Amber Archive Jun 2010: by messages with attachments

[AMBER] discontinuous residues Jio M (Tue Jun 01 2010 - 00:05:02 PDT)
1. my.pdb (1817 bytes)
[AMBER] Error: No potential terms in sander output! vaibhav dixit (Wed Jun 02 2010 - 03:37:15 PDT)
1. 2PRG_rosi.pdb (189073 bytes)
2. _MMPBSA_avgcomplex.pdb (313748 bytes)
Fwd: Re: Re: [AMBER] error - binding_energy.mmpbsa run Andrew Voronkov (Wed Jun 02 2010 - 06:15:56 PDT)
1. binding_energy.mmpbsa (8612 bytes)
[AMBER] gb working but not pb & gives No potential terms in sander output! error vaibhav dixit (Fri Jun 04 2010 - 22:25:43 PDT)
1. FINAL_RESULTS_MMPBSA.dat (4038 bytes)
[AMBER] MMPBSA.py calculations...bad atom type RANAJIT SHINDE (Fri Jun 04 2010 - 22:45:16 PDT)
1. FINAL_RESULTS_MMPBSA.dat (963 bytes)
[AMBER] Re: gb working but not pb & gives No potential terms in sander output! error vaibhav dixit (Sun Jun 06 2010 - 02:37:55 PDT)
1. _MMPBSA_complex_pb.mdout (5493 bytes)
2. _MMPBSA_ligand_pb.mdout (39794 bytes)
3. _MMPBSA_receptor_pb.mdout (5493 bytes)
[AMBER] Entropy calculation using nmode in mm_pbsa.pl Sushil Mishra (Sun Jun 06 2010 - 05:22:26 PDT)
1. snap_com.all.out (1032 bytes)
2. snap_lig.all.out (1002 bytes)
3. snap_rec.all.out (1032 bytes)
4. binding_energy.mmpbsa (14364 bytes)
Re: [AMBER] MMPBSA.py calculations...bad atom type RANAJIT SHINDE (Sun Jun 06 2010 - 21:49:37 PDT)
1. _MMPBSA_complex_gb.mdout (154141 bytes)
2. FINAL_RESULTS_MMPBSA.dat (9597 bytes)
[AMBER] Fwd: FW: Requesting your help in amber Jenny Iskrenova (Mon Jun 07 2010 - 07:26:49 PDT)
1. ala-neb_300K_equil.in (290 bytes)
2. ala-neb-smallk_1.in (397 bytes)
Re: [AMBER] Error on running ptraj Daniel Roe (Tue Jun 08 2010 - 07:46:10 PDT)
1. ptraj_AT1.4_fixMaxFrames.patch (9027 bytes)
Re: [AMBER] random number generators visible from nab: choice necessary? M. L. Dodson (Tue Jun 08 2010 - 09:16:46 PDT)
1. lecuyer.c (1767 bytes)
Re: [AMBER] about ewald error estimate Navanath Kumbhar (Tue Jun 08 2010 - 09:56:53 PDT)
1. md1.out (79107 bytes)
Re: [AMBER] SURFTEN / SURFOFF values are not consistent across *.all.out files Sushil Mishra (Tue Jun 08 2010 - 13:04:40 PDT)
1. binding_energy.mmpbsa (14749 bytes)
[AMBER] Strange results for vaibhav dixit (Wed Jun 09 2010 - 04:24:31 PDT)
1. FINAL_RESULTS_MMPBSA.dat (2363 bytes)
2. progress.log (691 bytes)
Re: [AMBER] regarding forcefield for rna Asfa Ali (Wed Jun 09 2010 - 04:35:21 PDT)
1. 2KBP.pdb (640791 bytes)
Re: [AMBER] MMPBSA.py nmode maxcyc problem Jason Swails (Thu Jun 10 2010 - 21:19:47 PDT)
1. mmpbsa.patch (1055 bytes)
Re: [AMBER] regarding forcefield for rna Asfa Ali (Fri Jun 11 2010 - 04:09:24 PDT)
1. 2kbp_md2_pdb1.png (24578 bytes)
Re: [AMBER] regarding forcefield for rna Asfa Ali (Fri Jun 11 2010 - 23:03:38 PDT)
1. 2kbp_openup.odt (576290 bytes)
[AMBER] Ptraj problems Samuel Genheden (Mon Jun 14 2010 - 01:47:25 PDT)
1. m1 (138780 bytes)
2. pdb.1 (436000 bytes)
3. prmtop (865954 bytes)
4. ptraj.in (69 bytes)
[AMBER] Polarizability and induced dipoles Mag. Thomas Taylor (Tue Jun 15 2010 - 01:53:33 PDT)
1. dipoles.patch (15938 bytes)
2. chamber.patch (3756 bytes)
[AMBER] to understand 1-4 interactions in Amber FF Alan (Tue Jun 15 2010 - 04:16:31 PDT)
1. HATP_amber.pdb (3809 bytes)
[AMBER] FW: frcdump for CHARMM Ross Walker (Wed Jun 16 2010 - 08:10:35 PDT)
1. patch.txt (1747 bytes)
[AMBER] high bidning energy MMPBSA kamlesh sahu (Wed Jun 16 2010 - 18:45:55 PDT)
1. snaps_statistics.out (2143 bytes)
2. extract_coords.mmpbsa (954 bytes)
3. binding_energy_Example.log (19548 bytes)
4. extract_coords.log (127242 bytes)
5. binding_energy_Example.mmpbsa (1073 bytes)
[AMBER] Fwd: high bidning energy MMPBSA kamlesh sahu (Wed Jun 16 2010 - 18:51:11 PDT)
1. snaps_statistics.out (2143 bytes)
2. extract_coords.mmpbsa (954 bytes)
3. binding_energy_Example.log (19548 bytes)
4. extract_coords.log (127242 bytes)
5. binding_energy_Example.mmpbsa (1073 bytes)
[AMBER] antechamber issue and parameters for heme of cyp3a4 vaibhav dixit (Fri Jun 18 2010 - 22:00:47 PDT)
1. cyx.lib.txt (7546 bytes)
2. heme_cys_w.pdb (4054 bytes)
[AMBER] Query- Heating after Equilibration Jagdeesh C (Sat Jun 19 2010 - 23:16:19 PDT)
1. 143d.prmtop (301177 bytes)
2. 143d.inpcrd (26106 bytes)
3. min_143d.rst (461590 bytes)
Re: [AMBER] Problem with pmed installation: Amber 10 Jason Swails (Mon Jun 21 2010 - 07:18:19 PDT)
1. config.h (653 bytes)
Re: [AMBER] parallel compiling failure of Amber 11 Yubo Fan (Tue Jun 22 2010 - 07:56:54 PDT)
1. config.log (5468 bytes)
2. fftw2_config.log (4971 bytes)
Re: [AMBER] parallel compiling failure of Amber 11 Yubo Fan (Tue Jun 22 2010 - 10:49:25 PDT)
1. compile.err (17880 bytes)
2. compile.log (56482 bytes)
[AMBER] dna monica.imtech.res.in (Wed Jun 23 2010 - 02:16:48 PDT)
1. oligo.nab (102 bytes)
2. oligo.pdb (92834 bytes)
Re: [AMBER] Query- Heating after Equilibration Jagdeesh C (Wed Jun 23 2010 - 04:28:15 PDT)
1. polak_new.out (7102 bytes)
2. polak_previous.out (45878 bytes)
Re: [AMBER] dna monica.imtech.res.in (Wed Jun 23 2010 - 08:40:18 PDT)
1. leap.log (38091 bytes)
2. oligo.nab (102 bytes)
3. oligo.pdb (92834 bytes)
Re: [AMBER] unexpected "vlimit exceeded for step" error Ross Walker (Wed Jun 23 2010 - 09:46:31 PDT)
1. frame2.jpg (70169 bytes)
2. frame0.jpg (76449 bytes)
Re: [AMBER] pre-processing of trajectories hannes.loeffler.stfc.ac.uk (Wed Jun 23 2010 - 12:41:24 PDT)
1. winmail.dat (3791 bytes)
[AMBER] [Fwd: Re: pre-processing of trajectories] moitrayee.mbu.iisc.ernet.in (Thu Jun 24 2010 - 00:21:16 PDT)
1. PC_protein_RNA.tif (394490 bytes)
[AMBER] RESP charge of heavy metal contained complex Jia Xu (Thu Jun 24 2010 - 08:37:00 PDT)
1. 0624.png (92006 bytes)
Re: [AMBER] MMPBSA.py NameError: global name 'diffstdev' is not defined Jason Swails (Fri Jun 25 2010 - 07:02:07 PDT)
1. mmpbsa.patch.3 (1809 bytes)
Re: [AMBER] Segmentation fault Jagdeesh C (Sat Jun 26 2010 - 23:01:18 PDT)
1. minx_ntmin1.out (392852 bytes)
2. minx_ntmin2.out (13076 bytes)
Re: [AMBER] Segmentation fault case (Wed Jun 30 2010 - 09:31:54 PDT)
1. Run.dhfr.min_prcg (580 bytes)

Amber Archive Jun 2010 by messages with attachments