Amber Archive Jun 2015 by thread
- [AMBER] Entropy Ramin Ekhteiari (Sun May 31 2015 - 23:25:36 PDT)
- [AMBER] How to Simulate Monoclinic crystal packing arrangement. srilaxmi reddy (Mon Jun 01 2015 - 02:55:20 PDT)
- [AMBER] How to generate Phi_Psi by cpptraj ? Michael Shokhen (Mon Jun 01 2015 - 12:27:19 PDT)
- Re: [AMBER] Arsenic force field parametrization Pengfei Li (Mon Jun 01 2015 - 15:56:59 PDT)
- [AMBER] Bug or feature of tleap Julio Dominguez (Mon Jun 01 2015 - 16:01:27 PDT)
- [AMBER] torsions in parm10.dat Jeffrey Teillet (Tue Jun 02 2015 - 01:28:58 PDT)
- [AMBER] How can I do a thermodynamic integration using Simpson's rules ? Jinfeng Huang (Tue Jun 02 2015 - 02:20:25 PDT)
- [AMBER] Density for a protein ligand complex run Mrinda Jones (Tue Jun 02 2015 - 05:16:03 PDT)
- [AMBER] GPU machines in the UK. Peter Winn (Tue Jun 02 2015 - 06:49:33 PDT)
- [AMBER] Only -mpi option creates the python modules. Is this right? Eduardo Almeida Costa (Tue Jun 02 2015 - 07:26:47 PDT)
- [AMBER] Imaging & centering Angela de Manzanos (Tue Jun 02 2015 - 09:33:58 PDT)
- [AMBER] ERROR WHILE RUNNING ANTECHAMBER ROOPALI VERMA (Wed Jun 03 2015 - 01:08:00 PDT)
- [AMBER] force-momentum based SGLD algorithm barbara rossi (Wed Jun 03 2015 - 02:22:16 PDT)
- [AMBER] circle of correlation - PCA - AMBERtools Jose Manuel Gally (Wed Jun 03 2015 - 07:33:36 PDT)
- [AMBER] pmemd.cuda.MPI vs openmpi Victor Ma (Wed Jun 03 2015 - 10:54:44 PDT)
- [AMBER] Bad Frames in Corrupted Trajectories Amanda Li (Wed Jun 03 2015 - 12:22:55 PDT)
- [AMBER] cpptraj crosscorr command Gard Nelson (Wed Jun 03 2015 - 16:53:25 PDT)
- [AMBER] Fwd: GPU pmemd.cuda runs very slow (3ns/day)??? Chinh Su Tran To (Thu Jun 04 2015 - 01:13:55 PDT)
- [AMBER] Regarding dihedral scanning Soumendranath Bhakat (Thu Jun 04 2015 - 01:36:21 PDT)
- [AMBER] proxy configuration abdennour braka (Thu Jun 04 2015 - 02:48:45 PDT)
- [AMBER] Converting Gromacs topology files to Amber format Jason Swails (Thu Jun 04 2015 - 06:33:09 PDT)
- [AMBER] Abrupt RMSD change during DNA simulation for a short interval of time jacob wick (Thu Jun 04 2015 - 06:38:17 PDT)
- Re: [AMBER] Torsion restraints with pmemd.amoeba Karl Debiec (Thu Jun 04 2015 - 08:41:41 PDT)
- [AMBER] write PCA mode trajectory with cpptraj Vlad Cojocaru (Fri Jun 05 2015 - 01:18:35 PDT)
- [AMBER] how to convert pdb to rst file ? Indrajit Deb (Fri Jun 05 2015 - 08:26:47 PDT)
- [AMBER] Error unknown flag: –O Michael Shokhen (Sat Jun 06 2015 - 01:24:19 PDT)
- [AMBER] During MD simulation protein drifts out of periodic cell Michael Shokhen (Sun Jun 07 2015 - 03:35:23 PDT)
- [AMBER] How to avoid protein drift? Michael Shokhen (Sun Jun 07 2015 - 05:08:36 PDT)
- [AMBER] problem with extraction of potential energy for the ligand Maryam Hamzehee (Sun Jun 07 2015 - 10:14:26 PDT)
- [AMBER] Leap : problem with copying and combining DNA items Jérémie Knoops (Sun Jun 07 2015 - 23:58:18 PDT)
- [AMBER] Regarding creating Mg2+ ions topology and parameter file ROOPALI VERMA (Mon Jun 08 2015 - 03:31:53 PDT)
- [AMBER] Error while running leap for a protein containing Co2+ Suchetana Gupta (Mon Jun 08 2015 - 05:05:38 PDT)
- [AMBER] Fwd: Question about building a branched levan oligosaccharide Surasak Chunsrivirot (Mon Jun 08 2015 - 07:26:17 PDT)
- [AMBER] Few queries about membrane protein simulations anu chandra (Mon Jun 08 2015 - 07:45:18 PDT)
- [AMBER] Centre of Mass or geometry issue Soumendranath Bhakat (Tue Jun 09 2015 - 01:33:49 PDT)
- [AMBER] HMR Parker de Waal (Tue Jun 09 2015 - 11:09:43 PDT)
- [AMBER] problem with extraction of potential energy for the ligand Maryam Hamzehee (Wed Jun 10 2015 - 02:50:14 PDT)
- [AMBER] Parmed.py_ImportError: No module named ParmedTools.logos Sheehan, Alice (Wed Jun 10 2015 - 08:54:20 PDT)
- [AMBER] Announcement: AMBER Workshop - London, Mon July 6th to Fri July 10th 2015 - Registration deadline June 15th (this coming Monday!) Ross Walker (Wed Jun 10 2015 - 09:23:17 PDT)
- [AMBER] Steered Molecular Dynamics Brittany Boykin (Wed Jun 10 2015 - 09:35:53 PDT)
- [AMBER] Charges for H-atoms in GLYCAM? Chris (Wed Jun 10 2015 - 10:32:57 PDT)
- [AMBER] problem with extraction of potential energy for the ligand Maryam Hamzehee (Wed Jun 10 2015 - 10:45:29 PDT)
- [AMBER] basic question - sanity check Jonathan Gough (Wed Jun 10 2015 - 10:48:32 PDT)
- [AMBER] Restraining distance between molecules initially jacob wick (Wed Jun 10 2015 - 23:40:55 PDT)
- [AMBER] Regarding the protonation states of Histidine muhammad tahir ayub (Wed Jun 10 2015 - 23:50:10 PDT)
- [AMBER] Help - setting up parallel machine anu chandra (Thu Jun 11 2015 - 03:39:26 PDT)
- [AMBER] Antechamber on regular nucleotides Mrinda Jones (Thu Jun 11 2015 - 05:58:14 PDT)
- [AMBER] tinker_to_amber doesn't like AMOEBA reference frames for chloride Baker, Lewis Robert (Thu Jun 11 2015 - 10:30:02 PDT)
- [AMBER] cpptraj matrix dist modifications Gard Nelson (Thu Jun 11 2015 - 11:59:19 PDT)
- [AMBER] distance restrain Lara rajam (Thu Jun 11 2015 - 13:11:38 PDT)
- [AMBER] Problem with stripped combined mdcrd files Soong Jiaxin (Thu Jun 11 2015 - 19:48:06 PDT)
- [AMBER] MMPBSA sasopt problem Debodyuti Dutta (Thu Jun 11 2015 - 23:40:31 PDT)
- [AMBER] Pairwise Interaction Energy between two urea pairs MOHD HOMAIDUR RAHMAN (Thu Jun 11 2015 - 23:45:51 PDT)
- [AMBER] conserved water in MMPBSA Albert (Fri Jun 12 2015 - 06:03:15 PDT)
- [AMBER] modifying cpptraj Gard Nelson (Fri Jun 12 2015 - 10:16:32 PDT)
- [AMBER] Dimer Rotations Brittany Boykin (Fri Jun 12 2015 - 14:56:03 PDT)
- [AMBER] error encountered on extending production simulation on Amber14 Harmeet Kaur (Sat Jun 13 2015 - 01:30:01 PDT)
- [AMBER] Issue Lennard jones interaction Loic ETHEVE (Sat Jun 13 2015 - 02:01:33 PDT)
- [AMBER] Alternative Membrane System Tutorial Parker de Waal (Sat Jun 13 2015 - 18:08:29 PDT)
- [AMBER] Python: AttributeError: 'dict' object has no attribute 'property' Jean-Patrick Francoia (Sun Jun 14 2015 - 10:44:43 PDT)
- [AMBER] Population analysis Kshatresh Dutta Dubey (Mon Jun 15 2015 - 00:54:25 PDT)
- [AMBER] MMPBSA: Generalised Born Warning George Tzotzos (Mon Jun 15 2015 - 06:13:47 PDT)
- [AMBER] QM-MM Equilibration of the System Brittany Boykin (Mon Jun 15 2015 - 09:11:25 PDT)
- [AMBER] A problem in using tLeap Morteza Chehel Amirani (Mon Jun 15 2015 - 11:12:50 PDT)
- [AMBER] tcorr and order parameters Travis Hughes (Mon Jun 15 2015 - 16:08:30 PDT)
- Re: [AMBER] AMBER Digest, Vol 1220, Issue 1 Huang (Mon Jun 15 2015 - 21:45:01 PDT)
- [AMBER] what's the default radius? Albert (Mon Jun 15 2015 - 23:06:31 PDT)
- [AMBER] problem in .pdb after md simulation Vishal Nemaysh (Mon Jun 15 2015 - 23:52:58 PDT)
- [AMBER] Problem generating peptide Harshala Haldankar (Tue Jun 16 2015 - 04:38:50 PDT)
- [AMBER] Freezing atoms in space during a simulation Jonathan Gough (Tue Jun 16 2015 - 11:06:30 PDT)
- [AMBER] GPI-anchor protein cleavage Aditya Padhi (Tue Jun 16 2015 - 11:49:04 PDT)
- [AMBER] [cpptraj] Changing frames in a trajectory file Juan Eiros Zamora (Tue Jun 16 2015 - 12:19:08 PDT)
- [AMBER] NMR restraints with pmemd.cuda problem Miroslav Krepl (Tue Jun 16 2015 - 14:25:41 PDT)
- [AMBER] The respective references suggested by the developers of Amber and HADDOCK Zhichao Lou (Tue Jun 16 2015 - 20:01:30 PDT)
- [AMBER] error in ante-MMPBSA.py Chris (Tue Jun 16 2015 - 21:41:25 PDT)
- [AMBER] help in radial command Robin Jain (Wed Jun 17 2015 - 01:32:19 PDT)
- [AMBER] binding energy for the frames Maryam Hamzehee (Wed Jun 17 2015 - 04:14:53 PDT)
- [AMBER] Error: unspecified launch failure launching kernel kNLSkinTest zayan alhalabi (Wed Jun 17 2015 - 06:18:26 PDT)
- [AMBER] subroutine qm_write_pdb Hector A. Baldoni (Wed Jun 17 2015 - 06:30:25 PDT)
- [AMBER] cpptraj : gzip or bzip2 netcdf trajectory files not recognized Marion, Antoine (Wed Jun 17 2015 - 06:37:47 PDT)
- [AMBER] 2nd mail: subroutine qm_write_pdb Hector A. Baldoni (Wed Jun 17 2015 - 06:47:41 PDT)
- [AMBER] problem zayan alhalabi (Wed Jun 17 2015 - 06:52:01 PDT)
- [AMBER] savepdb command not working in xleap muhammad tahir ayub (Wed Jun 17 2015 - 08:20:02 PDT)
- [AMBER] Spreading water molecules over the simulation time Morteza Chehel Amirani (Wed Jun 17 2015 - 12:40:34 PDT)
- [AMBER] Free Energy Landscape for cMD bharat lakhani (Wed Jun 17 2015 - 12:53:05 PDT)
- [AMBER] combine multiple trajectory Yin, Guowei (Wed Jun 17 2015 - 13:33:18 PDT)
- [AMBER] Free Energy Landscape for cMD Help bharat lakhani (Wed Jun 17 2015 - 19:17:04 PDT)
- [AMBER] Get energy information loic etheve (Thu Jun 18 2015 - 00:28:09 PDT)
- [AMBER] To Add or Not To Add - Salt Conc in Explicit Solvent Yip Yew Mun (Thu Jun 18 2015 - 00:32:41 PDT)
- [AMBER] Connect atoms in a pdb created with nab Jean-Patrick Francoia (Thu Jun 18 2015 - 01:31:52 PDT)
- [AMBER] energy difference between GBSA and PBSA Chris (Thu Jun 18 2015 - 02:32:58 PDT)
- [AMBER] problems with relative TI calculations hannes.loeffler.stfc.ac.uk (Thu Jun 18 2015 - 02:35:42 PDT)
- [AMBER] Energy contribution of phosphorylated residues Parker de Waal (Thu Jun 18 2015 - 06:57:14 PDT)
- [AMBER] Recover .lib from .prmtop and .inpcrd Yin, Xing (Thu Jun 18 2015 - 08:35:14 PDT)
- [AMBER] QM-MM Equilibration Step Brittany Boykin (Thu Jun 18 2015 - 10:06:34 PDT)
- [AMBER] ERROR while running XLEAP Pierre Bertin (Thu Jun 18 2015 - 11:13:29 PDT)
- [AMBER] amber 15 compiled with multiple GPUs nam kim (Thu Jun 18 2015 - 22:43:01 PDT)
- [AMBER] solid surface interacting with organic Azade Yazdan Yar (Fri Jun 19 2015 - 03:12:55 PDT)
- [AMBER] About OH conformation in protonated Asp/Glu (ASH/GLH) Marc van der Kamp (Fri Jun 19 2015 - 04:29:02 PDT)
- [AMBER] RESP charge derivation Neelanjana Sengupta (Fri Jun 19 2015 - 10:56:08 PDT)
- [AMBER] accuracy of FEW free energy calculation Albert (Fri Jun 19 2015 - 13:44:15 PDT)
- [AMBER] Regarding hydrogen bond time correlation function in cpptraj MOHD HOMAIDUR RAHMAN (Sat Jun 20 2015 - 03:27:34 PDT)
- [AMBER] problem zayan alhalabi (Sat Jun 20 2015 - 06:25:59 PDT)
- [AMBER] Quasi harmonic bad eigenvalue error D.J. Pattinson (Sat Jun 20 2015 - 07:28:45 PDT)
- [AMBER] standard and non-standard residues Ramin Ekhteiari (Sat Jun 20 2015 - 08:09:43 PDT)
- [AMBER] resp: errors in reading the electrostatic potential Neelanjana Sengupta (Sun Jun 21 2015 - 02:51:03 PDT)
- [AMBER] Load "library" of custom residues Jean-Patrick Francoia (Sun Jun 21 2015 - 04:57:55 PDT)
- [AMBER] resp: errors in reading the electrostatic potential Neelanjana Sengupta (Sun Jun 21 2015 - 05:29:47 PDT)
- [AMBER] using AMBER 14sb force-field in CHARMM program Iceriver Forever (Sun Jun 21 2015 - 09:21:50 PDT)
- [AMBER] aMD and scaled MD simulation-NVT production runs Neha Gandhi (Sun Jun 21 2015 - 23:24:25 PDT)
- [AMBER] how to export pdb in 'cluster' with 'autoimage' windy (Mon Jun 22 2015 - 02:11:32 PDT)
- [AMBER] Recover the water model and periodic box from built parm files Yin, Xing (Mon Jun 22 2015 - 07:01:10 PDT)
- [AMBER] united atom force field anu chandra (Mon Jun 22 2015 - 07:26:54 PDT)
- [AMBER] Ligand entry and exit path Debodyuti Dutta (Mon Jun 22 2015 - 08:26:41 PDT)
- [AMBER] Use of OPLS-AA/M force field in AMBER via CHAMBER Karl Debiec (Mon Jun 22 2015 - 08:54:31 PDT)
- [AMBER] Is there a way to do simultaneous Cartesian position and distance restraints in amber? Arthur Roberts (Mon Jun 22 2015 - 09:53:42 PDT)
- Re: [AMBER] Per residue rmsd bharat lakhani (Mon Jun 22 2015 - 09:59:05 PDT)
- [AMBER] Required time for a typical MD run Morteza Chehel Amirani (Mon Jun 22 2015 - 14:10:39 PDT)
- [AMBER] MMGBSA on Protein-DNA/RNA complex Muthukumaran R (Tue Jun 23 2015 - 03:32:15 PDT)
- [AMBER] parmwrite in cpptraj: AmberTools13 vs. 15 Gerald Monard (Tue Jun 23 2015 - 05:15:21 PDT)
- [AMBER] MMPBSA on DNA-Protein-Ligand complex Norbert GARNIER (Tue Jun 23 2015 - 05:26:07 PDT)
- [AMBER] MMPBSA_API: AmberTools13 vs. 15 Gerald Monard (Tue Jun 23 2015 - 06:49:27 PDT)
- [AMBER] Error during action on loaded multiple trajectory in cpptraj 15 MOHD HOMAIDUR RAHMAN (Wed Jun 24 2015 - 05:52:14 PDT)
- [AMBER] Hydrogen bond bridges DEBOSTUTI GHOSHDASTIDAR (Wed Jun 24 2015 - 06:52:23 PDT)
- [AMBER] unsaturated sugars Lara rajam (Wed Jun 24 2015 - 07:06:07 PDT)
- [AMBER] generating topology without loading Frcmod file Arun Srikanth (Wed Jun 24 2015 - 10:07:08 PDT)
- [AMBER] cpptraj Help rmsd between two homologous proteins and their Trajectory bharat lakhani (Wed Jun 24 2015 - 10:56:18 PDT)
- [AMBER] hbond lifetime cpptraj Lara rajam (Wed Jun 24 2015 - 11:48:08 PDT)
- [AMBER] hbond zahra khatti (Wed Jun 24 2015 - 14:37:12 PDT)
- [AMBER] relaxation in t/xleap newamber list (Wed Jun 24 2015 - 15:33:51 PDT)
- [AMBER] Defining the box dimensions while making the top and crd files Iqbal, Muhammad Sajid (Wed Jun 24 2015 - 17:02:03 PDT)
- [AMBER] A possible bug in t leap when creating topology file ? Arun Srikanth (Wed Jun 24 2015 - 20:59:57 PDT)
- [AMBER] Problem in Radial command Robin Jain (Wed Jun 24 2015 - 22:43:01 PDT)
- [AMBER] error in MD simulation erik.laurini.di3.units.it (Thu Jun 25 2015 - 07:17:56 PDT)
- [AMBER] help in radial command Robin Jain (Thu Jun 25 2015 - 22:20:22 PDT)
- [AMBER] Align 1000 frames into one .crd file Hadeer ELHabashy (Fri Jun 26 2015 - 04:17:46 PDT)
- [AMBER] Regarding calculation of viscosity of system MOHD HOMAIDUR RAHMAN (Fri Jun 26 2015 - 05:09:56 PDT)
- [AMBER] Lipid 14 force field Ning Xiang (Fri Jun 26 2015 - 07:16:24 PDT)
- [AMBER] Defining the box dimensions while making the top and crd files Iqbal, Muhammad Sajid (Fri Jun 26 2015 - 11:48:46 PDT)
- [AMBER] Halogen at the dftb level Hector A. Baldoni (Fri Jun 26 2015 - 12:42:54 PDT)
- [AMBER] Amber14 compatibilty with GTX-760 GPU card Elvis Martis (Fri Jun 26 2015 - 20:46:37 PDT)
- [AMBER] some doubts about simulation analysis Mary Varughese (Sat Jun 27 2015 - 00:53:28 PDT)
- Re: [AMBER] Amber14 compatibility with GTX-760 GPU card Elvis Martis (Sat Jun 27 2015 - 12:35:28 PDT)
- [AMBER] lifetime analysis zahra khatti (Sat Jun 27 2015 - 15:12:00 PDT)
- [AMBER] Generating RESP Charges For Tightly-Bound Complexes - Charges from the complexes or the fragments? Damian G. Allis, Ph.D. (Sat Jun 27 2015 - 19:08:43 PDT)
- [AMBER] lifetime analysis zahra khatti (Sun Jun 28 2015 - 14:22:52 PDT)
- [AMBER] lifetime analysis zahra khatti (Sun Jun 28 2015 - 14:34:26 PDT)
- [AMBER] lifetime zahra khatti (Sun Jun 28 2015 - 14:53:54 PDT)
- [AMBER] lifetime zahra khatti (Sun Jun 28 2015 - 15:06:50 PDT)
- [AMBER] Experimental values about some orgnaic solvent BOX wangmt (Sun Jun 28 2015 - 23:43:41 PDT)
- [AMBER] Running amber forcefield in NAMD Yogeeshwar Ajjugal (Mon Jun 29 2015 - 05:02:32 PDT)
- [AMBER] built-in scc-dftb method amber15 Hector A. Baldoni (Mon Jun 29 2015 - 05:22:55 PDT)
- [AMBER] cuda7 not supported? Albert (Mon Jun 29 2015 - 10:34:15 PDT)
- [AMBER] Quantifying Membrane Contact or insertion Parker de Waal (Mon Jun 29 2015 - 11:39:35 PDT)
- [AMBER] acpype fails to run on provided tests Daniel Bork (Mon Jun 29 2015 - 13:27:14 PDT)
- [AMBER] Installation Question - Missing file? Jim Wu (Mon Jun 29 2015 - 15:36:19 PDT)
- [AMBER] Normal mode calculation was failed with MMPBSA.py wliu (Mon Jun 29 2015 - 19:30:00 PDT)
- [AMBER] PCA Calculations Parker de Waal (Mon Jun 29 2015 - 19:43:43 PDT)
- [AMBER] svdcmp in sander/ncsu-rmsd.F90 (AmberTools15) is sensitive to higher optimizations, suggest using lapack routine instead Åke Sandgren (Mon Jun 29 2015 - 23:41:35 PDT)
- [AMBER] RESP: charges on equivalent atoms Neelanjana Sengupta (Tue Jun 30 2015 - 01:55:20 PDT)
- [AMBER] Post processing of trajectory with sander MOHD HOMAIDUR RAHMAN (Tue Jun 30 2015 - 05:59:02 PDT)
- [AMBER] folding RNA using SGLD Asmita Gupta (Tue Jun 30 2015 - 07:11:21 PDT)
- [AMBER] simulation phosphorylated complex of protein Ziba Bahadori (Tue Jun 30 2015 - 07:24:36 PDT)
- [AMBER] RESP Charge Fit - Intramolecular Hydrogen Bond Yip Yew Mun (Tue Jun 30 2015 - 07:48:36 PDT)
- [AMBER] Output format in sander John Dood (Tue Jun 30 2015 - 10:03:01 PDT)
- [AMBER] error in parallel run Lara rajam (Tue Jun 30 2015 - 10:20:37 PDT)
- [AMBER] Rms fitting to a reference structure with a differnt number atoms to top file George Green (Tue Jun 30 2015 - 12:42:12 PDT)
- [AMBER] Explicit Solvent Constant pH MD Rahul Ramesh (Tue Jun 30 2015 - 13:53:13 PDT)
- [AMBER] Compile Failure Jim Wu (Tue Jun 30 2015 - 15:06:36 PDT)
- [AMBER] Cpptraj failure Lin Song (Tue Jun 30 2015 - 19:47:37 PDT)
- Last message date: Tue Jun 30 2015 - 21:30:02 PDT
- Archived on: Wed Dec 25 2024 - 05:55:12 PST
