Amber Archive Jun 2012 by messages with attachments

[AMBER] cuda errors Jonathan Gough (Thu May 31 2012 - 21:13:22 PDT)
1. 06-01_00-01-02.log.gz (1667 bytes)
2. 06-01_00-01-02.diff.gz (451213 bytes)
[AMBER] ptraj Hbond analysis shradhey gupta (Thu May 31 2012 - 21:55:09 PDT)
1. hbond.ptraj (358 bytes)
2. anal_hbond.out (9579 bytes)
[AMBER] ptraj Hbond analysis shradhey gupta (Thu May 31 2012 - 21:56:20 PDT)
1. hbond.ptraj (358 bytes)
2. anal_hbond.out (9579 bytes)
Re: [AMBER] MMPBSA_Error: Could not find necessary program [sander] Cao Yang (Fri Jun 01 2012 - 06:29:34 PDT)
1. FINAL_DECOMP_MMPBSA.dat (277047 bytes)
[AMBER] ptraj Hbond analysis shradhey gupta (Fri Jun 01 2012 - 22:51:36 PDT)
1. hbond.ptraj (358 bytes)
2. anal_hbond.out (9579 bytes)
Re: [AMBER] Problem in parameter file generation Asma Abro 28-FBAS/MSBI/F09 (Mon Jun 04 2012 - 03:02:35 PDT)
1. Dock_ste.pdb (364700 bytes)
2. ste.frcmod (2728 bytes)
3. ste (10958 bytes)
[AMBER] Amber11 Installation Problem arun kumar (Tue Jun 05 2012 - 23:35:20 PDT)
1. 06-06_16-42-05.log (71439 bytes)
2. 06-06_16-42-05.diff (11005 bytes)
Re: [AMBER] Problems installing AmberTools12 on Ubuntu Adam Jion (Thu Jun 07 2012 - 18:41:55 PDT)
1. build.log (602564 bytes)
[AMBER] FIX for Mac OS X Lion with Xcode 4.3.2 Jason Swails (Fri Jun 08 2012 - 05:21:26 PDT)
1. bugfix.8 (6961 bytes)
Re: [AMBER] Entropy from MMPBSA.py and MM_PBSA.pl Nan Li (Fri Jun 08 2012 - 09:17:21 PDT)
1. mm_pbsapl.in (9892 bytes)
2. mmpbsapy.in (125 bytes)
[AMBER] QM/MM minimization Ewa Chudyk (Mon Jun 11 2012 - 08:17:43 PDT)
1. 0.7_3.5.out2-12 (499352 bytes)
2. 0.7_3.5.out2-11 (145962 bytes)
Re: [AMBER] MMPBSA calculation reproducibility Sangita Kachhap (Mon Jun 11 2012 - 11:56:33 PDT)
1. TG_1-3-prod-30ns.rms.pdf (105899 bytes)
[AMBER] force field library for protonated cytosine Asmita Gupta (Thu Jun 14 2012 - 11:24:32 PDT)
1. o1.mol2 (3636 bytes)
2. convert_mol_to_off (917 bytes)
Re: [AMBER] R: strange POPC under lipids 11 FF Ross Walker (Fri Jun 15 2012 - 02:26:20 PDT)
1. popc.jpg (227828 bytes)
[AMBER] Fail to read hem parameters written by P. Rydberg 崔颖璐 (Fri Jun 15 2012 - 05:08:07 PDT)
1. hem_ryd.in (8084 bytes)
2. frcmod.hemryd (5596 bytes)
Re: [AMBER] Facing problem on TUTORIAL A1 sudipta (Fri Jun 15 2012 - 12:05:30 PDT)
1. plc.frcmod (1272 bytes)
2. cua.pdb (80 bytes)
[AMBER] chiral Sulfur atom Yun Shi (Fri Jun 15 2012 - 15:30:00 PDT)
1. Sulf.png (7002 bytes)
[AMBER] modeling GDP Brandon Sim (Mon Jun 18 2012 - 11:43:52 PDT)
1. GDP.pdb (3087 bytes)
[AMBER] PB Bomb in epsmap(): epsy out of range Xiao Ba (Tue Jun 19 2012 - 14:37:12 PDT)
1. pbsasfe.out (112105 bytes)
[AMBER] Specifying disulfide bonds in a protein model Beale, John (Thu Jun 21 2012 - 02:18:09 PDT)
1. image001.jpg (23871 bytes)
[AMBER] TI calculation Amber 12 Anna Bauß (Thu Jun 21 2012 - 02:42:53 PDT)
1. anna_bauss.vcf (348 bytes)
Re: [AMBER] TI calculation Amber 12 Anna Bauß (Thu Jun 21 2012 - 04:31:35 PDT)
1. anna_bauss.vcf (348 bytes)
Re: [AMBER] TI calculation Amber 12 Anna Bauß (Thu Jun 21 2012 - 05:53:54 PDT)
1. 04-12_15-44-32.log (84312 bytes)
2. anna_bauss.vcf (348 bytes)
Re: [AMBER] Sander Error Melissa Buskes (Fri Jun 22 2012 - 01:15:20 PDT)
1. PKA1.tar.gz (344734 bytes)
Re: [AMBER] R: strange POPC under lipids 11 FF Gould, Ian R (Fri Jun 22 2012 - 01:50:25 PDT)
1. Figure_Lipid.pdf (130996 bytes)
2. Table_Lipids.pdf (42935 bytes)
Re: [AMBER] NaN with GTX580 pmemd.cuda simulation with and without iwrap = 1 Ben Roberts (Sat Jun 23 2012 - 21:17:24 PDT)
1. smime.p7s (4373 bytes)
[AMBER] problem in antechamber jit mukherjee (Mon Jun 25 2012 - 01:30:20 PDT)
1. divcon.out (177487 bytes)
Re: [AMBER] (no subject) DEBOSTUTI GHOSHDASTIDAR (Mon Jun 25 2012 - 11:00:31 PDT)
1. acetate_newFF.frc (835 bytes)
[AMBER] problem in the bondtype judgement step in antechamber jit mukherjee (Tue Jun 26 2012 - 00:30:57 PDT)
1. swcnt_ad3_sidewall_closedshell.pdb (35337 bytes)
2. ANTECHAMBER_BOND_TYPE.AC0 (26646 bytes)
3. ANTECHAMBER_BOND_TYPE.AC (26646 bytes)
4. ATOMTYPE.INF (83505 bytes)
[AMBER] AMBER Error: unable to achieve consistency Asma Abro 28-FBAS/MSBI/F09 (Tue Jun 26 2012 - 20:40:12 PDT)
1. ligand.pdb (2728 bytes)
Re: [AMBER] AMBER Error: unable to achieve consistency Asma Abro 28-FBAS/MSBI/F09 (Tue Jun 26 2012 - 22:20:21 PDT)
1. lig_h.pdb (2775 bytes)
Re: [AMBER] AMBER Error: unable to achieve consistency Jodi Ann Hadden (Wed Jun 27 2012 - 08:32:28 PDT)
1. ligand_H.pdb (5790 bytes)
Re: [AMBER] Low POPC area per lipid - LIPID11 Ross Walker (Thu Jun 28 2012 - 12:34:14 PDT)
1. Fig_4.TIF (410128 bytes)
Re: [AMBER] CHAMBER with RNA BERGY (Fri Jun 29 2012 - 00:28:15 PDT)
1. error_chamber.zip (159086 bytes)
[AMBER] update for POPE test Albert (Fri Jun 29 2012 - 05:28:44 PDT)
1. pope.jpeg (100317 bytes)
[AMBER] update for POPE test Albert (Fri Jun 29 2012 - 05:32:16 PDT)
1. pope_plot.jpg (81115 bytes)
Re: [AMBER] update for POPE test Albert (Fri Jun 29 2012 - 07:16:46 PDT)
1. 100ns.jpg (149254 bytes)
Re: [AMBER] Problem while running MMPBSA qiqi (Fri Jun 29 2012 - 13:08:44 PDT)
1. raf_top_mdcrd_MMPBSA_files.tar.gz (355722 bytes)

Last message date: Sat Jun 30 2012 - 15:30:03 PDT
Archived on: Fri Nov 22 2024 - 05:54:32 PST

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