Amber Archive Aug 2008 by thread
- Re: AMBER: Prepgen Grange Hermitage (Thu Jul 31 2008 - 19:29:45 PDT)
- AMBER: Compailation problum in Amber 10 srinivas sudani (Thu Jul 31 2008 - 23:59:00 PDT)
- AMBER: bacteriochlorophyll ff Anna Karawajczyk (Fri Aug 01 2008 - 03:04:44 PDT)
- AMBER: Bonds getting shorter in sander Peter Gannett (Fri Aug 01 2008 - 05:47:02 PDT)
- Fwd: AMBER: prepare an initial structure in Amber Lachele Foley (Lists) (Fri Aug 01 2008 - 07:52:50 PDT)
- Re: AMBER: silhouette width/coefficient after clustering by PTRAJ9.9 Jianyin Shao (Fri Aug 01 2008 - 12:43:14 PDT)
- AMBER: Simulating protein conformational changes? Sasha Buzko (Fri Aug 01 2008 - 15:42:07 PDT)
- AMBER: respgen -a charge groups function ineffective unless Grange Hermitage (Fri Aug 01 2008 - 22:00:29 PDT)
- AMBER: PDB files in Amber10 Francesco Pietra (Sat Aug 02 2008 - 00:21:58 PDT)
- AMBER: error in parallel amber 9 test Jaber Jahanbin Sardroodi (Sat Aug 02 2008 - 14:12:07 PDT)
- Re: AMBER: Trans proline Brent Krueger (Sat Aug 02 2008 - 20:47:16 PDT)
- AMBER: Problem with setting the NMR restraints Alex Spasic (Mon Aug 04 2008 - 07:15:25 PDT)
- AMBER: Set 251 is corrupted, ptraj error... Waqas Nasir (Mon Aug 04 2008 - 07:54:09 PDT)
- AMBER: Biased MD with Amber 10 Francesco Pietra (Mon Aug 04 2008 - 11:35:31 PDT)
- AMBER: divcon.rst ?? IN SUK JOUNG (Mon Aug 04 2008 - 17:06:43 PDT)
- AMBER: help me for filling a nanotube with water?? Jaber Jahanbin Sardroodi (Mon Aug 04 2008 - 18:39:05 PDT)
- AMBER: NMR structure as initial structure Siddharth Rastogi (Mon Aug 04 2008 - 23:40:54 PDT)
- AMBER: addles Urszula Uciechowska (Tue Aug 05 2008 - 01:30:20 PDT)
- AMBER: Need help with force field parameters for Lipopolysaccharide (LPS) dipti lele (Tue Aug 05 2008 - 03:03:10 PDT)
- AMBER: MM_PBSA snapshot statistic calc problem Hannes Wallnoefer (Tue Aug 05 2008 - 05:45:48 PDT)
- AMBER: NAB: getseq_from_pdb() IN SUK JOUNG (Tue Aug 05 2008 - 17:00:21 PDT)
- AMBER: Problems with the charge (membrane simulation) rebeca.mmb.pcb.ub.es (Wed Aug 06 2008 - 11:20:30 PDT)
- AMBER: entropy of released water Swarup Gupta (Thu Aug 07 2008 - 05:36:32 PDT)
- AMBER: Re: entropy of released water Swarup Gupta (Thu Aug 07 2008 - 05:40:26 PDT)
- AMBER: aggregation or cluster detection fatima.chami.durham.ac.uk (Thu Aug 07 2008 - 06:41:24 PDT)
- AMBER: linear interaction energy Urszula Uciechowska (Thu Aug 07 2008 - 06:55:18 PDT)
- AMBER: NAB conjgrad returns error? Carra, Claudio (JSC-SK)[USRA] (Thu Aug 07 2008 - 08:04:38 PDT)
- AMBER: problem with minimization luzhenw1.msu.edu (Thu Aug 07 2008 - 08:13:17 PDT)
- AMBER: value of Pi in Amber Alan (Fri Aug 08 2008 - 03:36:06 PDT)
- AMBER: PBCAL in MM_PBSA Hannes Wallnoefer (Fri Aug 08 2008 - 07:19:30 PDT)
- AMBER: Is G_disp calculated in MM_PBSA now? cgji (Sat Aug 09 2008 - 05:51:55 PDT)
- AMBER: Minimization methods teresa.ierano.unina.it (Mon Aug 11 2008 - 05:11:23 PDT)
- AMBER: GPCR membrane simulation, setting surface tension Fiona McRobb (Mon Aug 11 2008 - 18:42:47 PDT)
- AMBER: questions about previous posts Naser Alijabbari (Mon Aug 11 2008 - 21:17:40 PDT)
- AMBER: Querry about simulating a glycopeptide dipti lele (Tue Aug 12 2008 - 03:23:24 PDT)
- AMBER: Using RDCs for structure refinement David Witte (Tue Aug 12 2008 - 00:52:53 PDT)
- AMBER: MM-PBSA Issue in Amber 10 Peterson, Matthew W. (Tue Aug 12 2008 - 10:44:29 PDT)
- AMBER: empty frcmod file but missing parameters moitrayee.mbu.iisc.ernet.in (Tue Aug 12 2008 - 14:20:19 PDT)
- AMBER: frcmod:attn needs revision moitrayee.mbu.iisc.ernet.in (Tue Aug 12 2008 - 15:18:02 PDT)
- AMBER: glycoprotein setup Arturas Ziemys (Tue Aug 12 2008 - 20:35:35 PDT)
- AMBER: general question Gigil Toton (Tue Aug 12 2008 - 23:49:12 PDT)
- AMBER: amber 9 on Intel Harpertown Geoff Wood (Wed Aug 13 2008 - 02:45:36 PDT)
- AMBER: problem with prep file generation aneesh cna (Wed Aug 13 2008 - 05:05:58 PDT)
- AMBER: modified parmtop file from ptraj? Hannes Wallnoefer (Wed Aug 13 2008 - 05:14:34 PDT)
- AMBER: Querry dipti lele (Wed Aug 13 2008 - 05:15:11 PDT)
- AMBER: mm-pbsa / sander.MPI ? Arturas Ziemys (Wed Aug 13 2008 - 15:26:56 PDT)
- AMBER: Compile AMBER 9 on TACC Ranger super computer jialei (Wed Aug 13 2008 - 15:26:07 PDT)
- AMBER: how to choose the appropriate ensemble for a given problem Ruchi Sachdeva (Wed Aug 13 2008 - 21:09:28 PDT)
- AMBER: MD with NMR restraints Sally Pias (Wed Aug 13 2008 - 21:25:56 PDT)
- AMBER: amber9 hangas after job submission Vijay Manickam Achari (Wed Aug 13 2008 - 23:40:03 PDT)
- AMBER: minimization stops or does not write anything rebeca.mmb.pcb.ub.es (Thu Aug 14 2008 - 02:01:17 PDT)
- AMBER: Glycoprotein once again.......... dipti lele (Thu Aug 14 2008 - 05:10:10 PDT)
- AMBER: constph shubhra srivastava (Thu Aug 14 2008 - 04:54:57 PDT)
- AMBER: interaction energies Arturas Ziemys (Thu Aug 14 2008 - 08:21:34 PDT)
- AMBER: Help compiling Nab programs for AMBER tools Ragnarok sdf (Thu Aug 14 2008 - 12:36:04 PDT)
- AMBER: generate topology file for alanine scanning (mmpbsa) luzhenw1.msu.edu (Thu Aug 14 2008 - 12:32:56 PDT)
- AMBER: Proton Parameters Shultz, Jack (Thu Aug 14 2008 - 13:34:54 PDT)
- AMBER: impropers over bonds between sidechains Grange Hermitage (Thu Aug 14 2008 - 18:12:05 PDT)
- AMBER: solvatebox TIP4PEWBOX amb2gmx gives TIP3P in top TIP4PEW in gro Grange Hermitage (Sun Aug 17 2008 - 19:28:17 PDT)
- AMBER: Negative dihedral coefficients in amber99 - Possible? Ilyas Yildirim (Sun Aug 17 2008 - 19:33:16 PDT)
- AMBER: trying ff99SP Grange Hermitage (Sun Aug 17 2008 - 23:12:33 PDT)
- AMBER: unsubscribe khuram sb (Mon Aug 18 2008 - 01:56:36 PDT)
- AMBER: RDF output file format aneesh cna (Mon Aug 18 2008 - 02:48:45 PDT)
- AMBER: Initial structure from NMR structures Siddharth Rastogi (Mon Aug 18 2008 - 23:15:44 PDT)
- AMBER: How to convert a CHARMM trajectory to AMBER format? Jeffrey (Tue Aug 19 2008 - 04:30:35 PDT)
- AMBER: Compile Error Shultz, Jack (Tue Aug 19 2008 - 08:44:25 PDT)
- AMBER: Amber compile Shultz, Jack (Tue Aug 19 2008 - 11:21:18 PDT)
- AMBER: IGB=10 in Amber10 In Hee Park (Tue Aug 19 2008 - 11:55:05 PDT)
- AMBER: Problem loading the leaprc.amoeba force field file in Amber 10. Zhao, Zhen (zhaozh) (Tue Aug 19 2008 - 13:20:00 PDT)
- AMBER: Problems with sleap and amoeba Neil J. Henson (Tue Aug 19 2008 - 16:16:17 PDT)
- Re: AMBER: Problems with sleap and amoeba Bill Ross (Tue Aug 19 2008 - 16:51:18 PDT)
- AMBER: Questions about Locally enhanced sampling (LES) and Replica exchange xiaonan zhang (Wed Aug 20 2008 - 00:25:43 PDT)
- AMBER: Trouble installing Amber 9 Sampath Koppole (Wed Aug 20 2008 - 03:28:58 PDT)
- AMBER: Silicon parameters Abdul Hameed, MohamedDiwanMo (Wed Aug 20 2008 - 09:15:56 PDT)
- AMBER: Using Na+ ions as input to leap? Pablo Englebienne (Wed Aug 20 2008 - 10:40:11 PDT)
- AMBER: NMR average structure Gigil Toton (Wed Aug 20 2008 - 10:42:08 PDT)
- Re: AMBER: Using Na+ ions as input to leap? - solved Pablo Englebienne (Wed Aug 20 2008 - 12:25:25 PDT)
- AMBER: Vlimit Exceeded and inhomogeneous system !!!!!! Piyush Wanjari (Wed Aug 20 2008 - 21:36:20 PDT)
- AMBER: new residues in AMOEBA Grange Hermitage (Thu Aug 21 2008 - 00:14:59 PDT)
- AMBER: Fwd: Welcome to amber Maicon Sartin (Thu Aug 21 2008 - 05:33:08 PDT)
- AMBER: SANDER Parallel Maicon Sartin (Thu Aug 21 2008 - 05:36:56 PDT)
- AMBER: Gohlke in-house iRED Simulated Order Parameter Script Titus, Jamie (bairdje) (Thu Aug 21 2008 - 05:53:09 PDT)
- AMBER: DFTB QMMM parameters ambiguity in AMBER10 docs M. L. Dodson (Thu Aug 21 2008 - 10:56:38 PDT)
- AMBER: Error when compiling and testing AmberTools Ben Roberts (Thu Aug 21 2008 - 14:46:43 PDT)
- AMBER: all & united atoms force field fatima.chami.durham.ac.uk (Thu Aug 21 2008 - 15:05:12 PDT)
- AMBER: Error runing Addles Shultz, Jack (Thu Aug 21 2008 - 20:25:17 PDT)
- AMBER: united atom force field Adrien Delmont (Fri Aug 22 2008 - 05:35:06 PDT)
- AMBER: vdw 6-9 potential fatima.chami.durham.ac.uk (Fri Aug 22 2008 - 13:56:57 PDT)
- AMBER: Dell 2 Quad Core System Performance Ilyas Yildirim (Fri Aug 22 2008 - 18:16:49 PDT)
- AMBER: LES trajectories Urszula Uciechowska (Mon Aug 25 2008 - 01:12:23 PDT)
- AMBER: pmemd iwrap trouble Lars Skjærven (Mon Aug 25 2008 - 03:25:09 PDT)
- AMBER: mol2, xleap, Segmentation fault Anna Karawajczyk (Mon Aug 25 2008 - 06:01:31 PDT)
- AMBER: Parameters for chloride ion in contact with a protein Francesco Pietra (Mon Aug 25 2008 - 07:25:13 PDT)
- AMBER: Problem with the prmtop file generated by sleap and leaprc.amoeba in Amber 10. Zhao, Zhen (zhaozh) (Mon Aug 25 2008 - 08:04:34 PDT)
- AMBER: tan luo radii Jacopo Sgrignani (Tue Aug 26 2008 - 02:06:39 PDT)
- AMBER: installation amber on suse11.0 selami ercan (Tue Aug 26 2008 - 03:57:12 PDT)
- AMBER: Bennett acceptance ratio with Amber10 Samuel Genheden (a03samge) (Tue Aug 26 2008 - 04:58:13 PDT)
- AMBER: latest update on residuegen Junmei Wang (Tue Aug 26 2008 - 06:55:09 PDT)
- AMBER: Querry dipti lele (Tue Aug 26 2008 - 04:50:32 PDT)
- AMBER: Source FIles of SANDER Maicon Sartin (Tue Aug 26 2008 - 12:17:39 PDT)
- Re: AMBER: Source FIles of SANDER Bill Ross (Tue Aug 26 2008 - 12:28:34 PDT)
- AMBER: net charge Gigil Toton (Tue Aug 26 2008 - 22:03:19 PDT)
- AMBER: coordinate change of pdb structure using xleap Henrik Öberg (Tue Aug 26 2008 - 23:26:42 PDT)
- AMBER: constant ph (cpinutil file) shubhra srivastava (Tue Aug 26 2008 - 23:46:36 PDT)
- AMBER: querry dipti lele (Wed Aug 27 2008 - 02:07:52 PDT)
- AMBER: MM-PBSA multiple trajectory problem Carra, Claudio (JSC-SK)[USRA] (Wed Aug 27 2008 - 07:16:38 PDT)
- AMBER: solvent interaction in active site Hakkim Boy (Wed Aug 27 2008 - 19:41:24 PDT)
- AMBER: Membrane simulations priya priya (Thu Aug 28 2008 - 01:31:57 PDT)
- AMBER: to understand how frcmod.ff99SB works Alan (Thu Aug 28 2008 - 03:29:18 PDT)
- AMBER: output file format in SANDER.MPI & PMEMD fatima.chami.durham.ac.uk (Thu Aug 28 2008 - 03:47:17 PDT)
- AMBER: Critical patch for pmemd 10 extra points code Robert Duke (Thu Aug 28 2008 - 08:20:59 PDT)
- AMBER: RE: Personal favor Ross Walker (Thu Aug 28 2008 - 09:39:59 PDT)
- AMBER: conversion from crd to netcdf returns almost identical file! Jose Borreguero (Thu Aug 28 2008 - 13:38:50 PDT)
- AMBER: Problem in calculation of resp charges using RED III moitrayee.mbu.iisc.ernet.in (Thu Aug 28 2008 - 23:56:24 PDT)
- AMBER: Solvent Accesible Surface Area (SASA) - Confused Deepangi Pandit (Fri Aug 29 2008 - 11:45:19 PDT)
- AMBER: wrapping w/ ptraj Arturas Ziemys (Fri Aug 29 2008 - 14:57:52 PDT)
- AMBER: compilation problem john smith (Sat Aug 30 2008 - 04:51:07 PDT)
- AMBER: vlimit exceeded Wang,Ying (Sat Aug 30 2008 - 08:49:03 PDT)
- AMBER: RESP charges fitting for polarizable force fields Grange Hermitage (Sat Aug 30 2008 - 21:48:37 PDT)
- AMBER: AMBER under cygwin on 64 bit Vista Charles Letner, Ph.D. (Sun Aug 31 2008 - 14:30:08 PDT)
- Last message date: Wed Sep 03 2008 - 06:07:13 PDT
- Archived on: Mon Dec 23 2024 - 05:53:38 PST
