Amber Archive Jul 2009: by messages with attachments

[AMBER] antechamber R. A. (Wed Jul 01 2009 - 02:17:51 PDT)
1. t80p.pdb (22586 bytes)
2. ATT00002.txt (137 bytes)
[AMBER] antechamber R. A. (Wed Jul 01 2009 - 02:19:54 PDT)
1. t80p.pdb (22586 bytes)
2. ATT00002.txt (137 bytes)
[AMBER] amber9 in fedora10 Bala subramanian (Wed Jul 01 2009 - 07:09:15 PDT)
1. erro (34688 bytes)
2. ATT00002.txt (137 bytes)
Re: [AMBER] The problem of restart file Jeffrey (Wed Jul 01 2009 - 07:07:08 PDT)
1. ATT00002.txt (137 bytes)
Re: [AMBER] amber9 in fedora10 Bala subramanian (Thu Jul 02 2009 - 00:02:54 PDT)
1. erro (36310 bytes)
2. ATT00002.txt (137 bytes)
[AMBER] MM-PBSA problem Giorgos Lamprinidis (Fri Jul 03 2009 - 06:50:36 PDT)
1. snapshot_statistics.out (2125 bytes)
2. snapshot_statistics.out.snap (67028 bytes)
3. ATT00002.txt (137 bytes)
[AMBER] Boundary Condition Problem Pepe` Falahat (Sat Jul 04 2009 - 05:10:59 PDT)
1. g_tetra.pdb (7364 bytes)
2. Tetra_lattice.jpg (325190 bytes)
3. ATT00002.txt (137 bytes)
[AMBER] Leap Questions... Cihan Aydin (Sat Jul 04 2009 - 18:41:39 PDT)
1. wt-10A-Box.pdb.bz2 (763230 bytes)
2. wt-10A-Oct.pdb.bz2 (638698 bytes)
3. ATT00002.txt (137 bytes)
[AMBER] non standard residue Neha Gandhi (Mon Jul 06 2009 - 01:07:35 PDT)
1. ACA.pdb (1281 bytes)
2. protein.pdb (108043 bytes)
3. ACA.lib.x (3261 bytes)
4. ATT00002.txt (137 bytes)
[AMBER] RE: question about TUTORIAL A1 Ross Walker (Mon Jul 06 2009 - 09:58:47 PDT)
1. 1lw6.jpg (108446 bytes)
2. ATT00002.txt (137 bytes)
[AMBER] Tleap input error, atom not found in residue template Brothers, Michael Charles (Mon Jul 06 2009 - 18:25:00 PDT)
1. AAA.pdb (19931 bytes)
2. ATT00002.txt (137 bytes)
[AMBER] rdparm bug? Paul Mortenson (Tue Jul 07 2009 - 09:29:44 PDT)
1. test.tgz (231374 bytes)
2. ATT00002.txt (137 bytes)
[AMBER] ff parameters oguz gurbulak (Wed Jul 08 2009 - 07:35:40 PDT)
1. figure.zip (5690 bytes)
2. ATT00002.txt (137 bytes)
[AMBER] bug in antechamber David Mobley (Wed Jul 08 2009 - 09:19:12 PDT)
1. out_sybyl.mol2 (1704 bytes)
2. out_sybyl_1.mol2 (1704 bytes)
3. ATT00004.txt (6 bytes)
4. vinylpyridine_am1bcc_sybyl.mol2 (1689 bytes)
5. ATT00005.txt (166 bytes)
6. ATT00006.txt (137 bytes)
Re: [AMBER] Antechamber prep question Andrew Olson (Thu Jul 09 2009 - 08:22:18 PDT)
1. atp_H_1.pdb (2165 bytes)
2. ATT00002.txt (137 bytes)
Re: [AMBER] Antechamber prep question Andrew Olson (Thu Jul 09 2009 - 10:00:19 PDT)
1. atp_H_1_1.pdb (3638 bytes)
2. ATT00002.txt (137 bytes)
[AMBER] question of mm_pbsa 廖青华 (Thu Jul 09 2009 - 18:49:40 PDT)
1. 2obd_com.all.out (35480 bytes)
2. 2obd_lig.all.out (35072 bytes)
3. 2obd_rec.all.out (35072 bytes)
4. mm_pbsa.in (8612 bytes)
5. mm_pbsa.log (54887 bytes)
6. ATT00002.txt (137 bytes)
Re: [AMBER] amber10 installation problem Lan JIN (Fri Jul 10 2009 - 00:41:34 PDT)
1. TEST_FAILURES.diff (2613 bytes)
2. ATT00002.txt (137 bytes)
Re: [AMBER] Antechamber prep question gilbert.bluemarble.net (Fri Jul 10 2009 - 06:10:32 PDT)
1. atp_h_1_1.mol2 (4672 bytes)
2. ATT00002.txt (137 bytes)
[AMBER] ligand/protein minimization Andrew Olson (Fri Jul 10 2009 - 14:00:26 PDT)
1. LIGPRT.pdb (151188 bytes)
2. ATT00002.txt (137 bytes)
Re: [AMBER] Alpha-L-Methys Fucose structure problem bond 0fA.d.C1 OME.d.O "S" Shubhra Gupta (Wed Jul 15 2009 - 05:38:34 PDT)
1. a.pdb (831 bytes)
2. ATT00002.txt (137 bytes)
[AMBER] question of ibelly used in pmemd xiaoqin huang (Wed Jul 15 2009 - 10:34:20 PDT)
1. tus1.in (842 bytes)
2. tus1.out (30732 bytes)
3. 393297.out (2682 bytes)
4. logfile (307 bytes)
5. ATT00002.txt (137 bytes)
[AMBER] position v time graph Shozeb Haider (Wed Jul 15 2009 - 11:21:35 PDT)
1. smime.p7s (3043 bytes)
2. ATT00002.txt (137 bytes)
[AMBER] ptraj-radial distribution function Nancy (Wed Jul 15 2009 - 23:34:12 PDT)
1. rdf.doc (74752 bytes)
2. ATT00002.txt (137 bytes)
Re: [AMBER] ptraj-radial distribution function Christof Jaeger (Thu Jul 16 2009 - 01:22:02 PDT)
1. christof_jaeger.vcf (275 bytes)
2. ATT00002.txt (137 bytes)
RE: [AMBER] Umbrella Sampling Seetin, Matthew (Thu Jul 16 2009 - 13:13:59 PDT)
1. ATT00002.txt (137 bytes)
RE: [AMBER] question of ibelly used in pmemd xiaoqin huang (Fri Jul 17 2009 - 07:54:55 PDT)
1. tus1.in (860 bytes)
2. tus1.out (30871 bytes)
3. yr.err.rtf (1322 bytes)
4. ATT00002.txt (137 bytes)
[AMBER] charge not zero on group: RESP Jio M (Fri Jul 17 2009 - 22:14:58 PDT)
1. eda_v_esp.ac (1913 bytes)
2. eda_v.in (83 bytes)
3. ATT00002.txt (137 bytes)
[AMBER] RE: charge not zero on group:''''.respin1 attached Jio M (Sat Jul 18 2009 - 07:40:18 PDT)
1. eda_v_esp.ac (1913 bytes)
2. eda_v.in (83 bytes)
3. eda_v.respin1 (406 bytes)
4. ATT00002.txt (137 bytes)
[AMBER] RE: DCCM Duggan, Brendan M. (Mon Jul 20 2009 - 07:29:46 PDT)
1. ATT00002.txt (137 bytes)
RE: [AMBER] question of ibelly used in pmemd xiaoqin huang (Mon Jul 20 2009 - 08:20:32 PDT)
1. pmemd (30987 bytes)
2. ATT00002.txt (137 bytes)
Re: [AMBER] Compiling Amber 10 (serial) on Mac OS X 10.5.7 w/ gcc, Intel Fortan 11.0 and MKL 10.0 vitor.felix (Tue Jul 21 2009 - 20:15:06 PDT)
1. ATT00002.txt (137 bytes)
[AMBER] saquinavir parameterization with antechamber Oliver Kuhn (Wed Jul 22 2009 - 08:42:49 PDT)
1. lig.pdb (3967 bytes)
2. ATT00002.txt (137 bytes)
Re: [AMBER] Regarding Running QM/MM NEB with PM3-PDDG using Amber10 Keith Van Nostrand (Wed Jul 22 2009 - 08:58:08 PDT)
1. NEB.tar (327680 bytes)
2. ATT00002.txt (137 bytes)
RE: [AMBER] Equilibration step Olotu Odunayo (Wed Jul 22 2009 - 09:46:12 PDT)
1. frcmod.NAD_ (1783 bytes)
2. NAD__walker.lib (9631 bytes)
3. Q556.frcmod (605 bytes)
4. Q556.prepin (3729 bytes)
5. ATT00002.txt (137 bytes)
[AMBER] MM-PBSA cannot finish without error message. Catein Catherine (Thu Jul 23 2009 - 02:57:00 PDT)
1. mm_pbsa_snapshot.in (4963 bytes)
2. mm_pbsa_snapshot.log (10391 bytes)
3. mm_pbsa_binding_nonm.log (5568 bytes)
4. mm_pbsa_binding_nonm.in (7337 bytes)
5. ATT00002.txt (137 bytes)
RE: [Subject Filtered] Re: [AMBER] PMEMD in a Cygwin Environment 8% Hopkins, Robert (Thu Jul 23 2009 - 13:37:12 PDT)
1. ATT00002.txt (137 bytes)
[AMBER] thymidine monophosphate parametrization Yvonne.Westermaier.unige.ch (Fri Jul 24 2009 - 08:18:18 PDT)
1. TMP.prepin (3186 bytes)
2. TMP.frcmod (739 bytes)
3. ATT00002.txt (137 bytes)
Re: [AMBER] loading a mol2 file in xleap vallespardojl.chem.leidenuniv.nl (Mon Jul 27 2009 - 05:40:13 PDT)
1. alexa.mol2 (26838 bytes)
2. ATT00002.txt (137 bytes)
RE: [AMBER] cpin error Rukman Hertadi (Mon Jul 27 2009 - 22:22:18 PDT)
1. cpin (28871 bytes)
2. ATT00002.txt (137 bytes)
[AMBER] MM/PBSA, MM/GBSA and NMODE Analysis Matthias Negri (Wed Jul 29 2009 - 03:55:46 PDT)
1. ALL_md55_lig.all.out (76352 bytes)
2. ALL_md55_lig.crd.20 (1643 bytes)
3. ALL_md55_com.crd.20 (167625 bytes)
4. com.top (1783698 bytes)
5. lig.top (28274 bytes)
6. m_negri.vcf (316 bytes)
7. ATT00002.txt (137 bytes)
[AMBER] Non-Standard Amino Acid Residue LEAP ERROR Brothers, Michael Charles (Thu Jul 30 2009 - 15:28:43 PDT)
1. GMBS.off (6525 bytes)
2. GMBSX.off (7930 bytes)
3. 33GMBS.pdb (23540 bytes)
4. A.pdb (19505 bytes)
5. ATT00002.txt (137 bytes)
[AMBER] problem from xleap Qinghua Liao (Fri Jul 31 2009 - 07:38:18 PDT)
1. pic.PNG (19989 bytes)
2. rec.pdb (219593 bytes)
3. ATT00002.txt (137 bytes)
RE: [AMBER] Non-Standard Amino Acid Residue LEAP ERROR Brothers, Michael Charles (Fri Jul 31 2009 - 10:36:10 PDT)
1. leaprc.ff09 (5534 bytes)
2. ATT00002.txt (137 bytes)

Amber Archive Jul 2009 by messages with attachments