Amber Archive Oct 2010 by messages with attachments

[AMBER] MMPBSA.py - very high energy terms Senthil Natesan (Fri Oct 01 2010 - 06:27:18 PDT)
1. results_mmpbsa.dat_old (7141 bytes)
Re: [AMBER] MMPBSA.py - very high energy terms Senthil Natesan (Fri Oct 01 2010 - 07:20:51 PDT)
1. results_mmpbsa.dat (11178 bytes)
Re: [AMBER] pmemd.cuda error with group restraint Ross Walker (Fri Oct 01 2010 - 16:59:30 PDT)
1. equil.pmemd11 (47998 bytes)
2. equil.pmemd11.cuda (432 bytes)
3. 10-01.cuda (47200 bytes)
4. 10-01.cuda_DPDP (47180 bytes)
Re: [AMBER] Segmentation fault Seibold, Stephen (Sat Oct 02 2010 - 15:53:54 PDT)
1. winmail.dat (3967 bytes)
Re: [AMBER] Segmentation fault Seibold, Stephen (Mon Oct 04 2010 - 16:18:25 PDT)
1. winmail.dat (4547 bytes)
Re: [AMBER] TI +- variance is coming out to be very high sunita gupta (Tue Oct 05 2010 - 02:09:28 PDT)
1. plots.docx (15582 bytes)
Re: [AMBER] TI +- variance is coming out to be very high sunita gupta (Wed Oct 06 2010 - 00:07:13 PDT)
1. plots.pdf (90200 bytes)
Re: [AMBER] Fwd: Incorrect handling of phenylalanine amide by antechamber Francesco Pietra (Wed Oct 06 2010 - 03:07:28 PDT)
1. pha.NXT.pdb (2529 bytes)
2. pha.NXT.mol2 (2651 bytes)
3. pha.NH3.pdb (2529 bytes)
[AMBER] Fwd: Fwd: Incorrect handling of phenylalanine amide by antechamber Francesco Pietra (Wed Oct 06 2010 - 04:17:03 PDT)
1. pha.NXT.pdb (2529 bytes)
2. pha.NXT.mol2 (2651 bytes)
3. pha.NH3.pdb (2529 bytes)
4. pha.NXT.frcmod (410 bytes)
Re: [AMBER] Fwd: Fwd: Incorrect handling of phenylalanine amide by antechamber Francesco Pietra (Wed Oct 06 2010 - 08:40:55 PDT)
1. antechamber_pha_4.tar.bz2 (14149 bytes)
2. antechamber_leap_NXT_pha_1_mol2.tar.bz2 (21978 bytes)
Re: [AMBER] Fwd: Incorrect handling of phenylalanine amide by antechamber Paul S. Nerenberg (Thu Oct 07 2010 - 10:17:11 PDT)
1. pha.pdb (1684 bytes)
2. pneumadin.pdb (9188 bytes)
3. setup_pha (125 bytes)
4. setup_pneumadin (183 bytes)
Re: [AMBER] ptraj- cluster analysis - Error Daniel Roe (Thu Oct 07 2010 - 14:13:07 PDT)
1. ptraj_cluster.2010-10-07.patch (938 bytes)
[AMBER] prepare the heme parameters juan zeng (Sat Oct 09 2010 - 00:18:08 PDT)
1. ligand_ant.pdb (3960 bytes)
2. ligand_esp.gjf (223 bytes)
3. ligand_esp.log (449590 bytes)
4. ligand.prepi (7571 bytes)
5. ligand.gjf (5155 bytes)
6. ligand.log (4737 bytes)
Re: [AMBER] xleap Siavoush Dastmalchi (Mon Oct 11 2010 - 22:36:38 PDT)
1. winmail.dat (4794 bytes)
Re: [AMBER] xleap Siavoush Dastmalchi (Tue Oct 12 2010 - 01:21:48 PDT)
1. winmail.dat (6274 bytes)
Re: [AMBER] xleap Siavoush Dastmalchi (Tue Oct 12 2010 - 01:24:28 PDT)
1. winmail.dat (7018 bytes)
[AMBER] xleap menu bar problem Siavoush Dastmalchi (Tue Oct 12 2010 - 06:11:46 PDT)
1. winmail.dat (3399 bytes)
Re: [AMBER] xleap menu bar problem Siavoush Dastmalchi (Tue Oct 12 2010 - 06:30:24 PDT)
1. winmail.dat (4759 bytes)
Re: [AMBER] advenced tutorial 13 (crystal simulations) Matthias Negri (Wed Oct 13 2010 - 04:32:34 PDT)
1. m_negri.vcf (644 bytes)
[AMBER] Issue regarding buckling of planar ligand during simulations abc def (Thu Oct 14 2010 - 04:43:31 PDT)
1. After_simulation.pdb (9864 bytes)
2. Before_simulation.pdb (11440 bytes)
[AMBER] antechamber error when processing the graphite structure Bongkeun Kim (Thu Oct 14 2010 - 13:02:13 PDT)
1. grap2.pdb (186200 bytes)
[AMBER] mm-pbsa yan zhang (Sun Oct 17 2010 - 07:19:21 PDT)
1. pbsa.rar (781926 bytes)
2. mm_pbsa_readinput.pm (16044 bytes)
[AMBER] question on antechamber parametrization / unable to find mopac charges error Andrew Voronkov (Sun Oct 17 2010 - 10:35:07 PDT)
1. gdp.pdb (2219 bytes)
[AMBER] Problem with formyl group parameters Carter M.K. (Mon Oct 18 2010 - 03:36:44 PDT)
1. butyraldehyde.pdb (802 bytes)
2. butyraldehyde.frcmod (318 bytes)
3. butyraldehyde.prepi (1317 bytes)
[AMBER] H-Bonding Beale, John (Tue Oct 19 2010 - 09:15:20 PDT)
1. image001.jpg (10569 bytes)
[AMBER] Problem using graphite strucute in equil MD Bongkeun Kim (Tue Oct 19 2010 - 22:24:19 PDT)
1. 20.prmtop (427551 bytes)
2. 20_min2.rst (102215 bytes)
3. 20_heat1.out (18103 bytes)
4. equil1.out (18383 bytes)
[AMBER] Problem in mm_pbsa Kshatresh Dutta Dubey (Wed Oct 20 2010 - 00:00:54 PDT)
1. 03.log (16832 bytes)
Re: [AMBER] Problem using graphite strucute in equil MD Bongkeun Kim (Wed Oct 20 2010 - 11:19:35 PDT)
1. 2c.pdb (527 bytes)
2. c2.prepi (494 bytes)
Re: [AMBER] Problem using graphite strucute in equil MD Bongkeun Kim (Wed Oct 20 2010 - 15:48:09 PDT)
1. 1.pdb (2728 bytes)
2. 4c.frcmod (879 bytes)
3. 4c.prepi (1686 bytes)
4. 44.pdb (14230 bytes)
Re: [AMBER] Problem using graphite strucute in equil MD Bongkeun Kim (Thu Oct 21 2010 - 11:13:45 PDT)
1. c7.prmtop (299751 bytes)
2. c7.inpcrd (63118 bytes)
3. c7_min1.rst (63121 bytes)
4. c7_min2.rst (63121 bytes)
5. init.png (166344 bytes)
6. final.png (148610 bytes)
Re: [AMBER] Problem using graphite structure in equil MD Bongkeun Kim (Thu Oct 21 2010 - 16:09:14 PDT)
1. c20.png (49216 bytes)
[AMBER] Triclinic box condition for PBC Bongkeun Kim (Fri Oct 22 2010 - 10:39:04 PDT)
1. c20w.png (80929 bytes)
[AMBER] pmemd installation error M. Reza Ganjalikhany (Mon Oct 25 2010 - 02:29:10 PDT)
1. config.h (1030 bytes)
[AMBER] water molecule positions Beale, John (Mon Oct 25 2010 - 06:03:47 PDT)
1. image001.jpg (10569 bytes)
[AMBER] HOW TO PREPARE MODIFIED NUCLEOSIDE Indrajit Deb (Tue Oct 26 2010 - 05:11:07 PDT)
1. DHU.zip (2623 bytes)
[AMBER] 2drms in ptraj Beale, John (Thu Oct 28 2010 - 06:03:37 PDT)
1. image001.jpg (10569 bytes)

Last message date: Sun Oct 31 2010 - 22:30:03 PDT
Archived on: Sun Dec 22 2024 - 05:54:10 PST

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