Amber Archive Jan 2011: by messages with attachments

[AMBER] calculations failed on GPU with ntr=1 (with bugfix 11 applied) Dmitry Mukha (Sun Jan 02 2011 - 06:12:13 PST)
1. dens.out (51611 bytes)
2. dens.out (49027 bytes)
Re: [AMBER] MMPBSA.py.MPI - Output discrepancies George Tzotzos (Tue Jan 04 2011 - 10:03:56 PST)
1. FINAL_DECOMP__MMPBSA.dat (116386 bytes)
2. FINAL_RESULTS_MMPBSA.dat (7594 bytes)
Re: [AMBER] about the Sietraj xuemeiwang1103 (Wed Jan 05 2011 - 05:03:17 PST)
1. eqxx.rar (286569 bytes)
[AMBER] heavy atom rms Beale, John (Wed Jan 05 2011 - 05:06:26 PST)
1. image001.jpg (10569 bytes)
2. spc_file.rms.txt (2520 bytes)
[AMBER] Drifting RMSD George Tzotzos (Fri Jan 07 2011 - 10:32:58 PST)
1. prod_rmsd.png (54199 bytes)
2. equil_rmsd.png (57981 bytes)
Re: [AMBER] how to add phosphate group in protein Sangita Kachhap (Sat Jan 08 2011 - 01:45:22 PST)
1. PHD_tleap.pdb (264150 bytes)
2. min1.pdb (264150 bytes)
[AMBER] How to build Amber topology and other files for inorganic crystalline material? malay rana (Sun Jan 09 2011 - 02:06:52 PST)
1. 1unit.xyz (19449 bytes)
[AMBER] water simulation subrata paul (Mon Jan 10 2011 - 06:21:38 PST)
1. 20_rdf_ow_ow_iwr_standard.ps (12283 bytes)
[AMBER] PowerEdge M710 with Intel Xeon Siavoush Dastmalchi (Thu Jan 13 2011 - 03:11:17 PST)
1. winmail.dat (2432 bytes)
[AMBER] bad atom type: IP MMPBSA.py sodium Na+ ion [SOLVED] Oliver Grant (Fri Jan 14 2011 - 03:03:30 PST)
1. sodium_gb.patch (536 bytes)
[AMBER] Protein-Water Interaction Energy Beale, John (Fri Jan 14 2011 - 05:00:18 PST)
1. image001.jpg (10569 bytes)
Re: [AMBER] Protein-Water Interaction Energy Jason Swails (Fri Jan 14 2011 - 05:49:51 PST)
1. energyvectors.sh (5680 bytes)
Re: [AMBER] Torsional parameters for S-C-C-N bond Jason Swails (Tue Jan 18 2011 - 10:26:52 PST)
1. scan.sh (2705 bytes)
[AMBER] antechamber is failing for a molecule Alan Wilter Sousa da Silva (Wed Jan 19 2011 - 03:30:04 PST)
1. TB11_prot.pdb (2054 bytes)
2. TB11_noprot.pdb (1975 bytes)
[AMBER] missing parameter not present in antechamber generated frcmod Sangita Kachhap (Wed Jan 19 2011 - 09:42:20 PST)
1. PHD_ideal.sdf (1483 bytes)
2. PHD_ideal.pdb (3584 bytes)
3. PHD_ideal.prepin (1922 bytes)
[AMBER] MMPBSA.py.MPI Nmode problem filip fratev (Wed Jan 19 2011 - 14:26:53 PST)
1. mmpbsa.out (5370 bytes)
Re: [AMBER] MMPBSA.py.MPI Nmode problem Jason Swails (Thu Jan 20 2011 - 09:13:24 PST)
1. MacOSX_gcc_44_accelerate.dat (2121 bytes)
2. Linux_em64t_gnu44.dat (2118 bytes)
3. Linux_x86_64_pgi10.6.dat (2118 bytes)
4. Linux_em64t_intel11.1.069_MKL.dat (2118 bytes)
Re: [AMBER] maximum number of atoms Marc-André Dubois (Thu Jan 20 2011 - 18:58:32 PST)
1. Trimer1.pdb (15553 bytes)
[AMBER] contacts Beale, John (Fri Jan 21 2011 - 07:01:01 PST)
1. image001.jpg (10569 bytes)
[AMBER] RE : Dihedral parameters for TFE with GAFF ABEL Stephane 175950 (Fri Jan 21 2011 - 09:21:52 PST)
1. winmail.dat (3375 bytes)
[AMBER] Ptraj for diffusion coefficient of water Ganesh Kamath (Fri Jan 21 2011 - 12:52:54 PST)
1. diffusion_water.agr (9807 bytes)
2. tip.top (415817 bytes)
Re: [AMBER] Ptraj for diffusion coefficient of water Sergio R Aragon (Fri Jan 21 2011 - 15:10:19 PST)
1. Case_Drot_MD_JPC_08.pdf (639481 bytes)
Re: [AMBER] Ptraj for diffusion coefficient of water Ganesh Kamath (Sat Jan 22 2011 - 12:32:33 PST)
1. frcmod.tip3p (275 bytes)
[AMBER] Query regarding unusual water box in vmd Hirdesh Kumar (Mon Jan 24 2011 - 22:05:38 PST)
1. tleap.png (729335 bytes)
2. pymold.png (818388 bytes)
Re: [AMBER] Fwd: Query regarding unusual water box in vmd Hirdesh Kumar (Tue Jan 25 2011 - 02:22:32 PST)
1. model_wat.rar (507708 bytes)
[AMBER] Query regarding parmchk poll.chemie.uni-hamburg.de (Wed Jan 26 2011 - 01:49:57 PST)
1. paullone.mol2 (3976 bytes)
[AMBER] GPU vs CPU test Massimiliano Porrini (Thu Jan 27 2011 - 07:06:29 PST)
1. GPUvsCPU.ps (60720 bytes)
Re: [AMBER] NaN error in .rst files filip fratev (Thu Jan 27 2011 - 07:33:30 PST)
1. 1out.rst.tar.gz (2843477 bytes)
Re: [AMBER] Doubts in the installation of Amber11 Ben Roberts (Mon Jan 31 2011 - 10:57:02 PST)
1. smime.p7s (2670 bytes)
Re: [AMBER] Doubts in the installation of Amber11 Ben Roberts (Mon Jan 31 2011 - 11:21:55 PST)
1. smime.p7s (2670 bytes)

Amber Archive Jan 2011 by messages with attachments