Amber Archive Jul 2013 by messages with attachments

[AMBER] The recommended way to create periodic box around lipid bilayer system ? Marek Maly (Mon Jul 01 2013 - 07:20:54 PDT)
1. boxes_fin.png (522315 bytes)
Re: [AMBER] The recommended way to create periodic box around lipid bilayer system ? Marek Maly (Mon Jul 01 2013 - 11:26:11 PDT)
1. 01_02.png (635476 bytes)
Re: [AMBER] The recommended way to create periodic box around lipid bilayer system ? Marek Maly (Mon Jul 01 2013 - 15:48:37 PDT)
1. autoimage.png (534070 bytes)
[AMBER] Amber11 AmberTools1.5 installation problem Sangeetha B (Tue Jul 02 2013 - 08:33:06 PDT)
1. 23.log (29107 bytes)
Re: [AMBER] 4x Asus Titan boards :) GB/nucleosome passed Tru Huynh (Wed Jul 03 2013 - 11:28:35 PDT)
1. deviceQuery.margy (8890 bytes)
[AMBER] about run REMD(replica exchange molecular dynamic) Biao Ma (Wed Jul 03 2013 - 17:47:32 PDT)
1. clip_image004.jpg (20252 bytes)
2. clip_image002.jpg (15226 bytes)
[AMBER] question of Radius of Gyration Chinh Su Tran To (Thu Jul 04 2013 - 04:55:38 PDT)
1. test_RoG.gif (7005 bytes)
[AMBER] installing Amber 11 and Amber tools 1.5 Muthukumaran R (Thu Jul 04 2013 - 21:06:25 PDT)
1. 23.log (29107 bytes)
Re: [AMBER] question of Radius of Gyration Chinh Su Tran To (Thu Jul 04 2013 - 22:00:48 PDT)
1. gag_RadGyr_40ns.gif (14793 bytes)
[AMBER] RE：Re: Re?Re: FATAL: Atom XXX does not have a type sunyeping.aliyun.com (Fri Jul 05 2013 - 11:05:56 PDT)
1. amber_NA.zip (189607 bytes)
Re: [AMBER] constant pressure simulation kirtana S (Fri Jul 05 2013 - 11:05:00 PDT)
1. methanol_box.prmtop (326774 bytes)
2. methanol_box.inpcrd (54831 bytes)
3. methanol.off (102479 bytes)
[AMBER] Fwd: Re: Copper parametrization for a laccase center mmaestre.gate.sinica.edu.tw (Tue Jul 09 2013 - 00:30:54 PDT)
1. distorted_cluster (107836 bytes)
2. Clusters_separate (34469 bytes)
3. laccase_H_sidechain_opt_full_input (4494 bytes)
[AMBER] 答复: timecorr Hongyi WU (Tue Jul 09 2013 - 05:34:45 PDT)
1. Correlation.jpg (78446 bytes)
[AMBER] instablity of ligand during minimization Ibrahim Said (Tue Jul 09 2013 - 13:09:15 PDT)
1. H2O-2.in (319 bytes)
Re: [AMBER] AMBER GPU Job Write Fails Jan-Philip Gehrcke (Wed Jul 10 2013 - 06:58:38 PDT)
1. cuda_device_temp_week_gpu_lockup_amber_label.png (49150 bytes)
[AMBER] Amber 12 on OSX 10.8.4 Wang Chern Hoe (Dr) (Wed Jul 10 2013 - 16:17:59 PDT)
1. smime.p7s (4815 bytes)
Re: [AMBER] Amber 12 on OSX 10.8.4 Wang Chern Hoe (Dr) (Wed Jul 10 2013 - 19:09:00 PDT)
1. smime.p7s (4815 bytes)
Re: [AMBER] Amber 12 on OSX 10.8.4 Wang Chern Hoe (Dr) (Wed Jul 10 2013 - 23:01:34 PDT)
1. smime.p7s (4815 bytes)
[AMBER] Wrong results in GTX TITAN, correct results on GTX580 iqtcub (Thu Jul 11 2013 - 00:35:47 PDT)
1. 3c4c_v600e_4_din.in (327 bytes)
[AMBER] MCPB Jinqiang (Thu Jul 11 2013 - 08:54:06 PDT)
1. 1AMP_OH_md.frcmod (3263 bytes)
2. 1AMP_OH_sem.frcmod (3263 bytes)
Re: [AMBER] GTX780 News Ross Walker (Thu Jul 11 2013 - 20:24:56 PDT)
1. Flyer_for_Starter_2U_4xGPU_System_for_Your_Carrying_Case.pdf (506177 bytes)
Re: [AMBER] Problem related to the umbrella sampling Sindrila Dutta banik (Thu Jul 11 2013 - 21:23:22 PDT)
1. JACS_2006_128_.pdf (332746 bytes)
[AMBER] Problems running NAB scripts in the manual Alexander Button (Wed Jul 17 2013 - 00:08:09 PDT)
1. program_5.nab (2191 bytes)
2. program_5.tat.in (49 bytes)
3. program_5_edit.nab (2197 bytes)
4. program_5_edit.tat.in (50 bytes)
5. taDT.energy.dat (2760 bytes)
6. taDT.triad.min.pdb (7734 bytes)
7. temp.pdb (7656 bytes)
8. tat.triad.min.pdb (5486 bytes)
9. construct_triplex.nab (2483 bytes)
10. program_6.nab (3434 bytes)
11. tat_min.pdb (7873 bytes)
12. program_5.cgc.in (49 bytes)
13. cttctt.pdb (44940 bytes)
[AMBER] antechamber issues Hannes Loeffler (Wed Jul 17 2013 - 02:02:47 PDT)
1. ring.pdb (2111 bytes)
2. sybyl.mol2 (1509 bytes)
3. ring_babel.mol2 (1422 bytes)
Re: [AMBER] Antechamber atom types and all_nuc94.in atom descriptions Kamali Sripathi (Fri Jul 19 2013 - 12:20:44 PDT)
1. 130719_RED_Server.png (67147 bytes)
[AMBER] the question about the atom type of my molecule lujing8556 (Mon Jul 22 2013 - 01:12:33 PDT)
1. VOXCU_IL1R__VO__CP_INWL.jpg (16978 bytes)
Re: [AMBER] MMPBSA Alanine scan terminal residues Jason Swails (Tue Jul 23 2013 - 05:23:25 PDT)
1. alamdcrd.py (18750 bytes)
Re: [AMBER] antechamber issues Junmei Wang (Tue Jul 23 2013 - 11:59:01 PDT)
1. mol2.c (12014 bytes)
2. antechamber.c (71515 bytes)
3. charge.c (33197 bytes)
[AMBER] MMPBSA.py problem on G gas Yi An (Tue Jul 23 2013 - 14:53:34 PDT)
1. single_traj.out (7204 bytes)
2. multi_traj.out (10424 bytes)
[AMBER] Problem in running antechamber.Unable to achieve self consistency to the tolerances specified devawati dutta (Wed Jul 24 2013 - 01:25:36 PDT)
1. Original_ligand.pdb (9389 bytes)
2. Modified_ligand.pdb (8809 bytes)
[AMBER] DNA Phosphate error mohit mazumder (Fri Jul 26 2013 - 23:36:17 PDT)
1. edited.pdb (31351 bytes)
2. leap.log (20657 bytes)
[AMBER] bond command sunyeping.aliyun.com (Sat Jul 27 2013 - 21:12:14 PDT)
1. 10_DEF.mod.pdb (275164 bytes)
Re: [AMBER] Interaction energy-based residue-residue correlation matrix anu chandra (Sun Jul 28 2013 - 23:36:13 PDT)
1. Article_correlation.pdf (672215 bytes)
[AMBER] mdread MMPBSA tianchuan1015 (Tue Jul 30 2013 - 03:19:27 PDT)
1. mdread.f (114144 bytes)
[AMBER] mdread 372133720 (Tue Jul 30 2013 - 03:36:25 PDT)
1. mdread.f (114144 bytes)

Last message date: Wed Jul 31 2013 - 20:30:04 PDT
Archived on: Wed Dec 25 2024 - 05:54:50 PST

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