Amber Archive Jan 2009 by messages with attachments

Re: AMBER: a question about ff03ua oguz gurbulak (Fri Jan 02 2009 - 07:30:46 PST)
1. dodecaneuamol2.mol2 (1345 bytes)
AMBER: ligand parameter Bo Baker (Mon Jan 05 2009 - 14:05:18 PST)
1. FADb1.prep (4799 bytes)
2. FADb1.prep (4799 bytes)
3. FMNa1.parm (1278 bytes)
4. FMNa1.prep (2959 bytes)
5. NAPa.parm (2863 bytes)
6. NAPa.prep (2871 bytes)
[AMBER] Re: AMBER: ligand parameter Bo Baker (Tue Jan 06 2009 - 19:59:19 PST)
1. ligand.rtf (3608 bytes)
Re: [AMBER] Re: AMBER: ligand parameter Bo Baker (Tue Jan 06 2009 - 21:05:00 PST)
1. FAD4.prep (4702 bytes)
2. FAD4a.prep (4702 bytes)
3. FAD4.pdb (4350 bytes)
4. 070109-1.rtf (4818 bytes)
Re: [AMBER] RE: AMBER: xleap problem Bala subramanian (Wed Jan 07 2009 - 02:53:24 PST)
1. ggp_b.pdb (216575 bytes)
[AMBER] PBSA: PB bomb in pb_setgrd() Larry Layne (Wed Jan 07 2009 - 07:33:57 PST)
1. pbsa_com.2.out (109479 bytes)
[AMBER] Can we use Amber? Casey,Richard (Thu Jan 08 2009 - 09:16:50 PST)
1. 4.jpg (30468 bytes)
[AMBER] Can we use AMBER? Casey,Richard (Thu Jan 08 2009 - 09:25:57 PST)
1. image001.jpg (3133 bytes)
[AMBER] ambpdb is changing atom names, a feature or bug? Markus Kaukonen (Fri Jan 09 2009 - 04:55:41 PST)
1. prmtop (17094 bytes)
2. prmcrd (811 bytes)
Re: [AMBER] Re: AMBER: ligand parameter Bo Baker (Sun Jan 11 2009 - 16:20:08 PST)
1. 090109.rtf (2885 bytes)
2. FAD4.pdb (4350 bytes)
[AMBER] antechamber cation failure Rausch, Felix (Wed Jan 14 2009 - 05:32:04 PST)
1. TCA.mol2 (2924 bytes)
2. TCA.pdb (2484 bytes)
Re: [AMBER] (no subject) Jenny Iskrenova (Fri Jan 16 2009 - 15:20:46 PST)
1. vmd.pdf (8364 bytes)
[AMBER] Atom types George Tzotzos (Mon Jan 19 2009 - 06:04:09 PST)
1. complex.pdb (81811 bytes)
RE: [AMBER] Problem with entropy calculation of bigger system using NMODE and NAB. Niel Henriksen (Tue Jan 20 2009 - 12:49:38 PST)
1. ATT2403835.txt (137 bytes)
Re: [AMBER] MM - PBSA problem musa özboyacı (Thu Jan 22 2009 - 11:52:10 PST)
1. binding_energy.mmpbsa (2986 bytes)
RE: [AMBER] MM - PBSA problem Niel Henriksen (Thu Jan 22 2009 - 16:52:09 PST)
1. ATT5417765.txt (137 bytes)
[AMBER] charge derivation for ATP molecule using antechamber prachi munjal (Fri Jan 23 2009 - 05:19:27 PST)
1. ATP_1.mol2 (4498 bytes)
[AMBER] Very weird topology problem ranqi zhu (Sat Jan 24 2009 - 13:14:24 PST)
1. 25-Trjs-protein3654.pdb (15415 bytes)
2. 25-Trjs-protein3654.pdb.1 (15280 bytes)
3. conf_amber.top (104087 bytes)
[AMBER] xleap problem oguz gurbulak (Sun Jan 25 2009 - 03:56:12 PST)
1. xleap_files.rar (260471 bytes)
[AMBER] xleap problem oguz gurbulak (Sun Jan 25 2009 - 03:49:28 PST)
1. c12.AA.mol2 (4128 bytes)
2. min.in (101 bytes)
3. dodecane.frcmod (62 bytes)
4. dodecane.prmtop (1390138 bytes)
5. dodecane.inpcrd (138708 bytes)
6. dodecane.packmol100.pdb (308392 bytes)
7. dodecane.leap.pdb (255004 bytes)
Re: [AMBER] MM - PBSA problem musa özboyacı (Mon Jan 26 2009 - 04:43:33 PST)
1. files.zip (3065 bytes)
Re: [AMBER] Antechamber Connectivity George Tzotzos (Mon Jan 26 2009 - 10:23:58 PST)
1. lig.pdb (3677 bytes)
Re: [AMBER] antechamber : missed atoms Khaled Barakat (Mon Jan 26 2009 - 11:15:33 PST)
1. NEWPDB.PDB (3965 bytes)
2. ref.pdb (9409 bytes)
[AMBER] RE:xleap problem oguz gurbulak (Mon Jan 26 2009 - 11:48:11 PST)
1. inpcrd.rar (148254 bytes)
Re: [AMBER] antechamber : missed atoms Khaled Barakat (Mon Jan 26 2009 - 12:22:14 PST)
1. ref.mol2 (6239 bytes)
Re: [AMBER] RE:xleap problem oguz gurbulak (Mon Jan 26 2009 - 13:40:22 PST)
1. xleap_files.zip (302967 bytes)
[AMBER] atom types deepti nayar (Tue Jan 27 2009 - 01:47:12 PST)
1. leap.log (294399 bytes)
Re: [AMBER] Antechamber ligand prep George Tzotzos (Tue Jan 27 2009 - 07:24:30 PST)
1. new.pdb (3675 bytes)
[AMBER] GAFF conjugated ring system dihedrals Floris Buelens (Wed Jan 28 2009 - 04:04:55 PST)
1. sybyl.mol2 (5777 bytes)
2. ante.mol2 (5753 bytes)
Re: [AMBER] large resp charges for non-natural amino acid Arturas Ziemys (Thu Jan 29 2009 - 07:10:50 PST)
1. GLAc.tar.gz (494321 bytes)
Re: [AMBER] RE:xleap problem oguz gurbulak (Thu Jan 29 2009 - 07:53:30 PST)
1. density.eps (48968 bytes)
Re: [AMBER] large resp charges for non-natural amino acid Arturas Ziemys (Thu Jan 29 2009 - 13:38:12 PST)
1. GLA.tar.gz (1327 bytes)
2. NAL.tar.gz (1642 bytes)
Re: [AMBER] Compilation and usage of NAB in parallel ? Marek Malý (Fri Jan 30 2009 - 06:59:07 PST)
1. config_scalapack.h (2970 bytes)
2. config_mpi.h (2964 bytes)
3. config_openmp.h (2991 bytes)
[AMBER] REMD fixed atoms Maxime Louet (Fri Jan 30 2009 - 09:26:08 PST)
1. rms_replica1.jpg (147378 bytes)
2. rms_replica16.jpg (164426 bytes)
Re: [AMBER] large resp charges for non-natural amino acid Arturas Ziemys (Sat Jan 31 2009 - 09:03:09 PST)
1. GLA.tar.bz2 (530426 bytes)
Re: [AMBER] large resp charges for non-natural amino acid Arturas Ziemys (Sat Jan 31 2009 - 09:03:44 PST)
1. NAP.tar.bz2 (573071 bytes)

Last message date: Sun Feb 01 2009 - 01:22:26 PST
Archived on: Fri Nov 22 2024 - 05:53:44 PST

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