBER] Generate a pdb with unique atom names Jean-Patrick Francoia (Sun Apr 13 2014 - 12:38:37 PDT)
- [AMBER] Generate a pdb with unique atom names Jean-Patrick Francoia (Sun Apr 13 2014 - 12:40:18 PDT)
- [AMBER] MMPBSA Sourav Purohit (Sun Apr 13 2014 - 23:35:29 PDT)
- [AMBER] PCA analysis and histogram Neha Gandhi (Mon Apr 14 2014 - 04:45:42 PDT)
- [AMBER] Nonbond Energy for Single Water Molecule ? 黄 (Mon Apr 14 2014 - 07:59:20 PDT)
- [AMBER] SDS parameters in AMBER Rebeca García Fandiño (Tue Apr 15 2014 - 05:28:58 PDT)
- [AMBER] SDS parameters in AMBER ABEL Stephane 175950 (Tue Apr 15 2014 - 05:39:10 PDT)
- [AMBER] Announcement: Release of Amber14 and AmberTools14 David A Case (Tue Apr 15 2014 - 13:35:18 PDT)
- [AMBER] GTX780Ti consistent error "cudaMemcpy GpuBuffer::Download failed unspecified launch failure." Keiran Rowell (Tue Apr 15 2014 - 23:14:58 PDT)
- [AMBER] making test not successful in ambertool14 Mahendra B Thapa (Thu Apr 17 2014 - 05:55:05 PDT)
- [AMBER-Developers] AMBER Workshop Announcement Ross Walker (Thu Apr 17 2014 - 08:47:35 PDT)
- [AMBER] AMBER Workshop Announcement Ross Walker (Thu Apr 17 2014 - 09:26:43 PDT)
- Re: [AMBER] FW: making test not successful in ambertool14 Mahendra B Thapa (Fri Apr 18 2014 - 05:59:15 PDT)
- [AMBER] How to use "divergence" command Mahendra B Thapa (Fri Apr 18 2014 - 09:53:08 PDT)
- [AMBER] 【AMBER12】Including water when using General Amber Force Field leaprc.gaff 石坪江梨花 (Sat Apr 19 2014 - 03:22:48 PDT)
- [AMBER] Running parallel simulations on different no of cores Muthukumaran R (Sat Apr 19 2014 - 10:31:48 PDT)
- [AMBER] Combining trajectories with velocities Eugene Yedvabny (Sat Apr 19 2014 - 11:01:29 PDT)
- [AMBER] Can I do PCA on simply a particular domain of the whole protein? Yip Yew Mun (Sat Apr 19 2014 - 21:38:11 PDT)
- [AMBER] error in running entropy Arunima Shilpi (Sat Apr 19 2014 - 21:55:36 PDT)
- [AMBER] simulated annelaing condtions and requiremnets Nitin Sharma (Sun Apr 20 2014 - 06:47:42 PDT)
- [AMBER] Accelerated MD Sourav Purohit (Mon Apr 21 2014 - 02:34:29 PDT)
- [AMBER] Problems during installation of amber-14 with cuda-5 on GTX 670 James Starlight (Mon Apr 21 2014 - 02:43:15 PDT)
- [AMBER] updates for amber12 bugfix18 Ahmet yıldırım (Mon Apr 21 2014 - 03:43:14 PDT)
- [AMBER] Umbrella Slice module Geoffrey Gray (Mon Apr 21 2014 - 06:29:16 PDT)
- Re: [AMBER] FW: How to use "divergence" command Mahendra B Thapa (Mon Apr 21 2014 - 07:15:43 PDT)
- [AMBER] RESP procedure Ahmet Yıldırım (Mon Apr 21 2014 - 08:51:47 PDT)
- [AMBER] antechamber problem Carlos Romero (Mon Apr 21 2014 - 21:51:02 PDT)
- [AMBER] MMPBSA Mary Varughese (Mon Apr 21 2014 - 22:00:53 PDT)
- [AMBER] Native Contact Help kara tuong vi (Mon Apr 21 2014 - 22:59:38 PDT)
- [AMBER] strip some atoms to compute RMSD Marlet Martinez (Tue Apr 22 2014 - 04:56:40 PDT)
- [AMBER] diferent results zahra khatti (Tue Apr 22 2014 - 07:55:25 PDT)
- [AMBER] Error with quasi-harmonic MMPBSA.py calculations Kipp Johnson (Tue Apr 22 2014 - 16:21:42 PDT)
- [AMBER] xmin Fabiana Caporuscio (Wed Apr 23 2014 - 03:15:18 PDT)
- [AMBER] AMBER minimization problem Valentina Romano (Wed Apr 23 2014 - 09:11:54 PDT)
- [AMBER] FFTW3 related error when compiling AmberTools13 on Fedora20 Soren Wacker (Wed Apr 23 2014 - 13:51:31 PDT)
- [AMBER] OpenMP and MKL Eugene Yedvabny (Wed Apr 23 2014 - 16:21:23 PDT)
- [AMBER] temperature increments newamber list (Wed Apr 23 2014 - 19:30:54 PDT)
- [AMBER] positive value of delta G in MMPBSA calculation Arunima Shilpi (Wed Apr 23 2014 - 20:08:09 PDT)
- [AMBER] modified residues Lara rajam (Wed Apr 23 2014 - 20:32:45 PDT)
- [AMBER] Error: invalid argument launching kernel kNLGenerateSpatialHash ASFARINA AMIR HASSAN (Thu Apr 24 2014 - 02:01:44 PDT)
- [AMBER] distance restraints Neha Gandhi (Thu Apr 24 2014 - 03:04:32 PDT)
- [AMBER] Corresponding dry trajectory and PDB Soumendranath Bhakat (Thu Apr 24 2014 - 03:45:21 PDT)
- [AMBER] MM-PBSA for two drug molecules Fabian Glaser (Thu Apr 24 2014 - 03:46:58 PDT)
- [AMBER] could not extend the MD simulation sunita.tifrh.res.in (Thu Apr 24 2014 - 05:18:59 PDT)
- [AMBER] MMPBSA error Nitin Sharma (Thu Apr 24 2014 - 07:05:47 PDT)
- [AMBER] installation error zahra khatti (Thu Apr 24 2014 - 08:50:04 PDT)
- [AMBER] Question about volume when switching from NPT to NVE ensemble Quynh Vo (Thu Apr 24 2014 - 11:08:08 PDT)
- [AMBER] Reminder: AMBER Molecular Dynamics Workshop Barcelona Jun 2-6. Pre-Registration closes Apr 28th. Ross Walker (Thu Apr 24 2014 - 11:32:55 PDT)
- [AMBER] About Clustering arundhati dutta (Thu Apr 24 2014 - 15:05:10 PDT)
- [AMBER] average problem........ 전선희 (Thu Apr 24 2014 - 21:11:01 PDT)
- [AMBER] MMPBSA query Arunima Shilpi (Thu Apr 24 2014 - 23:07:32 PDT)
- [AMBER] LIPID14 force field for DPPC gel phase simulation Him Shweta (Fri Apr 25 2014 - 00:52:14 PDT)
- [AMBER] Calculation of charges, force constanst, bonds, angles of a ligand using antechamber and gaussian Ahmet yıldırım (Fri Apr 25 2014 - 01:07:26 PDT)
- [AMBER] MD run Lara rajam (Fri Apr 25 2014 - 07:32:58 PDT)
- [AMBER] How to use Divalent ion parameters in tleap mish (Fri Apr 25 2014 - 07:40:23 PDT)
- [AMBER] Hofmeister Effects Brown, Kyle (Fri Apr 25 2014 - 09:47:38 PDT)
- [AMBER] problem with installation amber12 and ambertools13 in ubuntu zahra khatti (Fri Apr 25 2014 - 11:21:42 PDT)
- [AMBER] simulated annelaing of protein ligand complex Nitin Sharma (Fri Apr 25 2014 - 11:46:17 PDT)
- [AMBER] problems with Amber12 installation - cuda and mpi zottisad (Fri Apr 25 2014 - 20:24:52 PDT)
- [AMBER] Accelerated MD Sourav Purohit (Sat Apr 26 2014 - 04:18:19 PDT)
- [AMBER] Accelerated MD Sourav Purohit (Sun Apr 27 2014 - 04:01:08 PDT)
- [AMBER] Corresponding PDB and snapshot PDB Soumendranath Bhakat (Sun Apr 27 2014 - 05:00:50 PDT)
- [AMBER] negative dihedral energy with ff14ipq Thomas Evangelidis (Sun Apr 27 2014 - 12:42:50 PDT)
- [AMBER] velocity information in restart file HM (Mon Apr 28 2014 - 04:54:29 PDT)
- [AMBER] Simulation of protein- cyclic nucleotide complex James Starlight (Mon Apr 28 2014 - 05:02:21 PDT)
- [AMBER] pmemd.cuda error amber14 Pierpaolo Cacciotto (Mon Apr 28 2014 - 09:05:09 PDT)
- [AMBER] Regarding simulation of alanine molecules in water box MOHD HOMAIDUR RAHMAN (Tue Apr 29 2014 - 03:47:33 PDT)
- [AMBER] Quantification of alpha helix Suchetana Gupta (Tue Apr 29 2014 - 08:06:56 PDT)
- [AMBER] Minimization with (0, 0, 0) coordinates Jean-Patrick Francoia (Tue Apr 29 2014 - 08:19:45 PDT)
- [AMBER] PCA analysis Ibrahim Said (Tue Apr 29 2014 - 08:40:05 PDT)
- [AMBER] Extract velocity from the restart file Yin, Guowei (Tue Apr 29 2014 - 14:03:42 PDT)
- [AMBER] Minimization with restraints Valentina Romano (Wed Apr 30 2014 - 02:42:02 PDT)
- [AMBER] How to extract each frame of a trajectory as individual .mdcrd files? Yip Yew Mun (Wed Apr 30 2014 - 06:28:48 PDT)
- [AMBER] ptraj in parallel zahra khatti (Wed Apr 30 2014 - 08:56:49 PDT)
- [AMBER] how to protonate phosphate groups of nucleotides Valentina D'Atri (Wed Apr 30 2014 - 10:13:32 PDT)
- Last message date: Wed Apr 30 2014 - 11:00:02 PDT
- Archived on: Wed Apr 17 2024 - 05:54:49 PDT
