Amber Archive Mar 2007 By Thread
- Re: AMBER: solvent accessible surface area (SASA) Carlos Simmerling (Thu Mar 01 2007 - 04:10:55 PST)
- AMBER: Disulfide Problem Beale, John (Thu Mar 01 2007 - 05:49:22 PST)
- Re: AMBER: RESP calculation of modified nucleotides mathew k varghese (Thu Mar 01 2007 - 06:33:00 PST)
- AMBER: Restart from restart file obtained from ptraj with added velocities j j (Thu Mar 01 2007 - 08:17:41 PST)
- Re: AMBER: momentum and periodic boundary condition David A. Case (Thu Mar 01 2007 - 08:52:00 PST)
- AMBER: [rsachdeva@imtech.res.in: A query] David A. Case (Thu Mar 01 2007 - 09:02:27 PST)
- Re: AMBER: SCF convergence issues Steven Winfield (Fri Mar 02 2007 - 05:43:58 PST)
- AMBER: qm/mm ti Ben Sattelle (Fri Mar 02 2007 - 05:54:53 PST)
- AMBER: Restart Files Steve Seibold (Fri Mar 02 2007 - 07:26:03 PST)
- AMBER: restraints during MD Seth Lilavivat (Fri Mar 02 2007 - 08:16:05 PST)
- AMBER: reproducibility between software Stern, Julie (Fri Mar 02 2007 - 08:34:32 PST)
- AMBER: Amber 9 make parallel fails with mpich Rene Salmon (Fri Mar 02 2007 - 09:45:37 PST)
- AMBER: ptraj average structure strip water Youyi Peng (Fri Mar 02 2007 - 11:52:02 PST)
- AMBER: Calcium parameters Lei Jia (Fri Mar 02 2007 - 11:58:27 PST)
- AMBER: Restraints on modified NA's Seth Lilavivat (Fri Mar 02 2007 - 13:56:07 PST)
- AMBER: calculate RMSD of only chain C ÕÔÑÇÑ© (Fri Mar 02 2007 - 18:21:33 PST)
- AMBER: TI calculation: charge is not zero in the perturbed state brmeher.iitg.ernet.in (Sat Mar 03 2007 - 12:32:02 PST)
- AMBER: denaturing salt conditions Sean Rathlef (Sat Mar 03 2007 - 14:35:45 PST)
- AMBER: Question about translational and rotational degree of freedom in MM-PBSA v9 computations Cenk Andac (Sun Mar 04 2007 - 04:06:22 PST)
- AMBER: prep file limit exceeding gurpreet singh (Sun Mar 04 2007 - 23:52:49 PST)
- AMBER: distance calculation! r. a. (Mon Mar 05 2007 - 00:43:45 PST)
- AMBER: psi , phi angles deepti nayar (Mon Mar 05 2007 - 03:07:41 PST)
- AMBER: pbsa installation problem bala (Mon Mar 05 2007 - 04:34:32 PST)
- AMBER: Beale, John (Mon Mar 05 2007 - 09:50:26 PST)
- AMBER: Beale, John (Mon Mar 05 2007 - 09:51:29 PST)
- AMBER: constraint pdb file Stern, Julie (Mon Mar 05 2007 - 13:06:47 PST)
- AMBER: mm_pbsa individual contributions of residues AYTUG TUNCEL (Mon Mar 05 2007 - 15:12:54 PST)
- AMBER: how to incorporate ismem =1 into mm_pbsa AYTUG TUNCEL (Mon Mar 05 2007 - 15:32:19 PST)
- AMBER: any general approach to create SiO2 wall Sisir Das (Mon Mar 05 2007 - 20:46:42 PST)
- AMBER: Trimannoside Problem Sandeep Kaushik (Tue Mar 06 2007 - 04:44:20 PST)
- AMBER: how is the standard deviations calculated in mm-pbsa? Magne Olufsen (Tue Mar 06 2007 - 04:58:17 PST)
- AMBER: DHAS_10_12 compilation aborted for egb.f Jesus Angulo (Tue Mar 06 2007 - 06:31:28 PST)
- AMBER: how to modify map.DG-AMBER file? Seth Lilavivat (Tue Mar 06 2007 - 12:55:40 PST)
- AMBER: addles segmentation fault deepti nayar (Tue Mar 06 2007 - 23:18:39 PST)
- AMBER: Topology file problem in TI ! Pradipta Bandyopadhyay (Wed Mar 07 2007 - 03:08:39 PST)
- Re: AMBER: Amber 9, sander imin = 5, -y flag S.Sundar Raman (Wed Mar 07 2007 - 10:05:19 PST)
- Re: AMBER: Problems with QMMM tests on Altix Roberto Gomperts (Thu Mar 08 2007 - 15:39:14 PST)
- AMBER: van der Waals parameters and 6-12 potential parameters of NB in parm99.dat? Chengwen Chen (Fri Mar 09 2007 - 00:04:00 PST)
- AMBER: problem with ptraj with calculating auto time correlation functions Terry Lang (Fri Mar 09 2007 - 10:36:14 PST)
- AMBER: abnormal termination of tleap Pankaj R. Daga (Fri Mar 09 2007 - 14:24:37 PST)
- AMBER: rmsd calculation in ptraj gurpreet singh (Sat Mar 10 2007 - 05:24:50 PST)
- AMBER: rmsd calculation in ptraj gurpreet singh (Sat Mar 10 2007 - 05:38:28 PST)
- AMBER: rmsd calculation in ptraj II gurpreet singh (Sat Mar 10 2007 - 20:37:10 PST)
- AMBER: unable to run test Anju Sharma (Sun Mar 11 2007 - 22:14:03 PDT)
- AMBER: addles deepti nayar (Sun Mar 11 2007 - 23:29:37 PDT)
- AMBER: Essential ions and water molecules in MMPBSA computations Cenk Andac (Mon Mar 12 2007 - 02:13:56 PDT)
- AMBER: NEB tutorial deepti nayar (Mon Mar 12 2007 - 03:03:17 PDT)
- AMBER: The parallel test fails while sander.MPI seems to be installed correctly Mostafa Sadighi (Mon Mar 12 2007 - 04:43:14 PDT)
- AMBER: DNA Helicoïdal Plots over time Stéphane Téletchéa (Mon Mar 12 2007 - 05:31:02 PDT)
- AMBER: Can I measure improper torsion by ptarj? Chengwen Chen (Mon Mar 12 2007 - 09:21:55 PDT)
- AMBER: hi.. Anju Sharma (Tue Mar 13 2007 - 04:59:24 PDT)
- AMBER: problem with mm_pbsa Yves Boulard (Tue Mar 13 2007 - 07:21:22 PDT)
- AMBER: poor performance of sander on a quad-core linux machine Lillian chong (Tue Mar 13 2007 - 10:27:31 PDT)
- AMBER: problem while running minimisation Anju Sharma (Tue Mar 13 2007 - 21:10:15 PDT)
- AMBER: Problem Solved Anju Sharma (Tue Mar 13 2007 - 21:19:57 PDT)
- AMBER: NEB tutorial and addles deepti nayar (Tue Mar 13 2007 - 21:28:20 PDT)
- AMBER: problem while analysing result Anju Sharma (Tue Mar 13 2007 - 22:38:37 PDT)
- AMBER: Need help in Analysis Anju Sharma (Wed Mar 14 2007 - 02:13:03 PDT)
- AMBER: torsion angle deepti nayar (Wed Mar 14 2007 - 05:03:08 PDT)
- AMBER: Question about Boron Kara Di Giorgio (Wed Mar 14 2007 - 10:15:22 PDT)
- AMBER: mmpbsa free energy pairwise decomposition Gianluca Degliesposti (Wed Mar 14 2007 - 11:54:32 PDT)
- AMBER: Regarding counter ions Rafi Ahmad (Wed Mar 14 2007 - 13:00:59 PDT)
- AMBER: Segmentation fault (iforrtoccurs during minimization (Amber 9) Eric Shamay (Wed Mar 14 2007 - 18:12:49 PDT)
- AMBER: How to build organic compound in Amber Anju Sharma (Wed Mar 14 2007 - 21:24:09 PDT)
- AMBER: hii Anju Sharma (Thu Mar 15 2007 - 02:28:47 PDT)
- AMBER: Problem related simulation of dimer priya priya (Thu Mar 15 2007 - 04:23:31 PDT)
- AMBER: Dipolar and Inertia Moments kepa koldo burusco (Thu Mar 15 2007 - 04:46:17 PDT)
- AMBER: solvate shell janavi raghavan (Thu Mar 15 2007 - 09:33:13 PDT)
- AMBER: van der waals parameters. Stefano Tonzani (Thu Mar 15 2007 - 10:52:09 PDT)
- AMBER: Segmentation Fault when saving prmtop and inpcrd files in xleap Laura McDriscoll (Thu Mar 15 2007 - 22:59:33 PDT)
- AMBER: hi Anju Sharma (Fri Mar 16 2007 - 03:50:44 PDT)
- AMBER: vlimit error Amit Kumar (Fri Mar 16 2007 - 16:10:06 PDT)
- AMBER: antechamber error Ilyas Yildirim (Fri Mar 16 2007 - 23:44:57 PDT)
- AMBER: targeted MD problem gurpreet singh (Sat Mar 17 2007 - 05:17:27 PDT)
- AMBER: targetedMD problem gurpreet singh (Sun Mar 18 2007 - 06:32:40 PDT)
- AMBER: antechamber Ilyas Yildirim (Sun Mar 18 2007 - 10:56:00 PDT)
- AMBER: hi Anju Sharma (Sun Mar 18 2007 - 20:56:22 PDT)
- AMBER: Problem while creating structure in xLeap Anju Sharma (Sun Mar 18 2007 - 21:30:03 PDT)
- AMBER: Problem!! Anju Sharma (Sun Mar 18 2007 - 23:38:15 PDT)
- AMBER: MM-GBSA residues decomposition comparison Sergey Samsonov (Tue Mar 20 2007 - 07:17:26 PDT)
- AMBER: basis set for RESP calculation Michel Becker (Tue Mar 20 2007 - 13:43:10 PDT)
- AMBER: Problem while loading Pdb in xleap Anju Sharma (Tue Mar 20 2007 - 21:12:55 PDT)
- AMBER: Problem while running Antechamber Anju Sharma (Wed Mar 21 2007 - 02:35:28 PDT)
- AMBER: Modified Nucleic Acid Problem SHARAD gupta (Wed Mar 21 2007 - 06:22:10 PDT)
- AMBER: How to reimage the trajectories of LES calculations? Kailee (Wed Mar 21 2007 - 06:35:06 PDT)
- AMBER: ntt=1 or ntt= 3? Therese Malliavin (Wed Mar 21 2007 - 10:32:07 PDT)
- AMBER: xLeAP: TI calculation: the perturbed charge is not integral Ignacio Faustino (Wed Mar 21 2007 - 12:17:12 PDT)
- AMBER: TI calculation: the perturbed charge is not integral Ignacio Faustino (Wed Mar 21 2007 - 12:21:52 PDT)
- AMBER: restraint in minimization deepti nayar (Thu Mar 22 2007 - 01:21:32 PDT)
- AMBER: Holding NA Base syn during annealing Seth Lilavivat (Thu Mar 22 2007 - 08:23:20 PDT)
- AMBER: Generating structure of polyethylene glycol in AMBER Lili Peng (Thu Mar 22 2007 - 14:35:07 PDT)
- Re: AMBER: sander/topology problem Jin-Soo Kim (Fri Mar 23 2007 - 07:31:00 PDT)
- AMBER: anneal algorthm Seth Lilavivat (Fri Mar 23 2007 - 12:33:42 PDT)
- AMBER: Error - must define AMBERHOME environment variable bertrand russell (Fri Mar 23 2007 - 13:05:47 PDT)
- AMBER: Combining RESP with AM1-BCC Ilyas Yildirim (Fri Mar 23 2007 - 14:41:04 PDT)
- AMBER: water density Esther Brugger (Fri Mar 23 2007 - 15:47:33 PDT)
- AMBER: amber 9 - output of forces Eric Shamay (Fri Mar 23 2007 - 16:00:39 PDT)
- AMBER: Does Sander.MPI support coupling effect between different molecules at the same area at the same temperature in the mixture? Jin-Soo Kim (Sat Mar 24 2007 - 04:40:26 PDT)
- AMBER: Please check the total charge and your -nc flag snoze pa (Sun Mar 25 2007 - 21:54:52 PDT)
- AMBER: phe-phe simulation deepti nayar (Mon Mar 26 2007 - 00:25:19 PDT)
- AMBER: pmemd segmentation fault Vlad Cojocaru (Mon Mar 26 2007 - 02:14:50 PDT)
- AMBER: pdb file produced by vmd Rita Cassia (Mon Mar 26 2007 - 09:04:19 PDT)
- AMBER: DNA Flat Angle Restraints Kyle L. Brown (Mon Mar 26 2007 - 10:04:09 PDT)
- AMBER: distcovar in ptraj Zhenyu Lu (Mon Mar 26 2007 - 21:00:13 PDT)
- AMBER: Parameter file for Dipeptide Neelanjana Sengupta (Mon Mar 26 2007 - 22:23:32 PDT)
- AMBER: The ring number exceeds MAXRING, increase MAXRING and recompile the programs, exit j j (Tue Mar 27 2007 - 07:04:48 PDT)
- AMBER: Question about loadMol2 David LeBard (Tue Mar 27 2007 - 11:31:56 PDT)
- AMBER: amber 9 install: patch reject Stern, Julie (Tue Mar 27 2007 - 11:50:33 PDT)
- AMBER: amber 9: fortran/test failures Stern, Julie (Tue Mar 27 2007 - 11:55:43 PDT)
- AMBER: residue types for GLY/high pH Stern, Julie (Tue Mar 27 2007 - 13:19:47 PDT)
- AMBER: Amber 9 TI Details Lachele Foley (Lists) (Tue Mar 27 2007 - 14:03:20 PDT)
- AMBER: specifying psi and phi for a dipeptide deepti nayar (Wed Mar 28 2007 - 04:50:28 PDT)
- AMBER: DISAVE value1 Kyle L. Brown (Wed Mar 28 2007 - 14:42:16 PDT)
- AMBER: rms and rmsf in ptraj Mingfeng Yang (Wed Mar 28 2007 - 14:06:02 PDT)
- AMBER: problem in implcit simulation gurpreet singh (Wed Mar 28 2007 - 21:25:53 PDT)
- AMBER: benchmarking pmemd and sander (pmemd segmentation fault problem follow up) Vlad Cojocaru (Thu Mar 29 2007 - 02:50:29 PDT)
- AMBER: minimization not running deepti nayar (Thu Mar 29 2007 - 02:57:15 PDT)
- AMBER: minimization energy query deepti nayar (Thu Mar 29 2007 - 03:55:39 PDT)
- AMBER: is possible to compile pmemd using scali MPI? Andrea Bortolato (Thu Mar 29 2007 - 09:17:05 PDT)
- AMBER: Amber9 Sander Error A Box (Thu Mar 29 2007 - 19:26:21 PDT)
- AMBER: Sander error : Coordinate resetting (SHAKE) cannot be accomplished Pankaj R. Daga (Thu Mar 29 2007 - 20:59:08 PDT)
- AMBER: minimization + simulation deepti nayar (Fri Mar 30 2007 - 00:54:03 PDT)
- AMBER: RST can not be opened deepti nayar (Fri Mar 30 2007 - 02:21:58 PDT)
- AMBER: problem regarding water handling in explicit simu gurpreet singh (Fri Mar 30 2007 - 02:35:49 PDT)
- AMBER: Some problems during the testing of Amber. Liang, Lei (Fri Mar 30 2007 - 11:12:50 PDT)
- AMBER: A question about biomineral simulation, help!! WANG,YING (Fri Mar 30 2007 - 14:36:02 PDT)
- AMBER: Distance restraint to centre of mass Evan Kelly (Fri Mar 30 2007 - 15:41:32 PDT)
- Last message date: Sun Apr 01 2007 - 06:08:06 PDT
- Archived on: Sun Mar 14 2010 - 06:00:14 PDT
