Amber Archive Jun 2009 by messages with attachments

Re: [AMBER] MM-PBSA nmode statistics Dmitry Osolodkin (Mon Jun 01 2009 - 06:12:15 PDT)
1. 04_MMPBSA_Nmode.tar.gz (7265 bytes)
2. test.tar.gz (4326 bytes)
3. ATT00002.txt (137 bytes)
Re: [AMBER] how to choose different comformations for RESP cgji (Mon Jun 01 2009 - 22:14:02 PDT)
1. ATT00002.txt (137 bytes)
[AMBER] MMPBSA and mm_pbsa_statistics.pl error john smith (Mon Jun 01 2009 - 22:38:54 PDT)
1. snapshot_statistics_m12.out (2125 bytes)
2. ATT00002.txt (137 bytes)
[AMBER] Atom names Rose Tamil (Tue Jun 02 2009 - 03:53:50 PDT)
1. PD_PDB.pdb (3080 bytes)
2. PD_prep.prepin (2427 bytes)
3. Final.parm (24155 bytes)
4. Final.pdb (2730 bytes)
5. Final.crd (1760 bytes)
6. ATT00002.txt (137 bytes)
Re: [AMBER] Atom names Rose Tamil (Wed Jun 03 2009 - 07:53:51 PDT)
1. problem.txt (8826 bytes)
2. PDB.pdb (7389 bytes)
3. PD_prep.prepin (2427 bytes)
4. ATT00002.txt (137 bytes)
Re: [AMBER] use of random seed in multiple runs Marek Maly (Thu Jun 04 2009 - 12:16:50 PDT)
1. prod14_PPI_D_GEM91.out (36664 bytes)
2. ATT00002.txt (137 bytes)
[AMBER] atom type Taufik Al-Sarraj (Thu Jun 04 2009 - 18:03:14 PDT)
1. smcc.mol2 (5514 bytes)
2. ATT00002.txt (137 bytes)
[AMBER] Max filename length in Sander? Paul Mortenson (Mon Jun 08 2009 - 03:59:52 PDT)
1. inpcrd_test.tgz (1221598 bytes)
2. ATT00002.txt (137 bytes)
Re: [AMBER] Max filename length in Sander? David A. Case (Mon Jun 08 2009 - 05:36:32 PDT)
1. inpcrd_test.tgz (1221598 bytes)
2. ATT00002.txt (137 bytes)
[AMBER] problem with creation of prmtop and prmcrd files moitrayee.mbu.iisc.ernet.in (Mon Jun 08 2009 - 06:00:18 PDT)
1. error_file (15251 bytes)
2. prot.pdb (1109927 bytes)
3. ATT00002.txt (137 bytes)
[AMBER] Problem with modified trna[Fwd: problem with creation of prmtop and prmcrd files] moitrayee.mbu.iisc.ernet.in (Mon Jun 08 2009 - 07:28:14 PDT)
1. error_file (15251 bytes)
2. prot.pdb (1109927 bytes)
3. ATT00002.txt (137 bytes)
[AMBER] Problem with modified trna[Fwd: problem with creation of prmtop and prmcrd files]] moitrayee.mbu.iisc.ernet.in (Mon Jun 08 2009 - 07:30:21 PDT)
1. error_file (15251 bytes)
2. prot.pdb (1109927 bytes)
3. AET.in (4658 bytes)
4. ATT00002.txt (137 bytes)
[AMBER] Unknown residue: MOL number: 30 type: Terminal/last Workalemhu Berhanu (Mon Jun 08 2009 - 11:30:43 PDT)
1. solution.pdb (41240 bytes)
2. ATT00002.txt (137 bytes)
[AMBER] Strange contacts with water molecules Jordan MONNET (Mon Jun 08 2009 - 14:39:26 PDT)
1. traj.pdb.2000 (194272 bytes)
2. ATT00003.txt (330 bytes)
3. ATT00004.txt (137 bytes)
[AMBER] SOS - too high binding energy Marek Maly (Tue Jun 09 2009 - 03:49:43 PDT)
1. PPI4_malt_ssDNA.png (229114 bytes)
2. ATT00002.txt (137 bytes)
RE: [AMBER] (no subject) david.lisgarten.canterbury.ac.uk (Tue Jun 09 2009 - 06:56:32 PDT)
1. ATT00002.txt (137 bytes)
[AMBER] DNA as well as protein distorted during MD run in sander Jayalakshmi Sridhar (Tue Jun 09 2009 - 07:30:39 PDT)
1. jsridhar.vcf (203 bytes)
2. ATT00002.txt (137 bytes)
Re: [AMBER] DNA as well as protein distorted during MD run in sander Jayalakshmi Sridhar (Tue Jun 09 2009 - 08:33:51 PDT)
1. summary.PRES (13222 bytes)
2. summary.TEMP (14424 bytes)
3. summary.EKTOT (18030 bytes)
4. summary.EPTOT (18030 bytes)
5. summary.ETOT (18030 bytes)
6. polyAT_wat_backbone.rms (12000 bytes)
7. jsridhar.vcf (203 bytes)
8. ATT00002.txt (137 bytes)
Re: [AMBER] DNA as well as protein distorted during MD run in sander Jayalakshmi Sridhar (Tue Jun 09 2009 - 09:02:56 PDT)
1. jsridhar.vcf (203 bytes)
2. ATT00002.txt (137 bytes)
[AMBER] Generating LeAP file for helix containing non-standard amino acid Brothers, Michael Charles (Wed Jun 10 2009 - 11:26:32 PDT)
1. test2.pdb (22763 bytes)
2. ATT00002.txt (137 bytes)
Re: [AMBER] SOS - too high binding energy Marek Maly (Wed Jun 10 2009 - 12:47:58 PDT)
1. B_malt_ssDNA_11ns.png (437287 bytes)
2. standalone.png (26440 bytes)
3. COMPLEX.PNG (20562 bytes)
4. THREE-TRAJ-APPROACH.out (2528 bytes)
5. ONE-TRAJ-APPROACH.out (2528 bytes)
6. ATT00002.txt (137 bytes)
[AMBER] zinc coordination of benzimidazole Aust, Susanne (Thu Jun 11 2009 - 00:09:59 PDT)
1. c2k_bzim_correct.pdb (218641 bytes)
2. bzim_correct.frcmod (1290 bytes)
3. bzim_correct.mol2 (1828 bytes)
4. bzim_correct.prepin (2018 bytes)
5. ZNA.lib (1094 bytes)
6. frcmod.zna (79 bytes)
7. c2k_bzim_correct_min.pdb (269339 bytes)
8. ATT00002.txt (137 bytes)
RE: [AMBER] (no subject) david.lisgarten.canterbury.ac.uk (Thu Jun 11 2009 - 01:28:56 PDT)
1. ATT00002.txt (137 bytes)
[AMBER] PRINCIPAL QUESTION Marek Maly (Thu Jun 11 2009 - 08:41:42 PDT)
1. B_malt_ssDNA_11ns.png (437287 bytes)
2. ATT00002.txt (137 bytes)
[AMBER] Re: Residues KIRTANA S (Fri Jun 12 2009 - 18:15:20 PDT)
1. library.gz (3956 bytes)
2. t2.pdb (1599 bytes)
3. t2.pdb (1599 bytes)
4. t3.pdb (1599 bytes)
5. ATT00002.txt (137 bytes)
Re: 回复：回复： [AMBER] too high in binding energy (MM-PBSA) Ilyas Yildirim (Sat Jun 13 2009 - 11:19:09 PDT)
1. ATT00002.txt (137 bytes)
Re: [AMBER] Residues KIRTANA S (Sat Jun 13 2009 - 17:14:31 PDT)
1. lib.gz (8722 bytes)
2. ATT00002.txt (137 bytes)
RE:Re: [AMBER] partial charges from AM1-BCC and RESP differ a lot xueqin pang (Tue Jun 16 2009 - 00:57:25 PDT)
1. dppcin.pdb (3525 bytes)
2. dppcout.pdb (7150 bytes)
3. ATT00002.txt (137 bytes)
[AMBER] improper torsion problem Youn Kyeung Lee (Tue Jun 16 2009 - 19:36:14 PDT)
1. improper_mail.PNG (272485 bytes)
2. MC.frcmod (11287 bytes)
3. MC.mol2 (3497 bytes)
4. ATT00002.txt (137 bytes)
[AMBER] vlimit in TI with soft core potential Ye MEI (Wed Jun 17 2009 - 01:20:31 PDT)
1. leap.zip (30369 bytes)
2. TI.zip (96928 bytes)
3. ATT00002.txt (137 bytes)
Re: [AMBER] Strange contacts with water molecules Jordan MONNET (Wed Jun 17 2009 - 10:00:46 PDT)
1. box_wat.png (76025 bytes)
2. ATT00003.txt (1573 bytes)
3. ATT00004.txt (137 bytes)
RE: [AMBER] Generating LeAP file for helix containing non-standard amino acid Brothers, Michael Charles (Thu Jun 18 2009 - 10:38:53 PDT)
1. vIII.2.pl (164637 bytes)
2. Mol_red1.p2n (5127 bytes)
3. ATT00002.txt (137 bytes)
[AMBER] Postdoc position in biomolecular simulation Ivaylo, Ivanov (Thu Jun 18 2009 - 16:26:05 PDT)
1. positions.pdf (21058 bytes)
2. ATT00002.txt (137 bytes)
[AMBER] RED Geometry Calculation Error Brothers, Michael Charles (Fri Jun 19 2009 - 11:52:37 PDT)
1. Mol_red1.p2n (2658 bytes)
2. ATT00002.txt (137 bytes)
[AMBER] atom type no recognize - xleap version 10 but fine in v 9 Peter Gannett (Fri Jun 19 2009 - 12:40:47 PDT)
1. hem.prep (6005 bytes)
2. hem.frcmod (6566 bytes)
3. ATT00002.txt (137 bytes)
[AMBER] PMEMD compilation manoj singh (Fri Jun 19 2009 - 15:49:31 PDT)
1. config.h.intel (1309 bytes)
2. ATT00002.txt (137 bytes)
R: [AMBER] Amber10 Parallel Installation sgrignani.cerm.unifi.it (Sat Jun 20 2009 - 13:14:38 PDT)
1. ATT00002.txt (137 bytes)
[AMBER] Re: Regd: Fe4S4 case (Mon Jun 22 2009 - 11:39:57 PDT)
1. fe4s4.tar.gz (11694 bytes)
2. ATT00002.txt (137 bytes)
RE: [Subject Filtered] Re: [AMBER] Amber10 Parallel Installation 8% Hopkins, Robert (Mon Jun 22 2009 - 12:54:17 PDT)
1. ATT00002.txt (137 bytes)
Re: [AMBER] Trying to patch amber 9 Jack Shultz (Wed Jun 24 2009 - 08:18:23 PDT)
1. bugfix.all (1475863 bytes)
2. ATT00002.txt (137 bytes)
AW: [AMBER] atomtypes in gaff Aust, Susanne (Thu Jun 25 2009 - 02:24:07 PDT)
1. leap.log (556584 bytes)
2. c2k_bzim_correct_xleap.mol2 (322158 bytes)
3. ATT00002.txt (137 bytes)
[AMBER] Re: Error on equilibriation of Amber10 Masakazu SEKIJIMA (Thu Jun 25 2009 - 03:45:31 PDT)
1. FK506.pdb (10205 bytes)
2. FK506.prepin (9820 bytes)
3. FK506.frcmod (881 bytes)
4. leap.log (10965 bytes)
5. min1.csh (176 bytes)
6. FK506.top (61728 bytes)
7. FK506.crd (4610 bytes)
8. FK506_min.out (15478 bytes)
9. FK506_min.rst (4610 bytes)
10. test.csh (182 bytes)
11. test.in (183 bytes)
12. FK506_1.out (194 bytes)
13. min1.in (73 bytes)
14. ATT00002.txt (137 bytes)
AW: [AMBER] atomtypes in gaff Aust, Susanne (Thu Jun 25 2009 - 05:05:10 PDT)
1. bzim_correct.frcmod (1290 bytes)
2. bzim_correct.prepin (2018 bytes)
3. c2k_bzim_correct.pdb (218641 bytes)
4. ZNA.lib (1094 bytes)
5. frcmod.zna (79 bytes)
6. bzim_correct.mol2 (1828 bytes)
7. ATT00002.txt (137 bytes)
Re: [AMBER] Re: Error on equilibriation of Amber10 Masakazu SEKIJIMA (Thu Jun 25 2009 - 10:41:39 PDT)
1. fkbp_wat.top.gz (245559 bytes)
2. fkbp_wat_1.out (194 bytes)
3. fkbp_wat_min.rst.gz (297077 bytes)
4. md1.in (133 bytes)
5. test.csh (194 bytes)
6. ATT00002.txt (137 bytes)
Re: AW: [AMBER] atomtypes in gaff FyD (Thu Jun 25 2009 - 23:56:35 PDT)
1. ABI.jpg (40466 bytes)
2. ATT00002.txt (137 bytes)
[AMBER] error in tleap of AMBER 10 kureeckal ramesh (Fri Jun 26 2009 - 00:10:56 PDT)
1. TAZ.mol2 (3388 bytes)
2. ATT00002.txt (137 bytes)
Re: [AMBER] how to know that adequate equilibration from rmsd curve of equilibration Naser Alijabbari (Sat Jun 27 2009 - 11:19:23 PDT)
1. example_run.bmp (1378230 bytes)
2. ATT00002.txt (137 bytes)
[AMBER] Regd: parameter Fe4S4 KIRTANA S (Mon Jun 29 2009 - 09:11:49 PDT)
1. frcmod.fe4s4 (590 bytes)
2. d.off (81438 bytes)
3. ATT00002.txt (137 bytes)
Re: [AMBER] Fe-S topology Markus Kaukonen (Tue Jun 30 2009 - 00:28:51 PDT)
1. tleap.in (152 bytes)
2. fs4.pdb (572 bytes)
3. fs4_and4cym.pdb (3422 bytes)
4. fs4.dat (722 bytes)
5. fs4.in (827 bytes)
6. ATT00002.txt (137 bytes)

Last message date: Mon Jul 06 2009 - 12:23:12 PDT
Archived on: Sun Dec 22 2024 - 05:53:52 PST

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