Amber Archive Feb 2010 by thread
- [AMBER] Problem in setting parameters for non standard DG residue:O6-Methylguanine N.R. Jena (Mon Feb 01 2010 - 03:47:47 PST)
- [AMBER] MMPBSA s. Bill (Mon Feb 01 2010 - 03:43:11 PST)
- [AMBER] VDW parameter for Cobalt and Nickel Raja Pandian (Mon Feb 01 2010 - 06:17:21 PST)
- Re: [AMBER] Tutorial for Glycoprotein simulation Lachele Foley (Lists) (Mon Feb 01 2010 - 06:34:15 PST)
- [AMBER] Solvating a protein - tleap works where sleap does not? Ben Roberts (Mon Feb 01 2010 - 07:10:56 PST)
- [AMBER] errors in leap Beale, John (Mon Feb 01 2010 - 07:09:06 PST)
- [AMBER] Converting Gaussian output format to the RESP input format imtiaz shafiq (Mon Feb 01 2010 - 07:44:45 PST)
- Re: [AMBER] errors in leap Bill Ross (Mon Feb 01 2010 - 09:24:50 PST)
- [AMBER] Test log s. Bill (Mon Feb 01 2010 - 09:48:10 PST)
- [AMBER] interaction energy of single residue to its environment luzhenw1.msu.edu (Mon Feb 01 2010 - 10:49:56 PST)
- [AMBER] plotting RMS vs. residue number Beale, John (Mon Feb 01 2010 - 11:15:39 PST)
- [AMBER] mmpbsa error: No data for 0+2 MM BOND 200 xueqin pang (Mon Feb 01 2010 - 17:25:55 PST)
- [AMBER] How to construct the methyl-animo acid? Aurum Bai (Tue Feb 02 2010 - 01:17:02 PST)
- [AMBER] Announcement: Amber MD Workshop 2010 in Duesseldorf, Germany April 26-30th steinbrt.rci.rutgers.edu (Tue Feb 02 2010 - 02:45:53 PST)
- [AMBER] parameters for heme-CO Francesco Pietra (Tue Feb 02 2010 - 10:51:12 PST)
- [AMBER] MOL2 Output through LEAP Matthew Tessier (Tue Feb 02 2010 - 11:20:54 PST)
- [AMBER] If this is normal for 3 or 4 sander.MPI jobs appearing on one node MUHAMMAD IMTIA SHAFIQ (Tue Feb 02 2010 - 11:46:31 PST)
- [AMBER] deuterate protein atoms by editing the topology file Jose Borreguero (Tue Feb 02 2010 - 12:16:43 PST)
- [AMBER] tleap command for disulfide bonds: for chain A and Chain B ??? Siddharth Rastogi (Tue Feb 02 2010 - 17:19:28 PST)
- [AMBER] failure when doing bugfix patch for amber10 and tools V1.2 xueqin pang (Tue Feb 02 2010 - 22:52:56 PST)
- [AMBER] Information regarding how to group atoms for ionic liquid dhilip kumar ramalingam (Wed Feb 03 2010 - 01:10:31 PST)
- [AMBER] AMBER 9 parallel compilation problem on Mac OS X 10.6 pelaez.usal.es (Wed Feb 03 2010 - 04:15:43 PST)
- [AMBER] parmchk lists multiple values of the same parameter Sidney Elmer (Wed Feb 03 2010 - 09:12:39 PST)
- [AMBER] adding atom types to leapfrc Francesco Pietra (Wed Feb 03 2010 - 10:53:00 PST)
- Re: [AMBER] adding atom types to leapfrc Bill Ross (Wed Feb 03 2010 - 11:11:56 PST)
- [AMBER] Addles and makeDIST_RST Titus, Jamie (bairdje) (Wed Feb 03 2010 - 12:08:20 PST)
- [AMBER] dielectric constant in NMODE Jeffrey (Wed Feb 03 2010 - 18:45:26 PST)
- Re: [AMBER] TEST_FAILURES sikander azam (Thu Feb 04 2010 - 05:37:44 PST)
- [AMBER] Amber11 vs Amber10 Steve Seibold (Thu Feb 04 2010 - 10:58:59 PST)
- [AMBER] multiple intercalating waters wong105.llnl.gov (Thu Feb 04 2010 - 11:05:32 PST)
- [AMBER] loading parm7 and coords with tLeap? Nicholas Musolino (Thu Feb 04 2010 - 12:41:10 PST)
- [AMBER] Problem reading PDB residues in AmberTools-1.3 Hopkins, Robert (Thu Feb 04 2010 - 18:10:04 PST)
- [AMBER] What is the ".ac" files as input of respgen and how to generate it? Aurum Bai (Thu Feb 04 2010 - 21:42:37 PST)
- [AMBER] load pdb into xleap Jim Miller (Fri Feb 05 2010 - 01:12:12 PST)
- [AMBER] reimaging the trajectory Shaikh Abdul R S Ramaju (Fri Feb 05 2010 - 02:25:53 PST)
- [AMBER] Add charge on quaternary nitrogen Pol Boudard (Fri Feb 05 2010 - 05:40:34 PST)
- [AMBER] AMBER10 build - failing "jar" and "jar_multi" tests Mark Dixon (Fri Feb 05 2010 - 06:55:29 PST)
- [AMBER] About the err of antechamber's tutorial! Aurum Bai (Fri Feb 05 2010 - 07:07:49 PST)
- RE: [Possible Spam: 10%] Re: [AMBER] FW: Problem reading PDB residues in AmberTools-1.3 Hopkins, Robert (Fri Feb 05 2010 - 10:51:25 PST)
- [AMBER] softcore TI lambda values of 0 and 1 Hugh Heldenbrand (Fri Feb 05 2010 - 12:49:05 PST)
- [AMBER] positional restraints of different strengths Jose Borreguero (Fri Feb 05 2010 - 15:55:28 PST)
- Re: [AMBER] positional restraints of different strengths Bill Ross (Fri Feb 05 2010 - 16:51:16 PST)
- [AMBER] Problem in Ptraj Kshatresh Dutta Dubey (Fri Feb 05 2010 - 22:41:12 PST)
- [AMBER] antechamber with carbon monoxide Francesco Pietra (Sat Feb 06 2010 - 02:52:54 PST)
- [AMBER] Question of Tutorials-A: the total charge is not integer Tom Williams (Sun Feb 07 2010 - 00:00:39 PST)
- [AMBER] Energy Minimization of a Complex MUHAMMAD IMTIA SHAFIQ (Sun Feb 07 2010 - 16:22:57 PST)
- [AMBER] Regarding restraints during minimisation stage 1 in explicit solvent Asfa Ali (Sun Feb 07 2010 - 21:23:12 PST)
- [AMBER] 10_12 potential aapeters.ncsu.edu (Mon Feb 08 2010 - 00:14:39 PST)
- [AMBER] [Fwd: 10_12 potential] aapeters.ncsu.edu (Mon Feb 08 2010 - 03:01:35 PST)
- [AMBER] Charges of ASN in all_aminoct03 CR Gregor (Mon Feb 08 2010 - 05:27:20 PST)
- [AMBER] limit of joining residues Jio M (Mon Feb 08 2010 - 05:38:54 PST)
- [AMBER] sleap crash with single water molecule and amoeba Neil Henson (Mon Feb 08 2010 - 06:14:45 PST)
- Re: [AMBER] limit of joining residues Bill Ross (Mon Feb 08 2010 - 09:32:57 PST)
- [AMBER] Problem in creating cubic water box Sangita Kachhap (Mon Feb 08 2010 - 09:51:28 PST)
- Re: [AMBER] Problem in creating cubic water box Bill Ross (Mon Feb 08 2010 - 10:21:47 PST)
- [AMBER] Imaging difficulty Hopkins, Robert (Mon Feb 08 2010 - 12:39:59 PST)
- [AMBER] QM/MM new parameters s. Bill (Mon Feb 08 2010 - 15:32:59 PST)
- [AMBER] (no subject) mani grover (Mon Feb 08 2010 - 22:19:15 PST)
- [AMBER] Antechamber: imidazole=aromatic, imidazolium=not aromatic? Gabriel Rocklin (Mon Feb 08 2010 - 23:33:17 PST)
- [AMBER] how to fix or restraint atoms in molecules Jim Miller (Tue Feb 09 2010 - 00:30:20 PST)
- [AMBER] Reducing RMS errors in TI calculation ET (Tue Feb 09 2010 - 13:02:48 PST)
- [AMBER] mailing list manikanthan bhavaraju (Tue Feb 09 2010 - 13:22:45 PST)
- [AMBER] problem of chenge of the water box during equilibration Sangita Kachhap (Wed Feb 10 2010 - 08:48:34 PST)
- [AMBER] Re: Antechamber: imidazole=aromatic, imidazolium=not aromatic? Gabriel Rocklin (Wed Feb 10 2010 - 11:23:24 PST)
- [AMBER] Problem compiling Amber 10 after applying latest bugfix file Sanders, Larry R. (Wed Feb 10 2010 - 12:17:40 PST)
- [AMBER] MMPBSA.py error s. Bill (Wed Feb 10 2010 - 15:46:34 PST)
- [AMBER] About RAMD gokul algates (Thu Feb 11 2010 - 06:27:32 PST)
- [AMBER] RE: Problem compiling Amber 10 after applying latest bugfix file Sanders, Larry R. (Thu Feb 11 2010 - 06:35:06 PST)
- [AMBER] mm_pbsa statistics problem Marina Grabar (Thu Feb 11 2010 - 06:51:01 PST)
- [AMBER] Small Molecule Parameters imtiaz shafiq (Thu Feb 11 2010 - 10:44:18 PST)
- Re: [AMBER] Small Molecule Parameters Bill Ross (Thu Feb 11 2010 - 11:05:32 PST)
- [AMBER] strange behavior in QMMM simulation M. L. Dodson (Thu Feb 11 2010 - 12:35:25 PST)
- [AMBER] PMEMD compiling errors Dian Jiao (Thu Feb 11 2010 - 15:56:31 PST)
- [AMBER] Problems with PMEMD compilation Alex Rodriguez (Fri Feb 12 2010 - 02:45:09 PST)
- [AMBER] Problem with specifying mask for MMPBSA.py script Arvind Marathe (Fri Feb 12 2010 - 07:09:03 PST)
- [AMBER] compiling amber on intel xeon 5500 series cpu Max Wang (Fri Feb 12 2010 - 12:16:29 PST)
- Re: [AMBER] compiling amber on intel xeon 5500 series cpu Bill Ross (Fri Feb 12 2010 - 12:26:17 PST)
- [AMBER] MM PBSA problem Jagdeesh C (Sat Feb 13 2010 - 08:49:19 PST)
- [AMBER] mmpbsa.py ion radius s. Bill (Sat Feb 13 2010 - 18:02:43 PST)
- [AMBER] question about how to fix the number of water molecule mirage . (Sun Feb 14 2010 - 23:39:29 PST)
- [AMBER] how is better to measure ligand drift against protein in Amber Andrew Voronkov (Mon Feb 15 2010 - 06:21:02 PST)
- [AMBER] Binding energy calculation using MMPBSA.py: Sander from amber9 complains "mdfil: Error unknown flag: -y" Arvind Marathe (Mon Feb 15 2010 - 06:30:04 PST)
- [AMBER] Fitting Torsional parameters stephane acoca (Mon Feb 15 2010 - 07:48:07 PST)
- [AMBER] RDF with ptraj Dian Jiao (Mon Feb 15 2010 - 12:45:00 PST)
- [AMBER] Re: Antechamber: imidazole=aromatic, imidazolium=not aromatic? Gabriel Rocklin (Mon Feb 15 2010 - 15:21:45 PST)
- [AMBER] PARMSCAN E.M. (Mon Feb 15 2010 - 19:58:15 PST)
- [AMBER] enquiry regarding distance-dependent dielectric constant minimization bharat lakhani (Mon Feb 15 2010 - 23:35:44 PST)
- [AMBER] (no subject) Yubo Fan (Tue Feb 16 2010 - 00:31:46 PST)
- [AMBER] (no subject) Rebeca García Fandiño (Tue Feb 16 2010 - 10:14:45 PST)
- [AMBER] VMD and Amber coordinates Rebeca García Fandiño (Tue Feb 16 2010 - 10:25:25 PST)
- [AMBER] sander compilation s. Bill (Tue Feb 16 2010 - 17:23:47 PST)
- [AMBER] PARMSCAN E.M. (Tue Feb 16 2010 - 20:08:45 PST)
- [AMBER] Calcium and Phosphate sikander azam (Tue Feb 16 2010 - 22:12:22 PST)
- [AMBER] Virtual waters Fernando Martín García (Wed Feb 17 2010 - 02:59:05 PST)
- [AMBER] how to generate acetone box parvesh singh (Wed Feb 17 2010 - 03:10:09 PST)
- [AMBER] makeCHIR_RST and LES Titus, Jamie (bairdje) (Wed Feb 17 2010 - 08:34:13 PST)
- [AMBER] relaxed PES eric henon (Wed Feb 17 2010 - 11:58:50 PST)
- Re: [AMBER] ccl4 simulation FyD (Wed Feb 17 2010 - 15:10:30 PST)
- [AMBER] New Bursaries and Plenary Speaker - Molecular Modeling Workshop 2010 in Erlangen, Germany Harald Lanig (Thu Feb 18 2010 - 02:39:24 PST)
- [AMBER] Script Beale, John (Thu Feb 18 2010 - 04:35:26 PST)
- [AMBER] Segmentation fault with xleap while loading a leaprc Nicolas Sapay (Thu Feb 18 2010 - 05:48:00 PST)
- [AMBER] help vaibhav jain (Thu Feb 18 2010 - 05:54:02 PST)
- [AMBER] References of all force fields for citations Sushil Mishra (Thu Feb 18 2010 - 06:18:26 PST)
- [AMBER] amoeba--Too many dipole_dipole interactions for allocated Dian Jiao (Thu Feb 18 2010 - 08:25:45 PST)
- [AMBER] mm-pbsa receptor and ligand masking Workalemhu Berhanu (Thu Feb 18 2010 - 13:26:03 PST)
- [AMBER] Re: Antechamber: imidazole=aromatic, imidazolium=not aromatic? Gabriel Rocklin (Thu Feb 18 2010 - 15:21:27 PST)
- [AMBER] pmemd.cuda progress Trevor Gokey (Thu Feb 18 2010 - 16:44:15 PST)
- [AMBER] TI calculation of absolute dG with restraint and energy decomposition Samuel Genheden (Fri Feb 19 2010 - 01:10:45 PST)
- [AMBER] Question about transition from AMBER6 to AMBER9 坂庭 大輔 (Fri Feb 19 2010 - 02:19:27 PST)
- [AMBER] help on minimization bharat lakhani (Fri Feb 19 2010 - 05:44:18 PST)
- [AMBER] help on minimization bharat lakhani (Fri Feb 19 2010 - 05:51:29 PST)
- Re: [AMBER] MM-PBSA: decompose energy error Ryan Pavlovicz (Fri Feb 19 2010 - 11:30:54 PST)
- [AMBER] deriving charges for use with gaff Sidney Elmer (Fri Feb 19 2010 - 12:00:06 PST)
- [AMBER] are translations applied in the 'average' command of ptraj? Jose Borreguero (Fri Feb 19 2010 - 16:02:22 PST)
- [AMBER] parmscan Peter Charles Kahuna (Fri Feb 19 2010 - 19:13:56 PST)
- [AMBER] Amber 8 sander.f file, force.f file gokul algates (Fri Feb 19 2010 - 21:14:34 PST)
- [AMBER] how to identify closest waters to protein surface? Jose Borreguero (Sat Feb 20 2010 - 15:47:54 PST)
- [AMBER] enquire of NAB tutorial or any detailed introduction xueqin pang (Sun Feb 21 2010 - 06:41:08 PST)
- [AMBER] Perturbed charges and types s. Bill (Sun Feb 21 2010 - 08:01:14 PST)
- [AMBER] PARMSCAN Peter Charles Kahuna (Sun Feb 21 2010 - 18:38:14 PST)
- [AMBER] MPICH2 and AMBER9 dxli75 (Mon Feb 22 2010 - 12:37:25 PST)
- [AMBER] Protein Stability in amber mmpbsa tutorial MUHAMMAD IMTIA SHAFIQ (Mon Feb 22 2010 - 12:54:54 PST)
- [AMBER] ptraj.MPI issue with "uninterruptible sleep" Trevor Gokey (Mon Feb 22 2010 - 16:04:28 PST)
- [AMBER] RDF analysis Shaikh Abdul R S Ramaju (Tue Feb 23 2010 - 00:05:58 PST)
- [AMBER] installation problem gunajyoti das (Tue Feb 23 2010 - 00:51:52 PST)
- [AMBER] parallel test error Nicee (Tue Feb 23 2010 - 01:34:00 PST)
- [AMBER] trouble with cooling down the system song_jianing_hi (Tue Feb 23 2010 - 02:43:39 PST)
- [AMBER] AMBER MD simulation Nancy (Tue Feb 23 2010 - 02:56:50 PST)
- [AMBER] trouble with cooling down a system Nancy (Tue Feb 23 2010 - 02:56:49 PST)
- [AMBER] AmberTools1.3 installation error Anna Dejardin (Tue Feb 23 2010 - 03:23:54 PST)
- [AMBER] use tleap through stdin Peter Schmidtke (Tue Feb 23 2010 - 09:41:04 PST)
- [AMBER] Charge protocol for OLP, HYP Emmanuel Baribefe Naziga (Tue Feb 23 2010 - 17:52:43 PST)
- Re: [AMBER] Charge protocol for OLP, HYP FyD (Wed Feb 24 2010 - 06:20:29 PST)
- Re: [AMBER] Charge protocol for OLP, HYP Carlos Simmerling (Wed Feb 24 2010 - 06:28:17 PST)
- Re: [AMBER] Charge protocol for OLP, HYP Lachele Foley (Lists) (Wed Feb 24 2010 - 06:59:36 PST)
- Re: [AMBER] Charge protocol for OLP, HYP Emmanuel Baribefe Naziga (Wed Feb 24 2010 - 07:36:14 PST)
- Re: [AMBER] Charge protocol for OLP, HYP Lachele Foley (Lists) (Thu Feb 25 2010 - 09:27:15 PST)
- Re: [AMBER] Charge protocol for OLP, HYP Emmanuel Baribefe Naziga (Thu Feb 25 2010 - 09:33:32 PST)
- Re: [AMBER] Charge protocol for OLP, HYP Lachele Foley (Lists) (Fri Feb 26 2010 - 07:56:44 PST)
- Re: [AMBER] Charge protocol for OLP, HYP Emmanuel Baribefe Naziga (Fri Feb 26 2010 - 08:28:22 PST)
- Re: [AMBER] Charge protocol for OLP, HYP Lachele Foley (Lists) (Fri Feb 26 2010 - 10:12:18 PST)
- Re: [AMBER] Charge protocol for OLP, HYP FyD (Sat Feb 27 2010 - 09:10:22 PST)
- Re: [AMBER] Charge protocol for OLP, HYP Emmanuel Baribefe Naziga (Sat Feb 27 2010 - 16:29:55 PST)
- Re: [AMBER] Charge protocol for OLP, HYP FyD (Sat Feb 27 2010 - 23:24:44 PST)
- Re: [AMBER] Charge protocol for OLP, HYP FyD (Sat Feb 27 2010 - 23:27:48 PST)
- [AMBER] Final PDB after Energy minimization Shaandar Nyamtulga (Tue Feb 23 2010 - 19:03:15 PST)
- Re: [AMBER] How to unsolvate solvated protein? Bill Ross (Tue Feb 23 2010 - 21:34:52 PST)
- [AMBER] Question on applying restraints in absolute dG calculations with TI in Amber 10 Samuel Genheden (Wed Feb 24 2010 - 01:03:21 PST)
- [AMBER] GUI Competition Matthew Tessier (Wed Feb 24 2010 - 06:18:20 PST)
- [AMBER] design of peptides to stabilize proteins Simon Becker (Wed Feb 24 2010 - 06:55:24 PST)
- [AMBER] trajectory alignment to a reference frame Oliver Kuhn (Wed Feb 24 2010 - 07:17:39 PST)
- [AMBER] Sander jac benchmark segfaults with non-power of two processors Manjunath Sripadarao (Wed Feb 24 2010 - 23:05:52 PST)
- [AMBER] Query about xmin gunajyoti das (Wed Feb 24 2010 - 23:58:14 PST)
- [AMBER] Problem in MM-PBSA Hyma vathi (Thu Feb 25 2010 - 01:54:48 PST)
- [AMBER] Query about LMOD gunajyoti das (Thu Feb 25 2010 - 03:53:31 PST)
- [AMBER] ptraj, imaging for NAMD generated dcd files, Error in tokenize Monika Sharma (Thu Feb 25 2010 - 04:20:16 PST)
- [AMBER] Not runing the Nmode! Aurum Bai (Thu Feb 25 2010 - 07:02:18 PST)
- [AMBER] serial compilation of pmemd bbalta.itu.edu.tr (Thu Feb 25 2010 - 07:45:00 PST)
- [AMBER] NMR complex and vlimit exceeded Michael Durney (Thu Feb 25 2010 - 08:00:50 PST)
- [AMBER] Re: SOS: make CYX bond using xleap Jason Swails (Thu Feb 25 2010 - 18:34:53 PST)
- [AMBER] Periodic Boundary in AMBER(PMEMD) GPU Acceleration support ? Hiromasa WATANABE (Thu Feb 25 2010 - 19:05:41 PST)
- [AMBER] swiss cheese water shell Mark M Huntress (Fri Feb 26 2010 - 21:40:25 PST)
- [AMBER] msd calculation using ptraj diffusion Monika Sharma (Fri Feb 26 2010 - 22:05:39 PST)
- [AMBER] xmin_verbosity gunajyoti das (Sat Feb 27 2010 - 05:40:59 PST)
- [AMBER] Installation error of amber10 after compile Ambertools1.3 albert albert (Sat Feb 27 2010 - 12:37:51 PST)
- [AMBER] Instaltion parallel amber on macbook pro Christine Baranski (Sun Feb 28 2010 - 04:15:00 PST)
- [AMBER] Protein + Bilayer Simulations: Role of salt Lalit Dubey (Sun Feb 28 2010 - 13:32:05 PST)
- Last message date: Sun Feb 28 2010 - 17:00:04 PST
- Archived on: Wed Dec 25 2024 - 05:54:00 PST
