Amber Archive Feb 2009 by thread
- [AMBER] Citing AMBER Tools... Aydin, Cihan (Sat Jan 31 2009 - 21:08:36 PST)
- Re: [AMBER] Test run on Solaris 10 X 86 Atro Tossavainen (Sat Jan 31 2009 - 23:10:30 PST)
- [AMBER] Can bonded pair of atoms be restrainted by NMR distance restraint? liu junjun (Sat Jan 31 2009 - 23:51:39 PST)
- [AMBER] the output files oguz gurbulak (Sun Feb 01 2009 - 03:13:02 PST)
- Re: [AMBER] Question on heating for homology based model. Carlos Simmerling (Sun Feb 01 2009 - 09:47:02 PST)
- Re: [AMBER] REMD fixed atoms Carlos Simmerling (Sun Feb 01 2009 - 10:00:33 PST)
- Re: [AMBER] RE: Tutorial 5 George Tzotzos (Sun Feb 01 2009 - 13:04:36 PST)
- [AMBER] strip frames from crd file aneesh cna (Mon Feb 02 2009 - 01:33:16 PST)
- [AMBER] strip frames from crd file aneesh cna (Mon Feb 02 2009 - 01:35:11 PST)
- [AMBER] md simulation on parallel PMEMD oguz gurbulak (Mon Feb 02 2009 - 05:32:31 PST)
- Re: [AMBER] Dr. Ramesh here kureeckal ramesh (Mon Feb 02 2009 - 06:22:51 PST)
- [AMBER] precision in the trajectory files Jenny Iskrenova (Mon Feb 02 2009 - 06:43:38 PST)
- [AMBER] Radius of Gyration Beale, John (Mon Feb 02 2009 - 09:34:35 PST)
- [AMBER] Langevin dynamics Antonios Samiotakis (Mon Feb 02 2009 - 09:54:31 PST)
- [AMBER] DFT SK parameter for P atom Qizhi Cui (Mon Feb 02 2009 - 11:59:19 PST)
- [AMBER] Micelles set-up?? Alexander Schierholt (Tue Feb 03 2009 - 02:09:52 PST)
- [AMBER] creating a restart file from md.out oguz gurbulak (Tue Feb 03 2009 - 02:44:10 PST)
- [AMBER] nab compile error with -scalapack chaitanya koppisetty (Tue Feb 03 2009 - 05:23:46 PST)
- [AMBER] -MMTSB instalation flag ? Marek Malý (Tue Feb 03 2009 - 07:31:38 PST)
- [AMBER] Unit 5 Error on OPEN:mdin on clustuer with mpirun drugdesign (Tue Feb 03 2009 - 09:03:20 PST)
- [AMBER] out error . .. (Tue Feb 03 2009 - 10:58:46 PST)
- Re: [AMBER] adding MG2 problem Scott Brozell (Tue Feb 03 2009 - 11:09:32 PST)
- [AMBER] MKL error ? Marek Malý (Tue Feb 03 2009 - 15:00:03 PST)
- RE: [AMBER] adding MG2 problem Rausch, Felix (Wed Feb 04 2009 - 05:04:51 PST)
- [AMBER] a question about umbrella sampling (US) xiaoqin huang (Wed Feb 04 2009 - 09:12:02 PST)
- [AMBER] PDB of a specific frame Jason A. Ford-Green (Wed Feb 04 2009 - 11:46:52 PST)
- [AMBER] compiling errors Gard Nelson (Wed Feb 04 2009 - 16:30:22 PST)
- [AMBER] Restarting an MD Simulation Hopkins, Robert (Wed Feb 04 2009 - 16:34:16 PST)
- [AMBER] pmemd installation in intelmpi Vijay Manickam Achari (Wed Feb 04 2009 - 19:16:06 PST)
- [AMBER] Compiling Carnal Amber7 in Amber9 Vijay Manickam Achari (Wed Feb 04 2009 - 19:21:14 PST)
- [AMBER] production run terminates due to (*) symbols in xxx.rst Vijay Manickam Achari (Wed Feb 04 2009 - 20:17:38 PST)
- [AMBER] how can i deal with large number atoms Wang,Ying (Wed Feb 04 2009 - 21:04:23 PST)
- [AMBER] How to build reference coordinate file for targeted MD gmail (Wed Feb 04 2009 - 22:44:22 PST)
- [AMBER] error in executing sander.MPI in amber9 Vijay Manickam Achari (Thu Feb 05 2009 - 00:37:09 PST)
- [AMBER] Solvation potential and free energies guardiani.fi.infn.it (Thu Feb 05 2009 - 04:27:21 PST)
- [AMBER] parameter files for D-amino acid Vsatheesh Patil (Thu Feb 05 2009 - 05:04:12 PST)
- [AMBER] pmemd on BlueGene/P? Hannes Loeffler (Thu Feb 05 2009 - 05:09:45 PST)
- Re: [AMBER] REM_hybrid test fails on AIX Shan-ho Tsai (Thu Feb 05 2009 - 08:44:43 PST)
- Re: [AMBER] Compiling Carnal Amber7 in Amber9 Bill Ross (Thu Feb 05 2009 - 09:36:00 PST)
- [AMBER] amber9 installation problem in SMP IA64 Vijay Manickam Achari (Thu Feb 05 2009 - 23:00:16 PST)
- [AMBER] mpirun problem in HPC Vijay Manickam Achari (Thu Feb 05 2009 - 23:01:29 PST)
- [AMBER] second derivative matrix calculation Marie Brut (Fri Feb 06 2009 - 02:47:18 PST)
- [AMBER] extract frames from a .mdcrd vallespardojl.chem.leidenuniv.nl (Fri Feb 06 2009 - 02:48:23 PST)
- [AMBER] MSD and stress tensors oguz gurbulak (Fri Feb 06 2009 - 03:09:12 PST)
- [AMBER] script to convert GLYCAM ff in CHARMM format ABEL Stephane 175950 (Fri Feb 06 2009 - 06:39:04 PST)
- [AMBER] Resp charge . .. (Fri Feb 06 2009 - 09:34:12 PST)
- [AMBER] ptraj fails to recognize binary REMD output Kevin Wiehe (Fri Feb 06 2009 - 09:44:21 PST)
- [AMBER] distance calculation by reading in the restraint file xiaoqin huang (Fri Feb 06 2009 - 09:52:56 PST)
- [AMBER] MD analysis oguz gurbulak (Sat Feb 07 2009 - 06:56:10 PST)
- [AMBER] Stability of a long NPT md trajectory? Bill K (Sun Feb 08 2009 - 23:07:24 PST)
- [AMBER] second derivative matrix Marie Brut (Mon Feb 09 2009 - 00:53:01 PST)
- [AMBER] NAB md function prints strange output Jochen Heil (Mon Feb 09 2009 - 03:30:21 PST)
- [AMBER] APS & ff03 Mahmoud A. A. Ibrahim (Mon Feb 09 2009 - 06:49:56 PST)
- [AMBER] parmchk s. Bill (Mon Feb 09 2009 - 07:55:20 PST)
- [AMBER] hbond analysis aneesh cna (Mon Feb 09 2009 - 09:55:25 PST)
- [AMBER] Solvating inside of a channel Daniel Smith (Mon Feb 09 2009 - 13:03:16 PST)
- [AMBER] Confusion regarding box size parul sharma (Mon Feb 09 2009 - 23:20:01 PST)
- [AMBER] Irregularity in box during md parul sharma (Tue Feb 10 2009 - 02:35:18 PST)
- [AMBER] RED-vIII: Scratch directory for Gaussian [NOT FOUND] Patrick Schopf (Tue Feb 10 2009 - 06:15:42 PST)
- [AMBER] Scaling of dipole interactions Diddo Diddens (Tue Feb 10 2009 - 06:33:18 PST)
- [AMBER] formate parameters Dmitri Nilov (Tue Feb 10 2009 - 06:47:31 PST)
- [AMBER] array out of bound in Amber10 tests Shan-ho Tsai (Tue Feb 10 2009 - 08:19:42 PST)
- [AMBER] reg . run TMD balaji nagarajan (Tue Feb 10 2009 - 09:36:28 PST)
- [AMBER] Solvating the interior of a channel Daniel Smith (Tue Feb 10 2009 - 12:42:09 PST)
- [AMBER] AMBER: chiral restraint on protein amit jain (Tue Feb 10 2009 - 16:48:12 PST)
- [AMBER] how to get amber 10 Prem Prakash Pathak (Tue Feb 10 2009 - 18:42:37 PST)
- [AMBER] nmr refinement of dimer Sally Pias (Wed Feb 11 2009 - 01:05:56 PST)
- [AMBER] Chlorine containing molecule CHAMI F. (Wed Feb 11 2009 - 05:39:19 PST)
- [AMBER] Optimization problem Daniel Emery (Thu Feb 12 2009 - 02:01:49 PST)
- [AMBER] error in xleap: ligand binding using MMand QMMM tech kureeckal ramesh (Thu Feb 12 2009 - 02:27:41 PST)
- [AMBER] H-bond information Beale, John (Thu Feb 12 2009 - 07:32:30 PST)
- [AMBER] projections of trajectories onto the first 2 principal eigenvectors Carra, Claudio (JSC-SK)[USRA] (Thu Feb 12 2009 - 10:22:20 PST)
- [AMBER] atoms fly out of the box in NVT calculations iccy liu (Thu Feb 12 2009 - 13:48:24 PST)
- [AMBER] How to jude whether the trajectory is stable or not Jeffrey (Thu Feb 12 2009 - 18:33:53 PST)
- [AMBER] Beginner question Heath Watts (Fri Feb 13 2009 - 13:18:42 PST)
- [AMBER] Question about improper torsions... Antonios Samiotakis (Fri Feb 13 2009 - 14:57:03 PST)
- [AMBER] New atom type with 7 bonds Akansha Saxena (Fri Feb 13 2009 - 15:56:47 PST)
- [AMBER] install Amber 10 to Macbook Adrien Delmont (Sat Feb 14 2009 - 03:06:50 PST)
- [AMBER] Any link to a major QM code? Francesco Pietra (Sun Feb 15 2009 - 09:58:30 PST)
- [AMBER] Error running sander.MPI Vijay Manickam Achari (Mon Feb 16 2009 - 00:23:05 PST)
- [AMBER] Error installing Amber David Patiño (Mon Feb 16 2009 - 04:02:31 PST)
- [AMBER] Iron 2+ parameters Hrvoje Brkić (Mon Feb 16 2009 - 05:53:57 PST)
- [AMBER] density and volume in NVT ensamble oguz gurbulak (Mon Feb 16 2009 - 05:58:13 PST)
- [AMBER] contant force pulling simulation with amber 10 li hui (Mon Feb 16 2009 - 09:01:36 PST)
- [AMBER] can ptraj output the trajectory of the residue CM? Jose Borreguero (Mon Feb 16 2009 - 11:47:34 PST)
- [AMBER] using ptraj Molecular Dynamics (Mon Feb 16 2009 - 12:31:42 PST)
- [AMBER] Normal errors on job kill? ben rodriguez (Mon Feb 16 2009 - 18:35:43 PST)
- [AMBER] Amber 9 Install - AMBERBUILDFLAGS error ben rodriguez (Mon Feb 16 2009 - 19:39:14 PST)
- [AMBER] parallel run error balaji nagarajan (Tue Feb 17 2009 - 00:19:23 PST)
- [AMBER] constph tutorial help Prem Prakash Pathak (Tue Feb 17 2009 - 04:53:37 PST)
- [AMBER] (no subject) Beale, John (Tue Feb 17 2009 - 05:02:25 PST)
- [AMBER] MD simulation with a partially flexible system Jeffrey (Tue Feb 17 2009 - 06:38:10 PST)
- [AMBER] DM complexation . .. (Tue Feb 17 2009 - 07:10:49 PST)
- [AMBER] How to get the energy of a molecule in a whole system Wang,Ying (Tue Feb 17 2009 - 08:28:39 PST)
- [AMBER] restraint angle m m (Tue Feb 17 2009 - 09:17:00 PST)
- [AMBER] PMF calculation Arnaud (Tue Feb 17 2009 - 10:10:18 PST)
- [AMBER] Need suggestion on payment for Ph.D student majored in molecular simulation Xu Dong (Tue Feb 17 2009 - 10:54:58 PST)
- [AMBER] glycam and solvateoct command Heath Watts (Tue Feb 17 2009 - 11:51:13 PST)
- [AMBER] problem compiling nmode.c Shan-ho Tsai (Tue Feb 17 2009 - 12:38:00 PST)
- [AMBER] reg.Targeted molecular dynamics balaji nagarajan (Tue Feb 17 2009 - 21:26:49 PST)
- [AMBER] protein monomerizartion times and simulation with implicit solvent drugdesign (Wed Feb 18 2009 - 02:27:17 PST)
- [AMBER] Re: AMBER: GBSA EGB = NaN Markus Kaukonen (Wed Feb 18 2009 - 04:26:28 PST)
- [AMBER] IG not change at each restart of NPT simulation Jeffrey (Wed Feb 18 2009 - 04:49:47 PST)
- [AMBER] How to constrain the hydrogen bonding distances... Majeed Shaik (Wed Feb 18 2009 - 06:11:37 PST)
- [AMBER] ./configure_amber: line 1211: cd: netcdf/src: No such file or directory Andrew Olson (Wed Feb 18 2009 - 09:08:57 PST)
- [AMBER] question about ptraj hydrogen bond analysis monica bhattacharee (Wed Feb 18 2009 - 11:45:17 PST)
- [AMBER] (NTB /= 0 && NTP /= 0) but IFBOX == 0 error Majeed Shaik (Wed Feb 18 2009 - 12:09:17 PST)
- [AMBER] Re: AMBER: How do you evaluate forces on a fixed atom? Bill Kowallis (Wed Feb 18 2009 - 17:55:47 PST)
- [AMBER] test charge Dan Kaps (Wed Feb 18 2009 - 18:27:32 PST)
- [AMBER] distance matrix plot and secondary structure analysis Siddharth Rastogi (Wed Feb 18 2009 - 22:17:47 PST)
- [AMBER] Protein motions comparison Dmitry Osolodkin (Thu Feb 19 2009 - 03:58:24 PST)
- [AMBER] secstruct Beale, John (Thu Feb 19 2009 - 05:22:20 PST)
- [AMBER] dipole correlation function Jeffrey (Thu Feb 19 2009 - 06:18:20 PST)
- [AMBER] paper of interest for FF development/solvent models David Mobley (Thu Feb 19 2009 - 07:15:04 PST)
- [AMBER] (no subject) Andrew Olson (Thu Feb 19 2009 - 11:46:24 PST)
- [AMBER] Antechamber kureeckal ramesh (Thu Feb 19 2009 - 17:36:03 PST)
- [AMBER] Problem with NVT and NPT parul sharma (Fri Feb 20 2009 - 05:07:36 PST)
- [AMBER] Parmchk wrongly calculates missing parameters (fwd) Gijs Schaftenaar (Fri Feb 20 2009 - 05:16:17 PST)
- [AMBER] ACS computational chemistry awards - March 9th deadline Carlos Simmerling (Fri Feb 20 2009 - 08:27:18 PST)
- [AMBER] order of "upper" and "lower" bounds in the makeDIS_RST inputs Piotr Cieplak (Fri Feb 20 2009 - 13:40:14 PST)
- [AMBER] reg.targeted molecular dynamics balaji nagarajan (Fri Feb 20 2009 - 21:10:50 PST)
- [AMBER] A beginner's question for using AMBER to do cell membrane simulation and molecular transportation Xu Dong (Sat Feb 21 2009 - 12:27:29 PST)
- [AMBER] PME doesn't work parul sharma (Mon Feb 23 2009 - 01:43:40 PST)
- [AMBER] PMEMD vs GROMACS? Sasha Buzko (Mon Feb 23 2009 - 11:55:27 PST)
- [AMBER] problem with amber installation nicholus bhattacharjee (Mon Feb 23 2009 - 22:50:12 PST)
- [AMBER] follow-up to previous discussion: nmr refinement of dimer Sally Pias (Mon Feb 23 2009 - 23:50:41 PST)
- [AMBER] About the croase grainded FF James W (Mon Feb 23 2009 - 23:58:12 PST)
- [AMBER] (no subject) Beale, John (Tue Feb 24 2009 - 03:59:51 PST)
- [AMBER] amber tools reading netcdf files Jeremy Harris (Tue Feb 24 2009 - 07:54:09 PST)
- [AMBER] perform an analysis using ptraj oguz gurbulak (Tue Feb 24 2009 - 08:19:11 PST)
- [AMBER] Equilibration Scaling to System Size Hopkins, Robert (Tue Feb 24 2009 - 14:31:37 PST)
- [AMBER] problem about trajectory analysis Adrien Delmont (Wed Feb 25 2009 - 06:24:41 PST)
- [AMBER] (no subject) waleed zalloum (Wed Feb 25 2009 - 08:41:14 PST)
- [AMBER] ptraj analyze Beale, John (Wed Feb 25 2009 - 08:56:59 PST)
- [AMBER] Simulated annealing Ibrahim Moustafa (Wed Feb 25 2009 - 16:26:37 PST)
- [AMBER] Error in using Amber sri noraima othman (Wed Feb 25 2009 - 19:27:29 PST)
- [AMBER] tleap errors !! Sampath Koppole (Thu Feb 26 2009 - 01:47:48 PST)
- [AMBER] MD simulation at constant pH Francesco Pietra (Thu Feb 26 2009 - 02:52:47 PST)
- [AMBER] Current Amber10 bugfix.all doesn't apply cleanly Mark Dixon (Thu Feb 26 2009 - 03:54:03 PST)
- [AMBER] PLUMED release 1.0.0 available Massimiliano Bonomi (Thu Feb 26 2009 - 05:11:54 PST)
- [AMBER] extra torsion terms in tleap.top-file Astrid Maaß (Thu Feb 26 2009 - 06:32:30 PST)
- [AMBER] H-Bonds Beale, John (Thu Feb 26 2009 - 06:38:04 PST)
- [AMBER] (no subject) Lake, Thomas (Thu Feb 26 2009 - 08:19:53 PST)
- [AMBER] A problem with xleap and pdb file nancy4619 (Fri Feb 27 2009 - 04:28:01 PST)
- [AMBER] Re: Antechamber kureeckal ramesh (Fri Feb 27 2009 - 04:56:58 PST)
- [AMBER] I need a professional help about xleap and pdb file nancy4619 (Fri Feb 27 2009 - 05:56:14 PST)
- [AMBER] using Gromacs for analysis oguz gurbulak (Fri Feb 27 2009 - 09:03:54 PST)
- [AMBER] Partial entropy calculations ? Marek Malý (Fri Feb 27 2009 - 10:21:29 PST)
- [AMBER] PCL waleed zalloum (Sat Feb 28 2009 - 09:17:51 PST)
- [AMBER] a query Molecular Dynamics (Sat Feb 28 2009 - 11:45:46 PST)
- [AMBER] IMPORTANT INFO: Regarding Anonymous postings to the AMBER mailing list. Ross Walker (Sat Feb 28 2009 - 14:19:16 PST)
- [AMBER] Question about NAB module Wei Huang (Sat Feb 28 2009 - 16:23:49 PST)
- Last message date: Sun Mar 01 2009 - 01:09:59 PST
- Archived on: Fri Nov 22 2024 - 05:53:44 PST
