Amber Archive May 2012 by messages with attachments

[AMBER] Electrostatic potential calculation Sudarshan Debnath (Wed May 02 2012 - 05:54:08 PDT)
1. 1VJ5pbsa.out (31760 bytes)
2. 1VJ5pbsa.in (193 bytes)
3. 1VJ5pbsa.phi (275890 bytes)
4. pbsa.png (56438 bytes)
5. 1VJ5.top (82045 bytes)
6. 1VJ5.rst (6542 bytes)
Re: [AMBER] Electrostatic potential calculation Qin Cai (Wed May 02 2012 - 13:06:21 PDT)
1. mdin (179 bytes)
2. mdout (33189 bytes)
Re: [AMBER] using two GPUs Vijay Manickam Achari (Wed May 02 2012 - 16:37:46 PDT)
1. THERMO-RT-MD00-run1000.out (9790 bytes)
[AMBER] using two GPUs Vijay Manickam Achari (Wed May 02 2012 - 20:55:34 PDT)
1. THERMO-RT-MD00-run1000.out (9790 bytes)
[AMBER] am1d problem Gabriel Jara (Thu May 03 2012 - 15:10:38 PDT)
1. from-dftb.in (526 bytes)
[AMBER] add H-atoms automatic in tleap Zhou Gong (Fri May 04 2012 - 07:52:34 PDT)
1. 1aar_native.pdb (97605 bytes)
2. 1aar_amber.pdb (199505 bytes)
Re: [AMBER] Amber 11, Amber-Tools 1.5 and Amber-Tools 12 respgen Bug Marko Wehle (Fri May 04 2012 - 08:38:18 PDT)
1. test_RESP.IN (8140 bytes)
2. test_respgen.IN (2467 bytes)
[AMBER] A1. Conversion of Gaussian output into mol 2 file Debolina Mitra (Sun May 06 2012 - 06:23:51 PDT)
1. CTAB.zip (347119 bytes)
[AMBER] strange CUDA MD output in VMD Albert (Sun May 06 2012 - 23:22:41 PDT)
1. Screenshot.jpg (41971 bytes)
[AMBER] About the system temperature of QMMM simulations (amber12+ Terachem V1.5 ) Yeng-Tseng Wang (Mon May 07 2012 - 18:05:55 PDT)
1. input.txt (2852 bytes)
2. output.txt (20693 bytes)
Re: [AMBER] help with pmemd .in file Chris Chris (Mon May 07 2012 - 18:43:13 PDT)
1. heat.out (9617 bytes)
[AMBER] About the system temperature of QMMM simulations (amber12+ Terachem V1.5 ) c00jsw00.nchc.narl.org.tw (Mon May 07 2012 - 10:20:07 PDT)
1. input (2852 bytes)
2. output (20693 bytes)
Re: [AMBER] help with pmemd .in file Chris Chris (Tue May 08 2012 - 09:23:17 PDT)
1. heat.out (20550 bytes)
Re: [AMBER] charmmlipid2amber.x error Benjamin D Madej (Tue May 08 2012 - 11:36:14 PDT)
1. charmmlipid2amber.x (134683 bytes)
Re: [AMBER] help with pmemd .in file Chris Chris (Tue May 08 2012 - 21:49:28 PDT)
1. CTZ05.pdb (4376 bytes)
2. 2psj_ctz_complex_tleap_CTZ.pdb (275516 bytes)
[AMBER] Problems doing MD on protein complex Chris Chris (Wed May 09 2012 - 08:29:22 PDT)
1. CTZ05.pdb (4376 bytes)
2. 2psj_ctz_complex_tleap_CTZ.pdb (275516 bytes)
[AMBER] Question on Entropy and MMPBSA calculation Kumar, Sonu (Wed May 09 2012 - 09:09:57 PDT)
1. 37_RESULTS_MMPBSA.DAT (6624 bytes)
2. 38_RESULTS_MMPBSA.DAT (6624 bytes)
3. ATT00001.txt (4 bytes)
Re: [AMBER] Problems doing MD on protein complex Chris Chris (Wed May 09 2012 - 14:58:45 PDT)
1. leap.log (5667 bytes)
Re: [AMBER] job error Albert (Thu May 10 2012 - 00:40:15 PDT)
1. Screenshot.png (117085 bytes)
2. 1.png (250387 bytes)
[AMBER] Electrostatic potential calculation Sudarshan Debnath (Thu May 10 2012 - 10:34:33 PDT)
1. 1VJ5.rst (6542 bytes)
2. 1VJ5.top (82045 bytes)
3. 1VJ5pbsa.phi (275890 bytes)
4. pbsa.phi (275850 bytes)
5. 1vj5mdout (31698 bytes)
6. mdout (33188 bytes)
7. mdin (178 bytes)
[AMBER] sander.MPI error George Tzotzos (Fri May 11 2012 - 02:30:12 PDT)
1. min.out (1980 bytes)
Re: [AMBER] lipid11 force filed question Benjamin D Madej (Fri May 11 2012 - 12:21:47 PDT)
1. charmmlipid2amber.x (134683 bytes)
[AMBER] Large standard deviation of entropy obtained from NMODE Xioling Chuang (Sat May 12 2012 - 21:40:36 PDT)
1. nmode.DNA.tar.gz (375367 bytes)
[AMBER] problems with added hydrogens to non standard residue Urszula Uciechowska (Mon May 14 2012 - 01:26:00 PDT)
1. peptide_amber.pdb (12876 bytes)
Re: [AMBER] problems with added hydrogens to non standard residue Urszula Uciechowska (Mon May 14 2012 - 04:43:30 PDT)
1. leap1.log (42839 bytes)
2. MGR.off (6384 bytes)
3. pep1_H.pdb (14804 bytes)
4. leap2.log (37504 bytes)
5. pep2_amber.pdb (12876 bytes)
6. pep2_sugaroH.pdb (8189 bytes)
7. MGR.mol2 (4363 bytes)
[AMBER] Bug? Zero decomposed vdw and ele energies for explicit water molecules in the decomposed PB calculation. Qiong Zhang (Mon May 14 2012 - 11:45:40 PDT)
1. pbsa.dat (17044 bytes)
2. decomp-result.dat (5798 bytes)
3. result.dat (5801 bytes)
[AMBER] Fwd: Bug? Zero decomposed vdw and ele energies for explicit water molecules in the decomposed PB calculation. Ray Luo, Ph.D. (Mon May 14 2012 - 15:00:37 PDT)
1. pbsa.dat (17044 bytes)
2. decomp-result.dat (5798 bytes)
3. result.dat (5801 bytes)
[AMBER] How to implement a new energy function in AMBER Xin Geng (Mon May 14 2012 - 15:55:10 PDT)
1. ehpmf.f_ (20108 bytes)
Re: [AMBER] problem in reading pdb file Asmita Gupta (Tue May 15 2012 - 01:37:47 PDT)
1. test.pdb (69908 bytes)
Re: [AMBER] problems with added hydrogens to non standard residue Urszula Uciechowska (Tue May 15 2012 - 04:47:53 PDT)
1. leap.log (71294 bytes)
2. LYA.mol2 (2557 bytes)
3. MGR.mol2 (4363 bytes)
4. pep1_H.pdb (10560 bytes)
Re: [AMBER] problems with added hydrogens to non standard residue Urszula Uciechowska (Tue May 15 2012 - 06:27:14 PDT)
1. LYA.mol2 (2558 bytes)
2. leap.log (12880 bytes)
Re: [AMBER] problems with added hydrogens to non standard residue Urszula Uciechowska (Tue May 15 2012 - 07:28:41 PDT)
1. pep1_H.pdb (10560 bytes)
2. MGR.mol2 (4363 bytes)
Re: [AMBER] Problem regarding antechamber Asma Abro 28-FBAS/MSBI/F09 (Tue May 15 2012 - 22:32:49 PDT)
1. 05-16_09-52-33.log (90801 bytes)
[AMBER] Electrostatic potential calculation. Sudarshan Debnath (Wed May 16 2012 - 02:54:59 PDT)
1. 1VJ5_pbsa.rst (6542 bytes)
2. 1VJ5_pbsa.top (82045 bytes)
3. 1vj5mdout (31698 bytes)
4. mdout (33188 bytes)
5. 1VJ5pbsa.phi (275890 bytes)
6. pbsa.phi (275850 bytes)
7. mdin (178 bytes)
Re: [AMBER] new Mg parameters Jesper Sørensen (Wed May 16 2012 - 11:51:13 PDT)
1. magnesium.dat (192 bytes)
2. magnesium.prep (335 bytes)
Re: [AMBER] Amber 12 cuda test failed Fernando Martín García (Wed May 16 2012 - 23:55:12 PDT)
1. myoglobin_md.out (6855 bytes)
Re: [AMBER] sander error in the decomposed MMGBSA using Ambertools12 and Amber11 Qiong Zhang (Fri May 18 2012 - 14:37:01 PDT)
1. _MMPBSA_complex_gb.mdout.0 (2814 bytes)
Re: [AMBER] sander error in the decomposed MMGBSA using Ambertools12 and Amber11 Bill Miller III (Fri May 18 2012 - 17:20:53 PDT)
1. _MMPBSA_gb_decomp_com.mdin (280 bytes)
2. _MMPBSA_gb_decomp_lig.mdin (239 bytes)
3. _MMPBSA_gb_decomp_rec.mdin (238 bytes)
[AMBER] Amber tools 12 and esp visualization in VMD and PyMol Sudarshan Debnath (Mon May 21 2012 - 12:11:04 PDT)
1. 1VJ5.rst (6542 bytes)
2. 1VJ5.top (82045 bytes)
3. mdout (33011 bytes)
4. pbsa.phi (275890 bytes)
5. Doc1.docx (26725 bytes)
[AMBER] add new functions into Amber10 Xin Geng (Mon May 21 2012 - 12:59:51 PDT)
1. 1.f_ (20144 bytes)
Re: [AMBER] amber99tor and amber99ez force field David Condon (Mon May 21 2012 - 15:04:09 PDT)
1. frcmod.parmCEZ.parmbsc.parmBETA (7831 bytes)
2. residues.parmCEZ.parmbsc (81115 bytes)
Re: [AMBER] sander error in the decomposed MMGBSA using Ambertools12 and Amber11 Qiong Zhang (Mon May 21 2012 - 17:43:27 PDT)
1. _MMPBSA_complex_gb.mdout.0 (10926 bytes)
[AMBER] Amber tools 12 and esp visualization in VMD and PyMol Sudarshan Debnath (Wed May 23 2012 - 06:10:18 PDT)
1. Dear_Wes.docx (559695 bytes)
[AMBER] problem with mol2 to pdb conversion Chris Chris (Mon May 21 2012 - 20:46:04 PDT)
1. test.mol2 (455509 bytes)
2. test_vega.pdb (402637 bytes)
Re: [AMBER] Saving the original position of atoms on using LEaP case (Sun May 27 2012 - 06:25:50 PDT)
1. fix_charmmpdb (443 bytes)
[AMBER] Compile Amber 12 with IBM compilers Yubo Fan (Mon May 28 2012 - 08:33:28 PDT)
1. info_xlc (152059 bytes)
2. info_xlf (126242 bytes)
Re: [AMBER] large deviation on entropy value using ambertools1.5 Jason Swails (Tue May 29 2012 - 10:28:39 PDT)
1. std_dev.patch (1224 bytes)
Re: [AMBER] large deviation on entropy value using ambertools1.5 Cao Yang (Tue May 29 2012 - 19:45:47 PDT)
1. _MMPBSA_complex_nm.out (8220 bytes)
2. _MMPBSA_ligand_nm.out (8220 bytes)
3. _MMPBSA_receptor_nm.out (8220 bytes)
4. FINAL_RESULTS_MMPBSA.dat (2349 bytes)
Re: [AMBER] large deviation on entropy value using ambertools1.5 Jason Swails (Tue May 29 2012 - 20:30:01 PDT)
1. std_dev2.patch (1346 bytes)
Re: [AMBER] Amber 12 on x86_64 CentOS 5 Kevin Parkes (Wed May 30 2012 - 06:25:54 PDT)
1. configure2 (82273 bytes)
Re: [AMBER] Trouble compiling cuda, need help. Jonathan Gough (Wed May 30 2012 - 09:54:23 PDT)
1. compile_log.txt.gz (30015 bytes)
[AMBER] ptraj Hbond analysis shradhey gupta (Thu May 31 2012 - 04:51:14 PDT)
1. hbond.ptraj (358 bytes)
[AMBER] ptraj Hbond analysis shradhey gupta (Thu May 31 2012 - 06:51:00 PDT)
1. hbond.ptraj (358 bytes)
[AMBER] ptraj Hbond analysis shradhey gupta (Thu May 31 2012 - 06:53:26 PDT)
1. hbond.ptraj (358 bytes)
2. anal_hbond.out (9579 bytes)
[AMBER] ptraj Hbond analysis shradhey gupta (Thu May 31 2012 - 06:55:04 PDT)
1. hbond.ptraj (358 bytes)
2. anal_hbond.out (9579 bytes)
[AMBER] base pairs missing from nastruct analysis of canonical B-DNA dodecamer Dean Cuebas (Thu May 31 2012 - 12:00:09 PDT)
1. default.xml (3222 bytes)

Last message date: Thu May 31 2012 - 22:00:02 PDT
Archived on: Sun Dec 22 2024 - 05:54:35 PST

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