Amber Archive Oct 2008 by thread
- Re: AMBER: Ac-Co Parameters for Amber FyD (Tue Sep 30 2008 - 23:14:39 PDT)
- AMBER: F modified RNA is split in two parts when running sander simulated annealing Peter Podbevšek (Wed Oct 01 2008 - 02:01:52 PDT)
- Re: AMBER: How to set up a water slab in Amber? David A. Case (Wed Oct 01 2008 - 04:51:17 PDT)
- AMBER: Sources of disruption during NVE Naser Alijabbari (Wed Oct 01 2008 - 08:59:29 PDT)
- AMBER: MM-PBSA problem : Use of uninitialized value in multiplicatiom with Amber10 Carra, Claudio (JSC-SK)[USRA] (Wed Oct 01 2008 - 10:05:55 PDT)
- Re: AMBER: Temperature regulation julliane Yoneda (Wed Oct 01 2008 - 10:22:06 PDT)
- AMBER: amber10 installation on sgi_mips Rima Chaudhuri (Wed Oct 01 2008 - 12:05:06 PDT)
- AMBER: thermodynamic integration with Amber9 Sadhna Rana (Thu Oct 02 2008 - 08:12:47 PDT)
- Re: AMBER: Leap atoms CL and OXT do not have a type Francesco Pietra (Thu Oct 02 2008 - 08:47:31 PDT)
- AMBER: Oct 6 deadline for ACS computational chemistry awards Carlos Simmerling (Thu Oct 02 2008 - 10:45:35 PDT)
- AMBER: Support for intel mpi in pmemd 10; better support for intel MKL Robert Duke (Thu Oct 02 2008 - 13:56:07 PDT)
- AMBER: shake the molecule amit jain (Thu Oct 02 2008 - 22:26:33 PDT)
- AMBER: amber10 on SiCortex hardware Peter Varnai (Fri Oct 03 2008 - 09:27:21 PDT)
- AMBER: ptraj average structure Yunierkis Perez Castillo (Sat Oct 04 2008 - 06:25:42 PDT)
- AMBER: Parameters for alkali cations and halogen anions Francesco Pietra (Sun Oct 05 2008 - 00:29:45 PDT)
- AMBER: MM_PBSA problems in AMBER9 欧阳德方 (Sun Oct 05 2008 - 14:30:12 PDT)
- AMBER: internal energy INT is not zero from MM_GBSA Fan Yanping (Mon Oct 06 2008 - 23:08:14 PDT)
- AMBER: internal energy INT is not zero from MM_GBSA flyanping (Mon Oct 06 2008 - 23:18:49 PDT)
- AMBER: Amber heme parameters Shaikh Abdul R S Ramaju (Mon Oct 06 2008 - 23:31:34 PDT)
- AMBER: Zn2+ Bondi radius value Sergey Samsonov (Tue Oct 07 2008 - 01:50:10 PDT)
- AMBER: Once again, with feeling --- Support for intel mpi in pmemd 10; better support for intel MKL Robert Duke (Tue Oct 07 2008 - 10:02:51 PDT)
- AMBER: Question on Urea box Antonios Samiotakis (Tue Oct 07 2008 - 12:31:44 PDT)
- AMBER: saveamberparm error Shaikh Abdul R S Ramaju (Wed Oct 08 2008 - 04:33:31 PDT)
- AMBER: AMBER force field for glycolipid Stephane Abel (Wed Oct 08 2008 - 05:25:12 PDT)
- AMBER: ptraj - closest command Ryan Pavlovicz (Wed Oct 08 2008 - 10:36:17 PDT)
- AMBER: Jmol 11.7.1 pre-release version reads AMBER trajectory/coordinate files Robert Hanson (Wed Oct 08 2008 - 11:16:55 PDT)
- AMBER: velocity-verlet algorithm and ensembles oguz gurbulak (Wed Oct 08 2008 - 11:59:46 PDT)
- Re: AMBER: xleap fails to savemol2 taufik.alsarraj.utoronto.ca (Wed Oct 08 2008 - 14:57:30 PDT)
- Fwd: Re: AMBER: Jmol 11.7.1 pre-release version reads AMBER trajectory/coordinate files FyD (Thu Oct 09 2008 - 09:57:07 PDT)
- Re: [Jmol-users] AMBER: Jmol 11.7.1 pre-release version reads AMBER trajectory/coordinate files Robert Hanson (Thu Oct 09 2008 - 16:12:52 PDT)
- AMBER: nscm code Naser Alijabbari (Thu Oct 09 2008 - 22:05:59 PDT)
- AMBER: Question about resp charges for a charged molecule... Alberto Sergio Garay (Fri Oct 10 2008 - 03:54:22 PDT)
- AMBER: AddIons approach parul sharma (Fri Oct 10 2008 - 04:13:51 PDT)
- AMBER: Radius of Gyration Beale, John (Fri Oct 10 2008 - 04:27:22 PDT)
- AMBER: Ring flips Beale, John (Fri Oct 10 2008 - 10:09:52 PDT)
- AMBER: antechamber dipti lele (Sat Oct 11 2008 - 21:43:33 PDT)
- AMBER: removing COM and rotation in explicit solvation Naser Alijabbari (Sun Oct 12 2008 - 13:02:22 PDT)
- AMBER: pairwise interaction energies Thomas Leonard (Sun Oct 12 2008 - 23:12:11 PDT)
- AMBER: PDB standards Francesco Pietra (Mon Oct 13 2008 - 01:18:23 PDT)
- AMBER: Ptraj pucker for pyranose Neha Gandhi (Mon Oct 13 2008 - 02:43:33 PDT)
- AMBER: question about pression Yunierkis Perez Castillo (Mon Oct 13 2008 - 07:45:38 PDT)
- AMBER: LEU as first residue Francesco Pietra (Mon Oct 13 2008 - 09:20:00 PDT)
- AMBER: amber: parameters for 5' nucleotide monophosphates Jeff Schwinefus (Mon Oct 13 2008 - 10:52:55 PDT)
- AMBER: High Bfactor values for the terminal residues/atoms Siddharth Rastogi (Mon Oct 13 2008 - 21:19:52 PDT)
- AMBER: large number of solvent molecules were added for protein with 221 AA residues Siddharth Rastogi (Mon Oct 13 2008 - 21:34:58 PDT)
- AMBER: antechamber test failure john smith (Mon Oct 13 2008 - 22:47:28 PDT)
- Re: Re: RE: AMBER: the install problem hklwatergod (Tue Oct 14 2008 - 00:19:02 PDT)
- AMBER: LEaP problem with LEU first residue? Francesco Pietra (Tue Oct 14 2008 - 03:26:25 PDT)
- AMBER: amber10 installation problem in cygwin vijayaraj.clri.res.in (Tue Oct 14 2008 - 08:21:19 PDT)
- AMBER: Amber dipole printout. Zhao, Zhen (zhaozh) (Tue Oct 14 2008 - 10:25:40 PDT)
- AMBER: Installation Error Jagan Mohan (Wed Oct 15 2008 - 00:50:18 PDT)
- AMBER: Amber10: Problem with tgtmd and ncsu testing Dmitri Nilov (Wed Oct 15 2008 - 06:00:11 PDT)
- AMBER: Origin of periodic box Naser Alijabbari (Wed Oct 15 2008 - 18:34:00 PDT)
- AMBER: Differentiating the force constant of distance restraints Francesca Poletti (Thu Oct 16 2008 - 01:40:16 PDT)
- AMBER: regarding rigid molecules aneesh cna (Thu Oct 16 2008 - 02:34:36 PDT)
- AMBER: Clarification re qmmask Benjamin Roberts (Thu Oct 16 2008 - 10:24:45 PDT)
- AMBER: antechamber Marcela Madrid (Thu Oct 16 2008 - 13:37:07 PDT)
- AMBER: Using charmm force field in amber Harry (Yicun) Ni (Thu Oct 16 2008 - 14:20:45 PDT)
- AMBER: capping with non charged residues Francesco Pietra (Thu Oct 16 2008 - 15:24:44 PDT)
- AMBER: antechamber errors oguz gurbulak (Fri Oct 17 2008 - 06:07:37 PDT)
- AMBER: Restricting the system to simulate Francesco Pietra (Fri Oct 17 2008 - 09:00:50 PDT)
- AMBER: NAD+ parameters problem using tleap Dmitri Nilov (Fri Oct 17 2008 - 09:24:50 PDT)
- AMBER: using ptraj Adrien Delmont (Fri Oct 17 2008 - 14:44:16 PDT)
- AMBER: REDvIII_I_lack_of_charges_in_mol2 Karol Kaszuba (Sat Oct 18 2008 - 04:08:53 PDT)
- AMBER: Addions in GB Mode? Rogelio Hernández (Sun Oct 19 2008 - 10:04:32 PDT)
- AMBER: question about simulation box Adrien Delmont (Sun Oct 19 2008 - 14:04:24 PDT)
- AMBER: Error in creating topology file musa özboyacı (Mon Oct 20 2008 - 04:00:48 PDT)
- AMBER: Contacts Beale, John (Mon Oct 20 2008 - 07:29:06 PDT)
- AMBER: about SASA and AMBER Yunierkis Perez Castillo (Mon Oct 20 2008 - 08:58:06 PDT)
- AMBER: mm_pbsa_statistics / 3 traj Arturas Ziemys (Mon Oct 20 2008 - 09:18:26 PDT)
- AMBER: drug/protein interaction modeling setup Sean Johnston (Mon Oct 20 2008 - 13:10:52 PDT)
- AMBER: cnstph test case failure or expected divergence? Melinda Layten (Mon Oct 20 2008 - 13:23:08 PDT)
- AMBER: scyld beowulf --amber10--openmpi Rima Chaudhuri (Mon Oct 20 2008 - 17:00:27 PDT)
- AMBER: Heme cysteine Shaikh Abdul R S Ramaju (Tue Oct 21 2008 - 00:16:50 PDT)
- AMBER: ptraj John Bennett (Tue Oct 21 2008 - 07:32:07 PDT)
- AMBER: Does LEaP understant capping with ACE/NME? Francesco Pietra (Tue Oct 21 2008 - 08:57:12 PDT)
- Re: AMBER: Heme cysteine Bill Ross (Tue Oct 21 2008 - 09:20:38 PDT)
- AMBER: Again: Installation problem of AMBER on cluster Dmitri Nilov (Tue Oct 21 2008 - 09:31:52 PDT)
- AMBER: MM_PBSA doesn't terminate Khaled Barakat (Tue Oct 21 2008 - 09:58:12 PDT)
- AMBER: DNA structure analysis Bert (Wed Oct 22 2008 - 04:27:38 PDT)
- AMBER: MM_PBSA doesn't terminate Khaled Barakat (Wed Oct 22 2008 - 08:27:55 PDT)
- AMBER: stripping water from a restart file CHAMI F. (Wed Oct 22 2008 - 09:11:46 PDT)
- Re: AMBER: stripping water from a restart file Bill Ross (Wed Oct 22 2008 - 10:12:29 PDT)
- AMBER: installing amber on new linux Jan Goeman (Wed Oct 22 2008 - 14:06:48 PDT)
- AMBER: MM-PBSA -energy decomposition error Cristina Sisu (Wed Oct 22 2008 - 15:07:43 PDT)
- AMBER: energy leakage? Sally Pias (Thu Oct 23 2008 - 00:25:59 PDT)
- AMBER: Metal parameter values musa özboyacı (Thu Oct 23 2008 - 04:59:13 PDT)
- AMBER: Non bond list error Wang,Ying (Thu Oct 23 2008 - 10:19:49 PDT)
- Re: AMBER: Metal parameter values Bill Ross (Thu Oct 23 2008 - 11:23:08 PDT)
- AMBER: problem with running mm-pbsa moitrayee.mbu.iisc.ernet.in (Fri Oct 24 2008 - 00:14:49 PDT)
- AMBER: something puzzled with mm_pbsa TaoPaul (Fri Oct 24 2008 - 03:50:04 PDT)
- AMBER: problem with amber8 installation moitrayee.mbu.iisc.ernet.in (Fri Oct 24 2008 - 05:20:17 PDT)
- AMBER: problem with amber8 installation moitrayee.mbu.iisc.ernet.in (Fri Oct 24 2008 - 05:22:40 PDT)
- AMBER: Regarding sleap - documentation and output behavior Keith Van Nostrand (Fri Oct 24 2008 - 08:26:58 PDT)
- AMBER: Atom names CL and four characters Francesco Pietra (Fri Oct 24 2008 - 11:55:05 PDT)
- AMBER: Restraining with PMEMD 10 Francesco Pietra (Sat Oct 25 2008 - 02:32:39 PDT)
- AMBER: the question about "RADIOPT" option in mm_pbsa TaoPaul (Sat Oct 25 2008 - 04:11:04 PDT)
- AMBER: Is it possible to recover the umbrella file in ABMD simulation after hard disk failure? Ye Mei (Sat Oct 25 2008 - 05:32:25 PDT)
- AMBER: Conversion between truncated octahedron and orthorohombic box #NGUYEN CONG TRI# (Sat Oct 25 2008 - 19:36:30 PDT)
- AMBER: Duplicate entries with different parameters in gaff.dat from AmberTools 1.2 John Chodera (Sun Oct 26 2008 - 18:16:48 PDT)
- AMBER: atom type for carbon and nitrogen atoms Catein Catherine (Mon Oct 27 2008 - 01:56:06 PDT)
- AMBER: atom type for carbon and nitrogen atoms Catein Catherine (Mon Oct 27 2008 - 01:58:51 PDT)
- AMBER: peptide MD Beale, John (Mon Oct 27 2008 - 08:38:48 PDT)
- AMBER: 2'-5'-branched RNA Volodymyr Zloy (Mon Oct 27 2008 - 09:10:00 PDT)
- AMBER: Identification of improper torsions in small molecules parameterized with GAFF by antechamber John Chodera (Mon Oct 27 2008 - 15:12:31 PDT)
- AMBER: aromatic bent ligand Arturas Ziemys (Mon Oct 27 2008 - 19:34:49 PDT)
- AMBER: SPCFW problems Naser Alijabbari (Mon Oct 27 2008 - 19:37:12 PDT)
- AMBER: antechamber bug? produces incorrect NEWPDB.PDB file Robert Hanson (Tue Oct 28 2008 - 09:46:08 PDT)
- AMBER: Problem installing PMEMD with intel mpi, ifort Rupesh Nanjunda (Tue Oct 28 2008 - 14:07:01 PDT)
- AMBER: ANAL Madhumalar Arumugam (Wed Oct 29 2008 - 01:44:57 PDT)
- AMBER: problem with Dihedral angle potentials aneesh cna (Wed Oct 29 2008 - 02:23:57 PDT)
- AMBER: Huge difference between pbtot and gbtot in mm-pbsa calculations moitrayee.mbu.iisc.ernet.in (Wed Oct 29 2008 - 06:07:23 PDT)
- AMBER: Folate parameters Michael Lerner (Wed Oct 29 2008 - 10:03:06 PDT)
- AMBER: Optimal compiling of amber on XT3 Patrick McCarren (Wed Oct 29 2008 - 21:30:56 PDT)
- AMBER: Packing density calculation Siddharth Rastogi (Thu Oct 30 2008 - 03:41:58 PDT)
- AMBER: Lone pairs in antechamber Diddo Diddens (Thu Oct 30 2008 - 06:25:35 PDT)
- amber-developers: FW: AMBER: Duplicate entries with different parameters in gaff.dat from AmberTools 1.2 Ross Walker (Thu Oct 30 2008 - 10:41:27 PDT)
- AMBER: minimization Jacopo Sgrignani (Thu Oct 30 2008 - 11:03:29 PDT)
- AMBER: MM_PBSA binding error Larry Layne (Thu Oct 30 2008 - 11:54:24 PDT)
- AMBER: Setting GROUP for pmemd Francesco Pietra (Thu Oct 30 2008 - 12:10:39 PDT)
- AMBER: Query on restart file Neha Gandhi (Thu Oct 30 2008 - 18:49:30 PDT)
- AMBER: error message of xleap Catein Catherine (Thu Oct 30 2008 - 20:40:49 PDT)
- AMBER: how to ger resp charge for a residue? WJ Ding (Thu Oct 30 2008 - 21:20:05 PDT)
- AMBER: problem with zMatrix in tleap WJ Ding (Thu Oct 30 2008 - 21:40:59 PDT)
- AMBER: minimization Jacopo Sgrignani (Fri Oct 31 2008 - 01:52:12 PDT)
- AMBER: Question on AMBER MD Implications Campbell, Patrick (Fri Oct 31 2008 - 09:27:41 PDT)
- AMBER: Trouble compiling Amber 9 leap programs on SGI Altix system John Finke (Fri Oct 31 2008 - 11:05:57 PDT)
- AMBER: MM-PBSA error in Amber10: possible bug? Pablo Englebienne (Fri Oct 31 2008 - 20:38:15 PDT)
- Last message date: Sun Nov 02 2008 - 05:09:41 PST
- Archived on: Wed Dec 25 2024 - 05:53:45 PST
