Amber Archive Jan 2012 by thread
- Re: [AMBER] Solvate a system in AMBER 11. Daniel Sindhikara (Sat Dec 31 2011 - 17:27:32 PST)
- Re: [AMBER] Regarding solvating a protein using amber Daniel Sindhikara (Sun Jan 01 2012 - 22:30:50 PST)
- Re: [AMBER] free energy calculation: turn off the VDW interaction between ligand and protein bxiong (Sun Jan 01 2012 - 22:32:53 PST)
- [AMBER] Using antechamber -Heme molecule יוכבד (Mon Jan 02 2012 - 03:24:26 PST)
- [AMBER] Ser/Thr phosphorylation support in AMBER-11 Michael Petukhov (Mon Jan 02 2012 - 09:58:24 PST)
- Re: [AMBER] Chloroform in Amber, a rigid model? case (Mon Jan 02 2012 - 19:36:39 PST)
- [AMBER] How to set the dist.RST file in SMD using Amber11? 潘显超 (Mon Jan 02 2012 - 23:12:00 PST)
- Re: [AMBER] studying the pH-dependent stability of a "large" homodimeric protein Jan-Philip Gehrcke (Tue Jan 03 2012 - 07:45:16 PST)
- [AMBER] rounding issue Dmitry Mukha (Tue Jan 03 2012 - 07:49:41 PST)
- [AMBER] Free Energy Calculations of Potassium and Chloride Sai Kumar Ramadugu (Tue Jan 03 2012 - 11:58:51 PST)
- Re: [AMBER] CUDA PMEMD on Longhorn: MPI_Win_free fatal error Ben Roberts (Tue Jan 03 2012 - 13:10:29 PST)
- [AMBER] how to set the dist.RST file in SMD using Amber11? pxc.cqu.edu.cn (Tue Jan 03 2012 - 17:20:56 PST)
- [AMBER] PMEMD installation error hari krishna (Tue Jan 03 2012 - 21:05:45 PST)
- Re: [AMBER] Which method is the best way to solve metalloprotein?MCPB or Only consider Electrostatic and VDW JiYuan Liu (Wed Jan 04 2012 - 00:07:08 PST)
- Re: [AMBER] chamber-fortran runtime error colvin (Wed Jan 04 2012 - 01:23:45 PST)
- [AMBER] Error while compiling AMBER11 Lucas A. Defelipe (Wed Jan 04 2012 - 08:17:30 PST)
- [AMBER] ptaj: RMSD George Tzotzos (Wed Jan 04 2012 - 10:15:38 PST)
- [AMBER] Deleting Cymal-6 from PDB Chris Bryant (Wed Jan 04 2012 - 10:20:52 PST)
- [AMBER] Problem with oxygens bonded to three atoms in metal clusters Ben Roberts (Wed Jan 04 2012 - 14:03:50 PST)
- [AMBER] Solvation of a system in AMBER11. Sudarshan Debnath (Wed Jan 04 2012 - 20:19:37 PST)
- [AMBER] Problem with generating topology file using tleap Devlina Chakravarty (Thu Jan 05 2012 - 00:19:14 PST)
- [AMBER] Solvation of a system in AMBER11. Sudarshan Debnath (Thu Jan 05 2012 - 04:52:07 PST)
- [AMBER] Origin of calculated system temperature (in mdout file) Jan-Philip Gehrcke (Thu Jan 05 2012 - 09:01:56 PST)
- [AMBER] Problem with clashing solvent molecules with solvateoct Gonzalo Jimenez Oses (Thu Jan 05 2012 - 09:07:33 PST)
- [AMBER] Problem with PB calculation using ff99SBildn: PB Bomb in pb_aaradi(): No radius assigned for atom Ryan Pavlovicz (Thu Jan 05 2012 - 09:53:31 PST)
- [AMBER] Gas Phase Simulations in PMEMD Aron Broom (Thu Jan 05 2012 - 13:20:34 PST)
- [AMBER] SANDER NMR violations Charles Johnson (Thu Jan 05 2012 - 13:40:21 PST)
- [AMBER] calculation of spectral density Mahendra B Thapa (Thu Jan 05 2012 - 14:51:35 PST)
- [AMBER] Ambertools installation. Sudarshan Debnath (Thu Jan 05 2012 - 23:10:20 PST)
- [AMBER] No leap in ambertool11 nicholus bhattacharjee (Fri Jan 06 2012 - 05:36:11 PST)
- [AMBER] installation subrata paul (Sat Jan 07 2012 - 02:55:05 PST)
- [AMBER] system breaks during simulation moitrayee.mbu.iisc.ernet.in (Sat Jan 07 2012 - 11:20:16 PST)
- [AMBER] clarification regarding the charge on the cluster in MCPB kanika singal (Mon Jan 09 2012 - 01:15:49 PST)
- Re: [AMBER] PMEMD parallelization on Ubuntu Lucid Mark Williamson (Mon Jan 09 2012 - 06:52:12 PST)
- [AMBER] gpu information Elisa Frezza (Mon Jan 09 2012 - 07:01:14 PST)
- [AMBER] Problems with amber topology in NAMD Osman, Roman (Mon Jan 09 2012 - 09:38:11 PST)
- [AMBER] antechamber parameter file issues? Thomas Pochapsky (Mon Jan 09 2012 - 10:15:40 PST)
- [AMBER] problem with ester bond between side chains moitrayee.mbu.iisc.ernet.in (Tue Jan 10 2012 - 02:33:17 PST)
- [AMBER] improper torsions in old prep form Andrew Voronkov (Tue Jan 10 2012 - 05:09:15 PST)
- [AMBER] installation amber10 subrata paul (Tue Jan 10 2012 - 05:46:11 PST)
- [AMBER] i7 extreme for Amber GPU computing? Raik Grünberg (Tue Jan 10 2012 - 12:34:32 PST)
- Re: [AMBER] mtkpp: parameters in metals.frcmod Patrick G Blachly (Tue Jan 10 2012 - 14:52:05 PST)
- [AMBER] Solvation of a system in Amber11 Sudarshan Debnath (Tue Jan 10 2012 - 22:07:25 PST)
- Re: [AMBER] AMBER11, pmemd.cuda: the system crashed. Chinh Su Tran To (Wed Jan 11 2012 - 00:04:48 PST)
- [AMBER] Amber 11 installation problem R. K. Kar (Wed Jan 11 2012 - 00:19:59 PST)
- Re: [AMBER] combination of CHAMBER prmtop and pmemd.cuda is causing serious instability Marc van der Kamp (Wed Jan 11 2012 - 08:53:08 PST)
- [AMBER] bad atom type: f Rajesh Singh (Wed Jan 11 2012 - 08:57:49 PST)
- [AMBER] q4md: When using red, it outputs incorrect primary amine geometry as tetrahedral instead of trigonal planar g t (Thu Jan 12 2012 - 03:23:51 PST)
- [AMBER] rism1d solvent models Meli Massimiliano (Thu Jan 12 2012 - 07:27:39 PST)
- [AMBER] closest water George Tzotzos (Thu Jan 12 2012 - 09:29:18 PST)
- [AMBER] Fwd: Re: [q4md-fft] When using red, it outputs incorrect primary amine geometry as tetrahedral instead of trigonal planar FyD (Thu Jan 12 2012 - 09:57:01 PST)
- [AMBER] Chirality restraints in Simulated Annealing Josmar R. da Rocha (Thu Jan 12 2012 - 14:07:38 PST)
- [AMBER] Running NAB Aleksandra Skoric (Thu Jan 12 2012 - 14:25:40 PST)
- [AMBER] PES for dialanine Ye MEI (Thu Jan 12 2012 - 19:25:51 PST)
- [AMBER] AMBERTOOL1.5 installation Hirdesh Kumar (Fri Jan 13 2012 - 00:43:14 PST)
- [AMBER] Problem with xleap installation Cristina Airoldi (Fri Jan 13 2012 - 02:20:12 PST)
- [AMBER] tleap/xleap segmenatation fault Marina Grabar Branilović (Fri Jan 13 2012 - 05:30:21 PST)
- [AMBER] Issue with HowToCompileAmberTools1.5AndAMBER11WithUbuntu10.04.3LTS.html Jan-Philip Gehrcke (Fri Jan 13 2012 - 06:34:06 PST)
- [AMBER] Upcoming of Amber Workshop in USA manikanthan bhavaraju (Fri Jan 13 2012 - 09:45:25 PST)
- [AMBER] ACE and NME caps Chris Bryant (Fri Jan 13 2012 - 11:53:57 PST)
- [AMBER] water molecules within a distance cutoff; ptraj analysis kanika singal (Fri Jan 13 2012 - 23:57:14 PST)
- [AMBER] Water considered in Amber11. Sudarshan Debnath (Sat Jan 14 2012 - 00:44:25 PST)
- [AMBER] Question related to the Force Field and water Sindrila Dutta banik (Sat Jan 14 2012 - 00:56:05 PST)
- [AMBER] strip water and save new trajectory Hirdesh Kumar (Sat Jan 14 2012 - 06:27:49 PST)
- [AMBER] Question related to the B factor Sindrila Dutta banik (Sat Jan 14 2012 - 09:03:19 PST)
- [AMBER] mpi4py installation for mmpbsa_py Vlad Cojocaru (Sat Jan 14 2012 - 14:39:58 PST)
- [AMBER] Using glycam06 under Amber8 john Kerk (Sun Jan 15 2012 - 10:45:19 PST)
- Re: [AMBER] ambertool question !!! Алексей Раевский (Sun Jan 15 2012 - 13:57:27 PST)
- [AMBER] nab string functions M. L. Dodson (Sun Jan 15 2012 - 16:34:33 PST)
- [AMBER] Calculate the cosine content of PC surasak chunsrivirot (Mon Jan 16 2012 - 02:44:20 PST)
- Re: [AMBER] What is the parameters for Mg2+? Jesper Sørensen (Mon Jan 16 2012 - 18:30:58 PST)
- [AMBER] Problem regarding Molecular Dynamics simulation of DNA using Parmbsc0 and ff99sb Muhammad Khaled Tumbi (Tue Jan 17 2012 - 05:12:51 PST)
- [AMBER] Conversion of binary velocity files to pdb style Ganesh Kamath (Tue Jan 17 2012 - 09:22:14 PST)
- [AMBER] :How to get 1PLC_mod.pdb from 1PLC.pdb [TUTORIAL A1 - SECTION 1] Mahendra B Thapa (Tue Jan 17 2012 - 14:24:19 PST)
- [AMBER] MCPB : addFragment in case of CYM kanika singal (Tue Jan 17 2012 - 22:50:08 PST)
- [AMBER] chamber segfault Hannes Loeffler (Wed Jan 18 2012 - 02:44:12 PST)
- [AMBER] Minimization problem for a homotrimer of small molecules Baptiste Legrand (Wed Jan 18 2012 - 03:22:36 PST)
- [AMBER] nmode error Urszula Uciechowska (Wed Jan 18 2012 - 03:42:30 PST)
- [AMBER] Adjusting density Beale, John (Wed Jan 18 2012 - 05:28:31 PST)
- [AMBER] AmberTools Installation Error Hevener, Kirk (Wed Jan 18 2012 - 08:59:15 PST)
- Re: [AMBER] FW: :How to get 1PLC_mod.pdb from 1PLC.pdb [TUTORIAL A1 - SECTION 1] Mahendra B Thapa (Wed Jan 18 2012 - 10:25:21 PST)
- Re: [AMBER] FW: FW: :How to get 1PLC_mod.pdb from 1PLC.pdb [TUTORIAL A1 - SECTION 1] Mahendra B Thapa (Wed Jan 18 2012 - 12:10:26 PST)
- [AMBER] simulation with implicit solvent runs longer than explicit? Victor Ma (Wed Jan 18 2012 - 13:48:01 PST)
- [AMBER] amber hangs on minimization Jorgen Simonsen (Thu Jan 19 2012 - 01:04:08 PST)
- [AMBER] Glycine in QM region Fernando Martín García (Thu Jan 19 2012 - 02:36:18 PST)
- [AMBER] error message for installing amber 10 Per Jr. Greisen (Thu Jan 19 2012 - 03:46:24 PST)
- [AMBER] MMPBSA analysis vaibhav dixit (Thu Jan 19 2012 - 04:44:58 PST)
- [AMBER] negative DeltaGsolv in MMPBSA vaibhav dixit (Thu Jan 19 2012 - 07:49:42 PST)
- [AMBER] Amber11 tests fail Massimiliano Porrini (Thu Jan 19 2012 - 10:05:10 PST)
- [AMBER] MCPB: error Pls help kanika singal (Fri Jan 20 2012 - 06:46:27 PST)
- [AMBER] MD trajectory extraction using ptraj Lianhu Wei (Fri Jan 20 2012 - 07:25:09 PST)
- [AMBER] which fitting methods should I use for OPLS FF? Albert (Fri Jan 20 2012 - 22:23:03 PST)
- [AMBER] MCPB: error Pls help kanika singal (Sat Jan 21 2012 - 02:18:56 PST)
- [AMBER] positive van der Waal energy and comparison Jio M (Sat Jan 21 2012 - 02:34:13 PST)
- [AMBER] ptraj contacts output query Rajeswari A. (Sat Jan 21 2012 - 04:04:41 PST)
- Re: [AMBER] [q4md-fft] which fitting methods should I use for OPLS FF? FyD (Sat Jan 21 2012 - 09:03:37 PST)
- [AMBER] Amber for monolayer Sindrila Dutta banik (Sat Jan 21 2012 - 19:40:41 PST)
- [AMBER] installation subrata paul (Sun Jan 22 2012 - 08:27:37 PST)
- [AMBER] md.crd file is very large! john Kerk (Mon Jan 23 2012 - 00:22:25 PST)
- [AMBER] adding hydrogens to protein crystal structure abinayar.imsc.res.in (Mon Jan 23 2012 - 04:43:45 PST)
- [AMBER] superimpose on first snapshot Simon Becker (Mon Jan 23 2012 - 06:05:03 PST)
- [AMBER] Molecular Modelling Workshop 2012 in Erlangen, Germany Harald Lanig (Mon Jan 23 2012 - 08:15:17 PST)
- [AMBER] AmberTools 1.5 & Centos6 Irene Newhouse (Mon Jan 23 2012 - 11:49:36 PST)
- [AMBER] Steered Molecular Dynamics: some questions George Tzotzos (Tue Jan 24 2012 - 05:40:57 PST)
- [AMBER] energy decomposition equation Anglea A. (Tue Jan 24 2012 - 08:53:13 PST)
- [AMBER] creating input files for a protein connected to a fatty acid chain - angle parameters missing error Amir Marcovitz (Tue Jan 24 2012 - 13:06:37 PST)
- [AMBER] GBSA decomposition per reside SANCHEZ MURCIA, PEDRO ALEJANDRO (Tue Jan 24 2012 - 13:48:58 PST)
- [AMBER] GBSA decomposition per reside SANCHEZ MURCIA, PEDRO ALEJANDRO (Tue Jan 24 2012 - 13:49:18 PST)
- [AMBER] GBSA decomposition per reside SANCHEZ MURCIA, PEDRO ALEJANDRO (Tue Jan 24 2012 - 13:53:09 PST)
- [AMBER] [qm2_pm6_hof_module.o] Error 1 Carlos Sosa (Tue Jan 24 2012 - 14:11:51 PST)
- [AMBER] velocities in restart files taken from ptraj Sidney Elmer (Tue Jan 24 2012 - 16:14:02 PST)
- [AMBER] anal in parallel Jio M (Wed Jan 25 2012 - 02:43:17 PST)
- [AMBER] analysis in all simulation time Atila Petrosian (Wed Jan 25 2012 - 02:44:40 PST)
- [AMBER] temperature and pressure coupling shahab shariati (Wed Jan 25 2012 - 03:53:45 PST)
- [AMBER] peptide+sugar Urszula Uciechowska (Wed Jan 25 2012 - 04:44:51 PST)
- [AMBER] solvation in a cubic box shahab shariati (Wed Jan 25 2012 - 05:11:49 PST)
- [AMBER] Problem related to the order parameter Sindrila Dutta banik (Wed Jan 25 2012 - 07:47:23 PST)
- [AMBER] installation of sander.MPI Jorgen Simonsen (Wed Jan 25 2012 - 09:18:15 PST)
- [AMBER] Review MD sampling techniques Thomas Exner (Wed Jan 25 2012 - 09:57:55 PST)
- [AMBER] divcon: error while loading shared libraries: libvml.so: cannot open shared object file rainy908 (Wed Jan 25 2012 - 11:21:16 PST)
- [AMBER] Workshop and Tutorial Announcement: State-of-the-Art Algorithms for Molecular Dynamics, April 30th to May 4th 2012, Edinburgh UK Ross Walker (Wed Jan 25 2012 - 11:38:24 PST)
- [AMBER] Cannot find $AMBERHOME/test/antechamber bin wang (Wed Jan 25 2012 - 13:28:03 PST)
- [AMBER] problem python compiling when install AmberTools 1.5 setyanto md (Thu Jan 26 2012 - 06:28:18 PST)
- [AMBER] makeDIST_RST command problem Olena Dobrovolska (Thu Jan 26 2012 - 08:39:05 PST)
- [AMBER] Splitting cyclic molecule into QM and MM parts Dmitry Nilov (Fri Jan 27 2012 - 05:12:33 PST)
- [AMBER] compiler-dependent error: "Invalid atom or grouping specified in restraint." Jan-Philip Gehrcke (Fri Jan 27 2012 - 05:51:27 PST)
- [AMBER] antechamber and parm.frosst thomas.fox.boehringer-ingelheim.com (Fri Jan 27 2012 - 07:19:33 PST)
- [AMBER] Building Wrapped DNA in NAB Ian Slaymaker (Fri Jan 27 2012 - 09:56:55 PST)
- [AMBER] Editing structure via Xleap James Starlight (Fri Jan 27 2012 - 10:28:06 PST)
- [AMBER] NMODE list index out of range error Sangeetha B (Fri Jan 27 2012 - 22:43:41 PST)
- [AMBER] problem with SASA calculation Maryam Hamzehee (Sat Jan 28 2012 - 01:21:42 PST)
- [AMBER] loading of fullerene2160 gargi borgohai (Sat Jan 28 2012 - 09:49:03 PST)
- [AMBER] Can I set the direction of the pulling force? Qian Wang (Sat Jan 28 2012 - 10:58:36 PST)
- [AMBER] syntax error in ambpdb leila karami (Sun Jan 29 2012 - 03:01:38 PST)
- [AMBER] Preparation of the topology file by means of Antechamber James Starlight (Sun Jan 29 2012 - 09:12:21 PST)
- [AMBER] loading of fullerene2160 gargi borgohai (Sun Jan 29 2012 - 20:49:41 PST)
- [AMBER] clustering in ptraj doesn't create mdrcd and pdb files Andrew Voronkov (Mon Jan 30 2012 - 02:29:29 PST)
- [AMBER] fortran error during installation Mettu, Ramgopal (Mon Jan 30 2012 - 17:16:44 PST)
- [AMBER] antechamber doesn't create mol2 file Dian Jiao (Mon Jan 30 2012 - 22:01:27 PST)
- [AMBER] AMBER9 Urszula Uciechowska (Tue Jan 31 2012 - 00:25:45 PST)
- [AMBER] Problem during pnetcdf build on CentOS 5 Jan-Philip Gehrcke (Tue Jan 31 2012 - 02:47:41 PST)
- [AMBER] ptraj.MPI Sel Ercan (Tue Jan 31 2012 - 03:55:12 PST)
- [AMBER] Constant pH George Tzotzos (Tue Jan 31 2012 - 04:26:04 PST)
- [AMBER] Ambiguous C0 atom type Vlastimil Zíma (Tue Jan 31 2012 - 05:23:47 PST)
- [AMBER] how to obtain prmtop and inpcrd files truely from initial pdb file? leila karami (Tue Jan 31 2012 - 06:09:07 PST)
- [AMBER] SMD: Segmentation fault George Tzotzos (Tue Jan 31 2012 - 10:32:28 PST)
- Last message date: Tue Jan 31 2012 - 19:30:02 PST
- Archived on: Sun Dec 22 2024 - 05:54:30 PST
