Amber Archive Nov 2011: by messages with attachments

Re: [AMBER] parameters for anchor-modified glycopeptides Urszula Uciechowska (Tue Nov 01 2011 - 01:49:48 PDT)
1. pep1.pdb (13978 bytes)
2. pep2.pdb (14198 bytes)
Re: [AMBER] AmberTools 1.5 build fails due to undefined symbols in libnetcdf.a Jan-Philip Gehrcke (Wed Nov 02 2011 - 03:48:29 PDT)
1. failed_netcdf_config.log (10525 bytes)
2. failed_netcdf_makelog (257155 bytes)
Re: [AMBER] 1JFF Antechamber, LEaP problems Matthew D Antalek (Wed Nov 02 2011 - 14:54:35 PDT)
1. short_taxolderivnoH.pdb (9474 bytes)
Re: [AMBER] Softcore TI. now with data! steinbrt.rci.rutgers.edu (Thu Nov 03 2011 - 03:39:47 PDT)
1. shake.png (205979 bytes)
2. shake2.png (89857 bytes)
[AMBER] problems in reading molecule in tleap/xleap Urszula Uciechowska (Thu Nov 03 2011 - 05:28:20 PDT)
1. pep4.mol2 (15580 bytes)
Re: [AMBER] AmberTools 1.5 build fails due to undefined symbols in libnetcdf.a Daniel Roe (Thu Nov 03 2011 - 07:43:55 PDT)
1. MyProcedure.txt (2362 bytes)
2. compile.log.gz (102035 bytes)
Re: [AMBER] sander error Charles Johnson (Thu Nov 03 2011 - 10:20:07 PDT)
1. anneal.in (2212 bytes)
Re: [AMBER] sander error Charles Johnson (Thu Nov 03 2011 - 11:11:51 PDT)
1. RST (77342 bytes)
Re: [AMBER] Issue with running sander with SHAKE Breuer, Marian (Sat Nov 05 2011 - 15:52:12 PDT)
1. CYX_only.pdb (3362 bytes)
Re: [AMBER] 1JFF Antechamber, LEaP problems Matthew D Antalek (Sun Nov 06 2011 - 18:47:45 PST)
1. sqm.out (24606 bytes)
[AMBER] Installation of amber11 on the latest Ubuntu 64bit Qinghua Liao (Sun Nov 06 2011 - 23:43:00 PST)
1. config.h (4441 bytes)
[AMBER] Installation of amber11 on the latest Ubuntu 64bit Qinghua Liao (Mon Nov 07 2011 - 05:19:46 PST)
1. config.h (4441 bytes)
Re: [AMBER] Installation of amber11 on the latest Ubuntu 64bit Qinghua Liao (Mon Nov 07 2011 - 06:33:42 PST)
1. netcdf_config.log (10511 bytes)
[AMBER] Protein structure heating into a mess Xiaozhou Li (Mon Nov 07 2011 - 09:18:13 PST)
1. md_result.png (407287 bytes)
[AMBER] problem in solvation Senthil Natesan (Tue Nov 08 2011 - 09:24:50 PST)
1. solvated_complex.png (685609 bytes)
[AMBER] help with antechamber jun kit (Wed Nov 09 2011 - 10:45:01 PST)
1. c.pdb (81882 bytes)
Re: [AMBER] problem in solvation Senthil Natesan (Wed Nov 09 2011 - 11:11:50 PST)
1. amber_error_report.txt (61308 bytes)
2. pdb1h9z.pdb (774627 bytes)
Re: [AMBER] problem in solvation Senthil Natesan (Wed Nov 09 2011 - 14:20:30 PST)
1. reimage.png (739878 bytes)
[AMBER] problem of generating prmtop and inpcrd files of a small molecule attached with several amino acids Qinghua Liao (Thu Nov 10 2011 - 05:20:43 PST)
1. 1OL.frcmod (441 bytes)
2. leap.log (27578 bytes)
3. lig.mol2 (11998 bytes)
4. 1OLm.mol2 (4510 bytes)
5. 1OL.off (4942 bytes)
Re: [AMBER] Xleap pdb editing James Starlight (Thu Nov 10 2011 - 10:31:42 PST)
1. after.pdb (37226 bytes)
2. before.pdb (42739 bytes)
Re: [AMBER] leap cannot read MOL2 file that it has written before: small fix suggested M. L. Dodson (Thu Nov 10 2011 - 13:09:35 PST)
1. test.mol2 (2664 bytes)
2. test.log (1428 bytes)
3. test.in (99 bytes)
Re: [AMBER] problem of generating prmtop and inpcrd files of a small molecule attached with several amino acids Qinghua Liao (Fri Nov 11 2011 - 03:06:00 PST)
1. M.mol2 (4247 bytes)
2. Mm.frcmod (441 bytes)
3. Mm.mol2 (4510 bytes)
4. Mm-edit.frcmod (4020 bytes)
5. Mm-edit.mol2 (4510 bytes)
[AMBER] Problems of generating prmtop and inpcrd files for ligand-receptor with two Mg2+ ions --please help Crystal.CHIA-YU Ku (Fri Nov 11 2011 - 13:48:18 PST)
1. TPS_500.gif (2622 bytes)
Re: [AMBER] Problems of generating prmtop and inpcrd files for ligand-receptor with two Mg2+ ions --please help David A Case (Tue Nov 15 2011 - 05:26:06 PST)
1. tps.pdb (3853 bytes)
Re: [AMBER] ambertools 1.5 compiling ERROR: Return type mismatch of function 'cgalf' at (1) (REAL(8)/REAL(4)) Jose Borreguero (Tue Nov 15 2011 - 08:15:14 PST)
1. 32F.gif (104 bytes)
Re: [AMBER] Problems of generating prmtop and inpcrd files for ligand-receptor with two Mg2+ ions --please help Irene Newhouse (Tue Nov 15 2011 - 11:26:15 PST)
1. lig.pdb (3499 bytes)
2. leapit.rc (404 bytes)
Re: [AMBER] Problems of generating prmtop and inpcrd files for ligand-receptor with two Mg2+ ions --please help Crystal.CHIA-YU Ku (Tue Nov 15 2011 - 14:24:00 PST)
1. pdb2hom.ent (179172 bytes)
Re: [AMBER] Problems of generating prmtop and inpcrd files for ligand-receptor with two Mg2+ ions --please help Crystal.CHIA-YU Ku (Tue Nov 15 2011 - 15:42:58 PST)
1. leap.log (22661 bytes)
2. 2HOM_1_addH.pdb (304677 bytes)
[AMBER] problem in leap Qinghua Liao (Wed Nov 16 2011 - 01:16:29 PST)
1. rec1.pdb (235321 bytes)
2. rec.pdb (480711 bytes)
[AMBER] pulling the ligand in different directions Sai Kumar Ramadugu (Wed Nov 16 2011 - 10:09:34 PST)
1. pulling.png (8134 bytes)
[AMBER] question to R.E.D server Urszula Uciechowska (Thu Nov 17 2011 - 05:20:26 PST)
1. out.p2n (3142 bytes)
Re: [AMBER] Problems of generating prmtop and inpcrd files for ligand-receptor with two Mg2+ ions --please help David A Case (Thu Nov 17 2011 - 08:33:26 PST)
1. tps_am1bcc.mol2 (3961 bytes)
[AMBER] compiling pmemd in amber9 Vijay Manickam Achari (Thu Nov 17 2011 - 17:08:00 PST)
1. pmemd_make_install.log (58417 bytes)
[AMBER] bonds problem in leap Qinghua Liao (Fri Nov 18 2011 - 05:32:16 PST)
1. lig.inpcrd (4574 bytes)
2. lig.prmtop (62420 bytes)
3. lig_leap.mol2 (12174 bytes)
4. lig_leap.pdb (10215 bytes)
[AMBER] problems with MCBP parametrization Andrew Voronkov (Fri Nov 18 2011 - 06:57:39 PST)
1. ZN2.prep (3080 bytes)
2. ZN2.frcmod (57064 bytes)
3. 3mhj2.pdb (136788 bytes)
[AMBER] frcmod file for metal-amino acid complex Soma Ghosh (Tue Nov 22 2011 - 03:42:12 PST)
1. apo1_H.mol2 (349404 bytes)
[AMBER] compilation of Amber Tools 1.5 with GCC 4.6.2 with "-nopython" Vlad Cojocaru (Tue Nov 22 2011 - 12:55:55 PST)
1. make_at_serial.log (452057 bytes)
Re: [AMBER] help with antechamber jun kit (Tue Nov 22 2011 - 18:14:42 PST)
1. amine.pdb (1809 bytes)
2. phenol.pdb (1315 bytes)
Re: [AMBER] ICST-Amber Install co nguyentruong (Wed Nov 23 2011 - 01:16:18 PST)
1. amber11_1.5.tar (102400 bytes)
2. amber111.4.tar (81920 bytes)
[AMBER] General Amber FF Parameters Caglar Bayar (Thu Nov 24 2011 - 14:08:47 PST)
1. gaff.dat (328503 bytes)
Re: [AMBER] help with antechamber jun kit (Sun Nov 27 2011 - 07:47:26 PST)
1. paa.pdb (10653 bytes)
[AMBER] MCPB execution error Soma Ghosh (Sun Nov 27 2011 - 22:01:31 PST)
1. 1AMP_OH_sidechain.bcl (3536 bytes)
[AMBER] pdb file with a covalently linked nerve agent Urszula Uciechowska (Mon Nov 28 2011 - 05:45:49 PST)
1. 3DL4_dA.pdb (357500 bytes)
[AMBER] Restarting an MD run Beale, John (Mon Nov 28 2011 - 05:56:29 PST)
1. image001.jpg (23871 bytes)
[AMBER] leap problem: TER cards disappearing thomas.fox.boehringer-ingelheim.com (Tue Nov 29 2011 - 06:33:40 PST)
1. 1ahp.pdb (450659 bytes)
2. leap1.in (302 bytes)
Re: [AMBER] glibc error while running Xleap Vlad Cojocaru (Tue Nov 29 2011 - 07:03:55 PST)
1. make_debug.log (88945 bytes)
Re: [AMBER] Problem running Ptraj with CHARMM psf and dcd trajectory file Puspita Halder (Tue Nov 29 2011 - 21:08:36 PST)
1. H107Y_all.psf.bz2 (439296 bytes)
Re: [AMBER] error by running MMPBSa Urszula Uciechowska (Wed Nov 30 2011 - 06:12:31 PST)
1. mm_pbsa_binding.in (11063 bytes)
2. REC.prmtop (78617 bytes)
3. snapshot_rec.crd.1 (6213 bytes)
[AMBER] Fwd: error by running MMPBSa Ray Luo, Ph.D. (Wed Nov 30 2011 - 09:42:40 PST)
1. mm_pbsa_binding.in (11063 bytes)
2. REC.prmtop (78617 bytes)
3. snapshot_rec.crd.1 (6213 bytes)
Re: [AMBER] combination of CHAMBER prmtop and pmemd.cuda is causing serious instability Marc van der Kamp (Wed Nov 30 2011 - 09:27:00 PST)
1. test_ross2.tgz (2185474 bytes)
Re: [AMBER] combination of CHAMBER prmtop and pmemd.cuda is causing serious instability Marc van der Kamp (Wed Nov 30 2011 - 09:51:56 PST)
1. test_ross2a.tgz (97074 bytes)
[AMBER] D-N-Sulfate-glucosamine net charge Massimiliano Porrini (Wed Nov 30 2011 - 11:23:58 PST)
1. leapfile.in (1032 bytes)
[AMBER] ATOM TYPES for MODIFIED dCTP Jana Sefcikova 1 (Wed Nov 30 2011 - 12:32:39 PST)
1. TDC.pdb (3086 bytes)
2. TDC.mol2 (4299 bytes)
[AMBER] CUDA NaN error occuring at "wrapping first mol" Bill Sinko (Wed Nov 30 2011 - 15:54:31 PST)
1. 11-30_12-43-53.diff (222527 bytes)
2. 11-30_12-43-53.log (12143 bytes)

Amber Archive Nov 2011 by messages with attachments