Amber Archive Dec 2012 by messages with attachments

[AMBER] need assistance to generate forcefield for Pyridoxal phosphate BALA SUBRAMANI G L (Mon Dec 03 2012 - 04:03:31 PST)
1. plp.pdb (1896 bytes)
2. plp_h.mol2 (3733 bytes)
[AMBER] PostDoc molecular modeling of enzymes Jan Brezovsky (Mon Dec 03 2012 - 05:17:17 PST)
1. 2012_PostDocs.pdf (518186 bytes)
Re: [AMBER] EGB discrepancy between sander and pmemd Eng H Yap (Tue Dec 04 2012 - 13:59:47 PST)
1. 1i85.tgz (119787 bytes)
[AMBER] problem with imposing planarity to a N3P3 ring Giovanni Pavan (Fri Dec 07 2012 - 10:36:08 PST)
1. N3P3.JPG (13272 bytes)
2. image.jpg (204589 bytes)
Re: [AMBER] [apbs-users] iapbs installation Robert Konecny (Sat Dec 08 2012 - 17:41:45 PST)
1. createinput.py.patch (640 bytes)
[AMBER] MMGBSA result difference from whether use &decomp or not Liu Denis (Tue Dec 11 2012 - 00:49:06 PST)
1. pj_mpdc2.out (5506 bytes)
2. pj_mpdc.out (5531 bytes)
[AMBER] MMPBSA.py.MPI import error marawan hussain (Wed Dec 12 2012 - 00:14:23 PST)
1. mpi4py_install.log (7515 bytes)
[AMBER] QM/MM AMBER-ORCA repulsion marawan hussain (Thu Dec 13 2012 - 19:47:45 PST)
1. MM_Gaussian_ORCA.rar (120568 bytes)
Re: [AMBER] glycam_06h atom types Urszula Uciechowska (Fri Dec 14 2012 - 09:54:11 PST)
1. test.mol2 (4364 bytes)
Re: [AMBER] FF99CHI and Modified nucleoside parameter combination Indrajit Deb (Fri Dec 14 2012 - 11:16:41 PST)
1. files.zip (83601 bytes)
[AMBER] branched disaccharide in leap Krisztina Feher (Sat Dec 15 2012 - 12:25:15 PST)
1. NML2.pdb (6831 bytes)
2. NMLwithGAffBasedLAC.png (23659 bytes)
[AMBER] H-REMD, pmemd fails to calculate potential energy of neighbor coordinates Jiri Wiesner (Sat Dec 15 2012 - 20:26:41 PST)
1. sander_run_16_rem.log (65209 bytes)
2. sander_run_64_rem.log (65209 bytes)
3. pmemd_run_32_rem.log (65209 bytes)
4. pmemd_run_64_rem.log (65209 bytes)
5. force_dumps.tar.gz (203327 bytes)
[AMBER] QM/MM AMBER-ORCA repulsion marawan hussain (Sat Dec 15 2012 - 21:16:14 PST)
1. MM_Gaussian_ORCA_2.rar (393628 bytes)
Re: [AMBER] cannot use more than one node Jiri Wiesner (Sun Dec 16 2012 - 05:24:38 PST)
1. run_refep (1555 bytes)
Re: [AMBER] H-REMD, pmemd fails to calculate potential energy of neighbor coordinates Jiri Wiesner (Sun Dec 16 2012 - 15:06:27 PST)
1. sander.diff (4236 bytes)
2. pmemd.diff (4284 bytes)
3. array_dumps.tar.bz2 (471232 bytes)
Re: [AMBER] Fwd: FF99CHI and Modified nucleoside parameter combination Indrajit Deb (Mon Dec 17 2012 - 14:57:36 PST)
1. files.zip (83601 bytes)
[AMBER] Fwd: Fwd: FF99CHI and Modified nucleoside parameter combination Indrajit Deb (Tue Dec 18 2012 - 04:49:27 PST)
1. files.zip (83601 bytes)
Re: [AMBER] QM/MM AMBER-ORCA repulsion Andreas Goetz (Tue Dec 18 2012 - 12:11:04 PST)
1. test.tar.bz2 (1184296 bytes)
Re: [AMBER] some problems in getting the parameters of GLYCAM in Leap 曾晓骏 (Wed Dec 19 2012 - 02:20:33 PST)
1. 3717A85D.92133C0F.4494D150.jpg (23849 bytes)
2. DBE5392C.92133C0F.4494D150.jpg (30717 bytes)
3. D5B5F662.92133C0F.4494D150.jpg (31958 bytes)
Re: [AMBER] some problems in getting the parameters of GLYCAM in Leap Lachele Foley (Lists) (Wed Dec 19 2012 - 11:00:51 PST)
1. 2ZYK_short_rev.pdb (7128 bytes)
Re: [AMBER] MMPBSA - GB is negative, but PB is positive? what am I missing? Jonathan Gough (Thu Dec 20 2012 - 10:58:42 PST)
1. _MMPBSA_complex_pb.mdout.0 (32781 bytes)
2. _MMPBSA_ligand_pb.mdout.0 (32780 bytes)
3. _MMPBSA_mutant_complex_pb.mdout.0 (32788 bytes)
4. _MMPBSA_mutant_ligand_pb.mdout.0 (32787 bytes)
5. _MMPBSA_mutant_receptor_pb.mdout.0 (32782 bytes)
6. _MMPBSA_receptor_pb.mdout.0 (32782 bytes)
[AMBER] Question in umbrella sampling Sajeewa Pemasinghe (Fri Dec 28 2012 - 06:08:39 PST)
1. reaction.histogram (47158 bytes)

Last message date: Mon Dec 31 2012 - 15:00:03 PST
Archived on: Fri Dec 20 2024 - 05:54:43 PST

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