Amber Archive Dec 2010 by thread
- [AMBER] GLYCAM with FF99SB Lishan Yao (Tue Nov 30 2010 - 17:55:16 PST)
- [AMBER] top and crd-reg.............. parasu raman (Tue Nov 30 2010 - 20:05:14 PST)
- [AMBER] solvent overlap when "iwrap=1" chicago.ecnu (Tue Nov 30 2010 - 20:58:25 PST)
- [AMBER] What is the Value of C° (standard concentration) sunita gupta (Tue Nov 30 2010 - 21:43:03 PST)
- Re: [AMBER] Benzene Stacking in AMBER Jiri Sponer (Wed Dec 01 2010 - 02:40:31 PST)
- [AMBER] AmberTools serial compilation with intel compiler 12.0.0: final link failed Vlad Cojocaru (Wed Dec 01 2010 - 03:34:24 PST)
- [AMBER] Distances between amino acid residues Beale, John (Wed Dec 01 2010 - 07:39:54 PST)
- Re: [AMBER] (no subject) case (Wed Dec 01 2010 - 08:05:30 PST)
- [AMBER] AMBER 11 on multiple GPUs Ross Walker (Wed Dec 01 2010 - 09:51:31 PST)
- [AMBER] energy calculation error after extracting peptide from the explicit water simulation Bongkeun Kim (Wed Dec 01 2010 - 11:49:04 PST)
- [AMBER] some problems of restart MD cwt (Wed Dec 01 2010 - 18:21:41 PST)
- [AMBER] MM-PBSA energy-decomposition yan zhang (Wed Dec 01 2010 - 22:15:59 PST)
- Re: [AMBER] j-restrained peptide Rossella Noschese (Thu Dec 02 2010 - 01:30:13 PST)
- Re: [AMBER] small organic molecule Rossella Noschese (Thu Dec 02 2010 - 01:31:54 PST)
- [AMBER] editing parm in LEAP Alex Rodriguez (Thu Dec 02 2010 - 08:15:36 PST)
- [AMBER] MMPBSA calculation of a zinc-enzyme zhihong ke (Thu Dec 02 2010 - 09:53:06 PST)
- Re: [AMBER] Serious problem at specific time point Hoshin Kim (Wed Dec 01 2010 - 20:34:44 PST)
- [AMBER] I've got an error msg, ptraj: double free or corruption Hoshin Kim (Wed Dec 01 2010 - 20:46:54 PST)
- [AMBER] what is correct atom type descriptor to add binding-site water molecules in tleap g t (Thu Dec 02 2010 - 10:51:43 PST)
- [AMBER] installing Amber 11 & tools 1.4 on Fedora 14 Andre Serobian (Thu Dec 02 2010 - 19:51:14 PST)
- [AMBER] AmberTools 1.4 serial tests failures Vlad Cojocaru (Fri Dec 03 2010 - 06:27:07 PST)
- [AMBER] amoeba waters Geoffrey Wood (Fri Dec 03 2010 - 13:12:48 PST)
- [AMBER] 'final link failed' error independent of intel compiler version Vlad Cojocaru (Sat Dec 04 2010 - 03:11:32 PST)
- [AMBER] Box volume calculated by sander Hopkins, Robert (Sat Dec 04 2010 - 09:48:58 PST)
- [AMBER] MM-PBSA with DELPHI Khaled Barakat (Sat Dec 04 2010 - 17:00:25 PST)
- [AMBER] hydrogen bond analysis of gromacs simulation by amber (direct and water mediated HB) leila karami (Sun Dec 05 2010 - 00:56:07 PST)
- [AMBER] problem with entropy computations by mm_pbsa_nabnmode Cenk \(Jenk\) Andac (Sun Dec 05 2010 - 01:17:07 PST)
- [AMBER] Query: ABMD Kshatresh Dutta Dubey (Sun Dec 05 2010 - 01:29:38 PST)
- [AMBER] High STD Value in pbsa Alice Wang (Sun Dec 05 2010 - 18:26:24 PST)
- [AMBER] building error of multi-GPU pmemd.cuda Masakazu SEKIJIMA (Sun Dec 05 2010 - 23:30:19 PST)
- [AMBER] hydrogen bond analysis of gromacs simulation by amber (direct and water mediated HB) leila karami (Mon Dec 06 2010 - 00:13:35 PST)
- [AMBER] Analytical and empirical parametrization of dihedrals in Amber Dmitry Nilov (Mon Dec 06 2010 - 00:43:56 PST)
- [AMBER] Installation problem on Mac George Tzotzos (Mon Dec 06 2010 - 05:28:29 PST)
- [AMBER] force constant parameters in amberports Jarmila Husby (Mon Dec 06 2010 - 06:11:52 PST)
- [AMBER] questions on molsurf program Senthil Natesan (Mon Dec 06 2010 - 07:36:33 PST)
- [AMBER] How to set up NMR distance restraint between surface and peptide? Bongkeun Kim (Mon Dec 06 2010 - 13:40:13 PST)
- [AMBER] Map function for custom residue to generate distace restraints? Bongkeun Kim (Mon Dec 06 2010 - 16:21:02 PST)
- [AMBER] What can we do with velocities file ? setyanto md (Mon Dec 06 2010 - 18:03:28 PST)
- [AMBER] Error: Sander output is missing values! VDWAALS = ************* kamlesh sahu (Mon Dec 06 2010 - 20:21:46 PST)
- [AMBER] hydrogen bond analysis of gromacs simulation by amber (direct and water mediated HB) leila karami (Mon Dec 06 2010 - 22:26:01 PST)
- [AMBER] vdW parameters steinbrt.rci.rutgers.edu (Mon Dec 06 2010 - 23:49:26 PST)
- [AMBER] solvatebox leila karami (Tue Dec 07 2010 - 04:00:09 PST)
- Re: [AMBER] pmemd.cuda on Snow Leopard 10.6.5 M. Shahid (Tue Dec 07 2010 - 04:33:57 PST)
- [AMBER] Illegal CONECT record in pdb file / The file contained 1 atoms not in residue templates leila karami (Tue Dec 07 2010 - 06:40:47 PST)
- [AMBER] Work Smarter, Not Harder - I will earn for you - You sit and relax. Kalpesh Sharma (Tue Dec 07 2010 - 20:43:59 PST)
- [AMBER] Regarding energy decomposition aneesh cna (Wed Dec 08 2010 - 04:40:17 PST)
- [AMBER] Closest waters Beale, John (Wed Dec 08 2010 - 04:44:42 PST)
- [AMBER] error for antecamber to establish small molecule Zhou Gong (Wed Dec 08 2010 - 06:58:49 PST)
- Re: [AMBER] REMD replicas blowing up Janzsó Gábor (Wed Dec 08 2010 - 08:44:27 PST)
- [AMBER] Umbrella Sampling lnedialkova.gmail.com (Wed Dec 08 2010 - 10:18:02 PST)
- [AMBER] MMPBSA calculation for chlorine anion zhihong ke (Wed Dec 08 2010 - 11:25:19 PST)
- [AMBER] Some errors in the Amber test cwt (Wed Dec 08 2010 - 18:14:53 PST)
- Re: [AMBER] Parameterization of ffamber99sb for octane box YUVRAJ UBOVEJA (Wed Dec 08 2010 - 20:21:21 PST)
- [AMBER] Tin-foil boundary condition kurisaki ikuo (Wed Dec 08 2010 - 20:51:14 PST)
- [AMBER] Does MMPBSA.py mutant only one residue? zjxu (Wed Dec 08 2010 - 23:31:39 PST)
- [AMBER] using mol2 files with tleap Jan Wahl (Thu Dec 09 2010 - 00:53:14 PST)
- [AMBER] cyclic peptide Rossella Noschese (Thu Dec 09 2010 - 02:50:41 PST)
- [AMBER] sleap loadmol2 bug Floris Buelens (Thu Dec 09 2010 - 04:39:40 PST)
- [AMBER] problem with resp charge generation with multiple orientations Thomas Schlesier (Thu Dec 09 2010 - 13:10:21 PST)
- Re: [AMBER] Trajectory John S (Thu Dec 09 2010 - 14:52:19 PST)
- [AMBER] Could the energy decomposition be carried out in the AmberTools? Yao-Chi Chen (Thu Dec 09 2010 - 17:23:19 PST)
- [AMBER] HEME parameters Karan Mehra (Thu Dec 09 2010 - 17:38:21 PST)
- [AMBER] Polyglycine simulation YUVRAJ UBOVEJA (Fri Dec 10 2010 - 02:28:53 PST)
- [AMBER] phosphorylated residues baljinder (Fri Dec 10 2010 - 02:54:05 PST)
- [AMBER] Fwd: simulation terminates for no apparent reason Gabriel Urquiza (Fri Dec 10 2010 - 05:14:22 PST)
- [AMBER] ambpdb error when usind mdcrd file lnedialkova.gmail.com (Fri Dec 10 2010 - 09:50:23 PST)
- [AMBER] compile pmemd using gcc Jorgen Simonsen (Fri Dec 10 2010 - 09:53:26 PST)
- [AMBER] Translate command with ptraj Logan Ahlstrom (Fri Dec 10 2010 - 17:21:24 PST)
- [AMBER] Residues lacking connect0/connect1 - these don't have chain types marked: leila karami (Sat Dec 11 2010 - 03:33:37 PST)
- [AMBER] comparision of gromacs and amber atila petrosian (Sat Dec 11 2010 - 04:55:49 PST)
- [AMBER] Atomic fluctuation John S (Sat Dec 11 2010 - 22:36:06 PST)
- [AMBER] error on running sander.MPI George Tzotzos (Sun Dec 12 2010 - 05:59:53 PST)
- [AMBER] Residues lacking connect0/connect1 - these don't have chain types marked: leila karami (Sun Dec 12 2010 - 01:05:47 PST)
- [AMBER] problem during MD process 蒋峻峰 (Sun Dec 12 2010 - 18:09:16 PST)
- [AMBER] error regarding periodic prmtop Jio M (Sun Dec 12 2010 - 20:55:13 PST)
- [AMBER] problem during TMD simulation Dachuan Guo (Mon Dec 13 2010 - 00:45:10 PST)
- [AMBER] use of packmol in amber subrata paul (Mon Dec 13 2010 - 02:43:03 PST)
- [AMBER] maxocc and life time atila petrosian (Mon Dec 13 2010 - 02:57:40 PST)
- [AMBER] reference for gbsa = 2 Jio M (Mon Dec 13 2010 - 06:25:03 PST)
- [AMBER] Using offsets to image with ptraj Logan Ahlstrom (Mon Dec 13 2010 - 12:17:36 PST)
- [AMBER] .mdin file content Bozell, Joseph John (Mon Dec 13 2010 - 13:36:15 PST)
- [AMBER] Are there polarized ion models in Amber? kurisaki ikuo (Mon Dec 13 2010 - 17:55:22 PST)
- [AMBER] running amber in amazon ec2 cloud environment Tomáš Kučera (Tue Dec 14 2010 - 01:58:46 PST)
- [AMBER] allocation failure in vector: problem in MMPBSA.py.MPI mish (Tue Dec 14 2010 - 04:11:48 PST)
- [AMBER] Problem on nmropt option in amber 11 Giachetti Andrea - CERM (Tue Dec 14 2010 - 06:24:36 PST)
- [AMBER] Building polymer John S (Tue Dec 14 2010 - 08:48:19 PST)
- [AMBER] Problems compiling pmemd.cuda.MPI for InfiniBand Sasha Buzko (Tue Dec 14 2010 - 15:02:02 PST)
- [AMBER] torsion parameters in parm99.dat xqkong (Tue Dec 14 2010 - 22:42:19 PST)
- [AMBER] Entropy calculation of a molecule in water Markus Kaukonen (Wed Dec 15 2010 - 02:07:31 PST)
- [AMBER] MMPBSA.py Internal energies Eliac Brown (Wed Dec 15 2010 - 05:58:41 PST)
- [AMBER] count number of solvent molecules inside the protein iccy liu (Wed Dec 15 2010 - 15:11:24 PST)
- Re: [AMBER] GRID-enabled web portal for the use of the AMBER Lucio Ferella (Thu Dec 16 2010 - 05:05:25 PST)
- [AMBER] QM/MM energy terms with DFTB Markus Kaukonen (Thu Dec 16 2010 - 07:49:50 PST)
- [AMBER] restart md simulation from different points Jorgen Simonsen (Thu Dec 16 2010 - 08:45:29 PST)
- [AMBER] cnts topology federica de leo (Thu Dec 16 2010 - 09:28:22 PST)
- [AMBER] NAMD cal with AMBER forces: Polarizable parameters in AMBER Xiao Ju Zhang (Thu Dec 16 2010 - 11:22:16 PST)
- [AMBER] Issues with Calculating P^2 values with RMS fits Daniel Scott (Thu Dec 16 2010 - 12:05:56 PST)
- [AMBER] force field John S (Thu Dec 16 2010 - 15:30:46 PST)
- [AMBER] Residue building and controlling the substitutes John S (Thu Dec 16 2010 - 15:39:48 PST)
- [AMBER] error in MD of modeled & docked protein - DAN complex Sangita Kachhap (Thu Dec 16 2010 - 01:22:38 PST)
- [AMBER] Is this output OK from the hybrid remd? Bongkeun Kim (Fri Dec 17 2010 - 00:13:31 PST)
- [AMBER] SCC-DFTB failure Dmitry Nilov (Fri Dec 17 2010 - 03:24:47 PST)
- [AMBER] MMPBAS.py.MPI George Tzotzos (Fri Dec 17 2010 - 07:37:24 PST)
- [AMBER] Generation of separate crd files Anindya Sarkar (Fri Dec 17 2010 - 09:21:37 PST)
- [AMBER] Error on applying MMPBSA.py Bug Fixes George Tzotzos (Fri Dec 17 2010 - 09:58:28 PST)
- [AMBER] MMPBSA test fail George Tzotzos (Fri Dec 17 2010 - 11:07:17 PST)
- [AMBER] problem with MM-PBSA Maryam Hamzehee (Sun Dec 19 2010 - 03:06:33 PST)
- [AMBER] Error with multiple GPU run: kCalculateMolecularVirial Andre Serobian (Sun Dec 19 2010 - 03:05:45 PST)
- [AMBER] reordering of atoms in mdcrd file leila karami (Sun Dec 19 2010 - 10:28:29 PST)
- [AMBER] problem of ptraj fancy2012 (Sun Dec 19 2010 - 18:54:16 PST)
- [AMBER] watershell / number of waters and which waters? leila karami (Mon Dec 20 2010 - 03:05:19 PST)
- [AMBER] AmberTools NAB corrections Markus Kaukonen (Mon Dec 20 2010 - 05:32:00 PST)
- [AMBER] compiling error for amber10 in parallel version with g++4.3.2, gfortan 4.3, mpich or lam or openmpi michelle.dupont.ulg.ac.be (Mon Dec 20 2010 - 07:52:49 PST)
- [AMBER] Flip chirality John S (Mon Dec 20 2010 - 10:21:50 PST)
- [AMBER] suppose.nab Mark Foster (Mon Dec 20 2010 - 11:53:08 PST)
- [AMBER] evaluating physical meaning of Amber results Bozell, Joseph John (Mon Dec 20 2010 - 13:54:19 PST)
- [AMBER] What is the Value of C° (standard concentration) in calculating Free Energy sunita gupta (Mon Dec 20 2010 - 22:56:52 PST)
- [AMBER] Regarding Anal energy decomposition aneesh cna (Tue Dec 21 2010 - 00:51:10 PST)
- [AMBER] RESP Dipole moment Eliac Brown (Tue Dec 21 2010 - 09:31:53 PST)
- [AMBER] Test Message - Do not reply. Ross Walker (Tue Dec 21 2010 - 23:35:20 PST)
- [AMBER] RMSD for two trajectories Maryam Hamzehee (Wed Dec 22 2010 - 04:31:26 PST)
- [AMBER] water molecules Beale, John (Wed Dec 22 2010 - 04:48:38 PST)
- [AMBER] Possibly wrong dihedrals assignment in the frcmod.parmbsc0 file Alex Spasic (Wed Dec 22 2010 - 10:26:10 PST)
- [AMBER] Using REDUCE George Tzotzos (Wed Dec 22 2010 - 10:44:38 PST)
- [AMBER] Could not find angle parameter: FE - o - c3 Ashutosh Shandilya (Wed Dec 22 2010 - 21:15:30 PST)
- [AMBER] Join my network on LinkedIn Maryam Hamzehee via LinkedIn (Thu Dec 23 2010 - 05:34:44 PST)
- [AMBER] 25th Molecular Modelling Workshop 2011 Announcement Tatyana Shubina (Thu Dec 23 2010 - 07:20:44 PST)
- [AMBER] native number of contacts Rilei Yu (Fri Dec 24 2010 - 07:17:49 PST)
- [AMBER] GAFF polarizability - source Jan.Heyda.seznam.cz (Fri Dec 24 2010 - 08:53:40 PST)
- [AMBER] GTX470 and Amber 11 Cuda tests filip fratev (Fri Dec 24 2010 - 23:14:04 PST)
- [AMBER] REMD number of replica Sangita Kachhap (Sat Dec 25 2010 - 04:53:28 PST)
- [AMBER] conversion of gromacs trajrctory file (xtc) to amber trajectory file (mdcrd) / problem in water moecules. leila karami (Sun Dec 26 2010 - 03:24:02 PST)
- [AMBER] watershell / number of waters and which waters? leila karami (Sun Dec 26 2010 - 06:01:07 PST)
- [AMBER] conversion of gromacs trajrctory file (xtc) to amber trajectory file (mdcrd) / problem in water moecules. leila karami (Sun Dec 26 2010 - 07:47:01 PST)
- [AMBER] QM/MM-MD binding energy Eliac Brown (Sun Dec 26 2010 - 08:49:51 PST)
- [AMBER] about the Sietraj xuemeiwang1103 (Sun Dec 26 2010 - 22:22:44 PST)
- [AMBER] conversion of gromacs trajectory file (xtc) to amber trajectory file (mdcrd) / problem in water molecules leila karami (Mon Dec 27 2010 - 01:28:03 PST)
- [AMBER] time in ptraj atila petrosian (Mon Dec 27 2010 - 01:43:51 PST)
- [AMBER] conversion of gromacs trajectory file (xtc) to amber trajectory file (mdcrd) / problem in water molecules leila karami (Mon Dec 27 2010 - 06:40:14 PST)
- [AMBER] conversion of gromacs trajectory file (xtc) to amber trajectory file (mdcrd) / problem in water molecules leila karami (Mon Dec 27 2010 - 10:27:54 PST)
- [AMBER] problem with MM-PBSA Maryam Hamzehee (Tue Dec 28 2010 - 03:17:03 PST)
- [AMBER] flag dihedrals in the .prmtop Z.Xiao (Tue Dec 28 2010 - 23:43:24 PST)
- [AMBER] conversion of gromacs trajectory file (xtc) to amber trajectory file (mdcrd) / problem in water molecules leila karami (Wed Dec 29 2010 - 02:47:59 PST)
- [AMBER] can I use ambmask for trajectory file (mdcrd)? atila petrosian (Wed Dec 29 2010 - 06:13:59 PST)
- [AMBER] MMPBSA binding energy Eliac Brown (Wed Dec 29 2010 - 17:11:44 PST)
- [AMBER] how to add phosphate group in protein Sangita Kachhap (Thu Dec 30 2010 - 01:45:02 PST)
- [AMBER] Fw: configuring options for Amber tools amit banerjee (Thu Dec 30 2010 - 02:16:47 PST)
- [AMBER] conversion of gromacs trajectory file (xtc) to amber trajectory file (mdcrd) / problem in water molecules leila karami (Thu Dec 30 2010 - 02:34:03 PST)
- [AMBER] dissacharide subrata paul (Thu Dec 30 2010 - 04:49:42 PST)
- [AMBER] can I use ambmask for trajectory file (mdcrd)? atila petrosian (Thu Dec 30 2010 - 05:39:36 PST)
- [AMBER] rdf subrata paul (Thu Dec 30 2010 - 07:26:53 PST)
- [AMBER] about the Sietraj xuemeiwang1103 (Thu Dec 30 2010 - 17:11:47 PST)
- [AMBER] Luck or Black Box Eliac Brown (Thu Dec 30 2010 - 20:55:59 PST)
- [AMBER] where are the parameters controlling the cis/trans configuration of Proline ? Jose Borreguero (Fri Dec 31 2010 - 09:32:06 PST)
- [AMBER] GTP parameters Jacopo Sgrignani (Fri Dec 31 2010 - 09:36:06 PST)
- Last message date: Fri Dec 31 2010 - 17:00:04 PST
- Archived on: Fri Nov 22 2024 - 05:54:09 PST
