Amber Archive Jan 2009 by thread
- AMBER: energy jumps during molecule minimization Paul Ledbetter (Thu Jan 01 2009 - 19:33:30 PST)
- Re: AMBER: SMD-related questions Gustavo Seabra (Fri Jan 02 2009 - 05:21:53 PST)
- Re: AMBER: RMS plot Carlos Simmerling (Fri Jan 02 2009 - 06:08:44 PST)
- Re: AMBER: a question about ff03ua oguz gurbulak (Fri Jan 02 2009 - 07:30:46 PST)
- AMBER: apparent error in closest function in ptraj 10 Roman Osman (Fri Jan 02 2009 - 07:54:48 PST)
- AMBER: Dielectric constant musa özboyacı (Sat Jan 03 2009 - 10:54:06 PST)
- AMBER: IMPORTANT INFORMATION: Notice regarding transition of AMBER mailing list to new address. Ross Walker (Sat Jan 03 2009 - 14:12:19 PST)
- AMBER: CHCl3 solvent box WJ Ding (Sun Jan 04 2009 - 14:24:48 PST)
- AMBER: reg sander crashing on more than 32 cores over IB Amit Bajaj (Sun Jan 04 2009 - 22:33:15 PST)
- AMBER: bug of the mm_pbsa module in ambertools 1.2 Ye Mei (Mon Jan 05 2009 - 07:28:02 PST)
- AMBER: ligand parameter Bo Baker (Mon Jan 05 2009 - 14:05:18 PST)
- AMBER: error in amber 10 archana sonawani (Mon Jan 05 2009 - 23:19:03 PST)
- AMBER: questions about equilibram wei zhang (Tue Jan 06 2009 - 03:18:47 PST)
- AMBER: Re: nmode error: bad nonbon (amber 10) Jeremy Harris (Tue Jan 06 2009 - 05:37:21 PST)
- AMBER: install amber10 wl2290.columbia.edu (Tue Jan 06 2009 - 09:23:01 PST)
- AMBER: problem with ptraj image command in Amber 10? Ryan Pavlovicz (Tue Jan 06 2009 - 09:28:27 PST)
- AMBER: xleap problem Bala subramanian (Tue Jan 06 2009 - 10:57:53 PST)
- Re: AMBER: install amber 10 on linux with openSUSE 10.2 (x86-64) Scott Brozell (Tue Jan 06 2009 - 11:23:29 PST)
- AMBER: IMPORTANT Information regarding AMBER Mailing List - please read. Ross Walker (Tue Jan 06 2009 - 12:40:00 PST)
- AMBER: mail list Mark M Huntress (Tue Jan 06 2009 - 15:06:57 PST)
- [AMBER] amber.ambermd.org open for business Ross Walker (Tue Jan 06 2009 - 15:34:31 PST)
- [AMBER] TEST Message - please ignore. Ross Walker (Tue Jan 06 2009 - 17:00:39 PST)
- [AMBER] AMBER: Problems in solvation with xleap vallespardojl.chem.leidenuniv.nl (Wed Jan 07 2009 - 05:39:56 PST)
- [AMBER] MD Beale, John (Wed Jan 07 2009 - 06:40:07 PST)
- [AMBER] four prepin/frcmod files be read simultaneously by leap Yi Mao (Wed Jan 07 2009 - 06:46:05 PST)
- [AMBER] PBSA: PB bomb in pb_setgrd() Larry Layne (Wed Jan 07 2009 - 07:33:57 PST)
- [AMBER] RE: RE: amber force filed for RNA Ross Walker (Wed Jan 07 2009 - 08:49:41 PST)
- [AMBER] RE: same result Ross Walker (Wed Jan 07 2009 - 08:59:39 PST)
- [AMBER] Amber Parameters for Iron Heme covalently boud to carbon monoxide Osmar Norberto de Souza (Wed Jan 07 2009 - 10:23:06 PST)
- [AMBER] PHOSPHOTHREONINE Khaled Barakat (Wed Jan 07 2009 - 11:11:43 PST)
- [AMBER] Using GAFF with a covalently bound ligand or label Sale, Kenneth L (Wed Jan 07 2009 - 17:30:10 PST)
- [AMBER] Non-planarity of amide atoms after optimization Sanghwa Han (Wed Jan 07 2009 - 19:17:18 PST)
- [AMBER] how many processors for parallel test michael (Thu Jan 08 2009 - 03:01:41 PST)
- [AMBER] Can we use Amber? Casey,Richard (Thu Jan 08 2009 - 09:16:50 PST)
- [AMBER] Can we use AMBER? Casey,Richard (Thu Jan 08 2009 - 09:25:57 PST)
- [AMBER] mairun wl2290.columbia.edu (Thu Jan 08 2009 - 09:30:05 PST)
- [AMBER] lone pairs on CYX and MET Beale, John (Thu Jan 08 2009 - 10:08:42 PST)
- [AMBER] Need help with point to plane distance calculation in nab M. L. Dodson (Thu Jan 08 2009 - 10:39:16 PST)
- RE: [AMBER] mpirun Ross Walker (Thu Jan 08 2009 - 15:28:12 PST)
- [AMBER] force-field for cyclic oligosaccharide using leap Madhurima Jana (Thu Jan 08 2009 - 20:50:18 PST)
- [AMBER] NAB entropy calcualtion chaitanya koppisetty (Fri Jan 09 2009 - 01:01:13 PST)
- [AMBER] ambpdb is changing atom names, a feature or bug? Markus Kaukonen (Fri Jan 09 2009 - 04:55:41 PST)
- [AMBER] problem building AmberTools/sleap on AIX Shan-ho Tsai (Fri Jan 09 2009 - 08:27:56 PST)
- [AMBER] "bad atom type" Akansha Saxena (Fri Jan 09 2009 - 09:15:11 PST)
- Re: [AMBER] ambpdb is changing atom names, a feature or bug? Bill Ross (Fri Jan 09 2009 - 09:53:23 PST)
- [AMBER] number-of-EPS-exceeds-MAXESP Karol Kaszuba (Fri Jan 09 2009 - 13:07:13 PST)
- [AMBER] implicit and explicit simulation: salt effect Catein Catherine (Fri Jan 09 2009 - 19:03:35 PST)
- [AMBER] mm-GBSA from implicit Catein Catherine (Fri Jan 09 2009 - 19:13:28 PST)
- [AMBER] Off topic. Hardware problem Francesco Pietra (Sat Jan 10 2009 - 00:26:55 PST)
- [AMBER] Can't reproduce RESP charges Sanghwa Han (Sun Jan 11 2009 - 21:57:15 PST)
- [AMBER] Amber 9 installation problem on Ubuntu drugdesign (Sun Jan 11 2009 - 22:26:34 PST)
- [AMBER] Release of the R.E.D.-III.1 tools FyD (Mon Jan 12 2009 - 03:59:14 PST)
- [AMBER] Parallelepiped periodic box Ian Streeter (Mon Jan 12 2009 - 07:57:55 PST)
- [AMBER] Writing out trajectory in NAB xxxzzzyyy xxxzzzyyy (Mon Jan 12 2009 - 08:43:33 PST)
- [AMBER] crystal waters Carmen Domene (Mon Jan 12 2009 - 12:04:24 PST)
- [AMBER] multisander error Justine Condo (Mon Jan 12 2009 - 14:03:37 PST)
- [AMBER] error in sander (Amber10) archana sonawani (Tue Jan 13 2009 - 00:21:09 PST)
- [AMBER] errorin sander---Amber10 archana sonawani (Tue Jan 13 2009 - 01:27:43 PST)
- [AMBER] amber9 in fedora10 Bala subramanian (Tue Jan 13 2009 - 09:51:49 PST)
- [AMBER] principal component vector onto C-alpha Carra, Claudio (JSC-SK)[USRA] (Tue Jan 13 2009 - 12:52:31 PST)
- [AMBER] Divcon or Mopac Cen Gao (Tue Jan 13 2009 - 15:54:33 PST)
- [AMBER] ptraj, CHARMM PSF and CMAP Hannes Loeffler (Wed Jan 14 2009 - 01:45:07 PST)
- [AMBER] charges in topology file vallespardojl.chem.leidenuniv.nl (Wed Jan 14 2009 - 02:33:35 PST)
- [AMBER] reaction coordinates Rausch, Felix (Wed Jan 14 2009 - 03:54:57 PST)
- [AMBER] antechamber cation failure Rausch, Felix (Wed Jan 14 2009 - 05:32:04 PST)
- [AMBER] NPT md with PME method for a water box Jeffrey (Wed Jan 14 2009 - 06:41:24 PST)
- [AMBER] molecular mechanic minimisation with amber momo momo (Wed Jan 14 2009 - 06:58:47 PST)
- [AMBER] Dipole command in ptraj musa özboyacı (Wed Jan 14 2009 - 07:41:07 PST)
- [AMBER] pmemd | Compilation problem with ifort and mvapich environment fohm fohm (Wed Jan 14 2009 - 09:23:50 PST)
- [AMBER] bad energy??!! momo momo (Wed Jan 14 2009 - 11:19:20 PST)
- [AMBER] Postdoc Position Available at SDSC/UCSD Ross Walker (Wed Jan 14 2009 - 12:35:52 PST)
- [AMBER] Dipole command in ptraj musa özboyacı (Wed Jan 14 2009 - 15:15:26 PST)
- [AMBER] xmgrace and plotting time evolution of a defined variable Naser Alijabbari (Wed Jan 14 2009 - 16:20:31 PST)
- [AMBER] Error in xleap archana sonawani (Wed Jan 14 2009 - 23:39:16 PST)
- [AMBER] Using a restart file Simone Swift (Thu Jan 15 2009 - 08:40:38 PST)
- [AMBER] Ligand Diffusion Studies? Jason A. Ford-Green (Thu Jan 15 2009 - 09:42:03 PST)
- [AMBER] restraint of REMD z g (Thu Jan 15 2009 - 18:51:46 PST)
- [AMBER] sander not working archana sonawani (Thu Jan 15 2009 - 21:52:48 PST)
- [AMBER] nab conjgrad min problem Jeremy Harris (Fri Jan 16 2009 - 07:11:12 PST)
- [AMBER] RE: Tutorial 5 Ross Walker (Fri Jan 16 2009 - 09:10:51 PST)
- [AMBER] (no subject) Lake, Thomas (Fri Jan 16 2009 - 09:38:09 PST)
- [AMBER] Heat and Equilibrate Hybrid GB solvent? Jason A. Ford-Green (Fri Jan 16 2009 - 13:14:41 PST)
- [AMBER] Use of Amber in distributed calculations drugdesign (Fri Jan 16 2009 - 23:33:55 PST)
- [AMBER] To stop the AMBER's list Furia Gargano (Sat Jan 17 2009 - 09:59:48 PST)
- [AMBER] to remove AMBER list Furia Gargano (Sat Jan 17 2009 - 10:02:26 PST)
- [AMBER] AMBER efficiency: Intel vs. AMD Swarup Gupta (Sun Jan 18 2009 - 17:43:32 PST)
- [AMBER] how to set up "Two molecules tied with an Elastic band of 20A in implicit solvent" Jagadeesh, M.N., Ph.D. (Mon Jan 19 2009 - 01:03:39 PST)
- [AMBER] RESP charges for Fe in heme Carina Backtorp (Mon Jan 19 2009 - 05:48:11 PST)
- [AMBER] Atom types George Tzotzos (Mon Jan 19 2009 - 06:04:09 PST)
- [AMBER] errors on REMD z g (Mon Jan 19 2009 - 18:41:35 PST)
- [AMBER] analysis Adrien Delmont (Tue Jan 20 2009 - 09:03:16 PST)
- [AMBER] Problem with entropy calculation of bigger system using NMODE and NAB. Marek Malý (Tue Jan 20 2009 - 10:24:55 PST)
- [AMBER] solvent mixture iccy liu (Tue Jan 20 2009 - 14:08:34 PST)
- [AMBER] How to calculate cavity volume from MD structures? ben rodriguez (Tue Jan 20 2009 - 14:21:43 PST)
- [AMBER] prot-DNA simulation deepti nayar (Wed Jan 21 2009 - 03:16:09 PST)
- [AMBER] AMBER External keyword Mahmoud A. A. Ibrahim (Wed Jan 21 2009 - 07:59:33 PST)
- [AMBER] how to use those water models off the list in amber? GZ Zhang (Wed Jan 21 2009 - 13:39:50 PST)
- [AMBER] reg . parallel run balaji nagarajan (Wed Jan 21 2009 - 21:34:03 PST)
- [AMBER] (no subject) Lake, Thomas (Thu Jan 22 2009 - 05:43:59 PST)
- [AMBER] MM - PBSA problem musa özboyacı (Thu Jan 22 2009 - 09:06:54 PST)
- [AMBER] non-natural amino acids Arturas Ziemys (Thu Jan 22 2009 - 09:32:11 PST)
- [AMBER] reg.parallel run error balaji nagarajan (Thu Jan 22 2009 - 10:41:25 PST)
- [AMBER] REM_hybrid test fails on AIX Shan-ho Tsai (Thu Jan 22 2009 - 12:28:04 PST)
- [AMBER] reg.error in parallel run balaji nagarajan (Fri Jan 23 2009 - 02:05:21 PST)
- [AMBER] charge derivation for ATP molecule using antechamber prachi munjal (Fri Jan 23 2009 - 05:19:27 PST)
- [AMBER] RE: errors on remd Ross Walker (Fri Jan 23 2009 - 08:38:06 PST)
- Re: [AMBER] "Could not find bond parameter" George Tzotzos (Fri Jan 23 2009 - 10:16:34 PST)
- [AMBER] reg.parallel.run error balaji nagarajan (Fri Jan 23 2009 - 17:59:21 PST)
- [AMBER] error on open distatance restraint gmail (Fri Jan 23 2009 - 18:58:27 PST)
- [AMBER] reg.parallel.run.error balaji nagarajan (Sat Jan 24 2009 - 07:09:49 PST)
- [AMBER] Very weird topology problem ranqi zhu (Sat Jan 24 2009 - 13:14:24 PST)
- [AMBER] AmberTools and ptraj clustering on Mac OS X David Watson (Sat Jan 24 2009 - 13:41:04 PST)
- [AMBER] xleap problem oguz gurbulak (Sun Jan 25 2009 - 03:56:12 PST)
- [AMBER] RE:xleap problem oguz gurbulak (Sun Jan 25 2009 - 08:08:26 PST)
- [AMBER] xleap problem oguz gurbulak (Sun Jan 25 2009 - 08:27:48 PST)
- [AMBER] xleap problem oguz gurbulak (Sun Jan 25 2009 - 08:34:39 PST)
- [AMBER] xleap problem oguz gurbulak (Sun Jan 25 2009 - 03:49:28 PST)
- [AMBER] deduce correlation from covariance matrix Yi Mao (Sun Jan 25 2009 - 13:01:05 PST)
- [AMBER] using binary trajectories from NAMD in PTRAJ karthik s (Sun Jan 25 2009 - 23:11:29 PST)
- [AMBER] thioglycoside Alexander Schierholt (Mon Jan 26 2009 - 06:46:28 PST)
- Re: [AMBER] Antechamber Connectivity George Tzotzos (Mon Jan 26 2009 - 10:23:58 PST)
- [AMBER] antechamber : missed atoms Khaled Barakat (Mon Jan 26 2009 - 10:54:07 PST)
- [AMBER] RE:xleap problem oguz gurbulak (Mon Jan 26 2009 - 11:48:11 PST)
- [AMBER] atom types deepti nayar (Tue Jan 27 2009 - 01:47:12 PST)
- [AMBER] reg: targeted molecular dynamics balaji nagarajan (Tue Jan 27 2009 - 05:02:03 PST)
- [AMBER] Rosetta Academic Training Workshop Nir London (Tue Jan 27 2009 - 05:07:24 PST)
- [AMBER] reg.Targeted molecular dynamics balaji nagarajan (Tue Jan 27 2009 - 05:56:54 PST)
- [AMBER] reg.Targeted molecular dynamics balaji nagarajan (Tue Jan 27 2009 - 05:57:01 PST)
- Re: [AMBER] Antechamber ligand prep George Tzotzos (Tue Jan 27 2009 - 06:48:11 PST)
- [AMBER] NOTICE: File size limits on AMBER reflector Ross Walker (Tue Jan 27 2009 - 08:35:50 PST)
- [AMBER] distance restraint and SHAKE Michael J Yonkunas (Tue Jan 27 2009 - 09:39:56 PST)
- Re: [AMBER] Building atom and angle parameters George Tzotzos (Tue Jan 27 2009 - 10:24:52 PST)
- [AMBER] topology file for GLY with amino and carboxyl group? Jose Borreguero (Tue Jan 27 2009 - 10:57:45 PST)
- [AMBER] large resp charges for non-natural amino acid Arturas Ziemys (Tue Jan 27 2009 - 14:40:49 PST)
- [AMBER] PhD position in Computational Structural Biology at Cambridge, UK Swanand Gore (Wed Jan 28 2009 - 02:31:16 PST)
- [AMBER] GAFF conjugated ring system dihedrals Floris Buelens (Wed Jan 28 2009 - 04:04:55 PST)
- [AMBER] Watercap... some querries Waqas Nasir (Wed Jan 28 2009 - 06:54:00 PST)
- [AMBER] generating top file using antechmaber sarvin moghaddam (Wed Jan 28 2009 - 11:49:20 PST)
- [AMBER] Compilation and usage of NAB in parallel ? Marek Malý (Wed Jan 28 2009 - 14:25:24 PST)
- [AMBER] atomic charge m m (Thu Jan 29 2009 - 00:08:47 PST)
- [AMBER] Problem in pb simulation, PB_Bomb Waqas Nasir (Thu Jan 29 2009 - 01:08:22 PST)
- [AMBER] Dr. Ramesh here kureeckal ramesh (Thu Jan 29 2009 - 02:41:10 PST)
- [AMBER] Atome Type Mahmoud A. A. Ibrahim (Thu Jan 29 2009 - 02:59:42 PST)
- [AMBER] Installation error - Amber10 Ananda Rama Krishnan Selvaraj (Thu Jan 29 2009 - 03:47:44 PST)
- [AMBER] Problem in watercap simulation, PB_Bomb Waqas Nasir (Thu Jan 29 2009 - 06:21:20 PST)
- [AMBER] Alpha helix plot Beale, John (Thu Jan 29 2009 - 12:10:11 PST)
- [AMBER] failure to run antechamber with amber 10 Francesco Pietra (Thu Jan 29 2009 - 14:29:18 PST)
- [AMBER] AmberTools 1.2 James W. Caldwell (Thu Jan 29 2009 - 16:04:36 PST)
- [AMBER] adding MG2 problem balaji nagarajan (Fri Jan 30 2009 - 01:45:58 PST)
- [AMBER] Xleap - solvatebox - counterions Arnaud (Fri Jan 30 2009 - 02:44:58 PST)
- [AMBER] help momo momo (Fri Jan 30 2009 - 04:35:22 PST)
- [AMBER] Amber top file to Charmm top file sarvin moghaddam (Fri Jan 30 2009 - 06:48:44 PST)
- [AMBER] REMD fixed atoms Maxime Louet (Fri Jan 30 2009 - 09:26:08 PST)
- Re: [AMBER] Xleap - solvatebox - counterions Bill Ross (Fri Jan 30 2009 - 10:40:07 PST)
- [AMBER] thermo, entropy by quasiharmonic method Carra, Claudio (JSC-SK)[USRA] (Fri Jan 30 2009 - 13:35:37 PST)
- [AMBER] RE: Tutorial 5 Ross Walker (Fri Jan 30 2009 - 17:32:03 PST)
- [AMBER] Test run on Solaris 10 X 86 Manikandan Chandrasekaran (Sat Jan 31 2009 - 10:39:14 PST)
- [AMBER] Question on heating for homology based model. drugdesign (Sat Jan 31 2009 - 10:43:06 PST)
- Last message date: Sun Feb 01 2009 - 01:22:26 PST
- Archived on: Fri Apr 19 2024 - 05:53:31 PDT
