Amber Archive Jan 2013 by messages with attachments

Re: [AMBER] bad atom type: f Vaibhav Dixit (Fri Jan 04 2013 - 20:16:58 PST)
1. mdread.F90 (127271 bytes)
Re: [AMBER] Query regarding GB calculation on a protein with FE using MMPBSA.py Prajwal Nandekar (Wed Jan 09 2013 - 06:04:25 PST)
1. mdread.f (112928 bytes)
Re: [AMBER] bad atom type: f Date, Mihir (Thu Jan 10 2013 - 13:06:03 PST)
1. mmpbsa_py.clean.out (814 bytes)
2. mmpbsa_py.stacktrace.out (191 bytes)
3. mmpbsa_py_decomp.clean.out (5535 bytes)
[AMBER] antechamber problem Changqing Yan (Thu Jan 10 2013 - 19:15:45 PST)
1. ligand.pdb (5066 bytes)
[AMBER] Simulating Folic Acid JD John (Thu Jan 10 2013 - 22:53:10 PST)
1. fol_msd.pdb (3455 bytes)
Re: [AMBER] installation problem JD John (Fri Jan 11 2013 - 09:38:37 PST)
1. amber12_install.sh (574 bytes)
[AMBER] Problem with Identification of bonds Volker Lesch (Mon Jan 14 2013 - 06:33:07 PST)
1. FSI.inpcrd (377 bytes)
2. FSI.prmtop (11066 bytes)
[AMBER] xlead aentrena (Tue Jan 15 2013 - 04:03:43 PST)
1. xleap_image.png (585586 bytes)
[AMBER] Is it possible to do TI calculations with pmemd? Anna Bauß (Tue Jan 15 2013 - 07:10:07 PST)
1. anna_bauss.vcf (348 bytes)
Re: [AMBER] Is it possible to do TI calculations with pmemd? Anna Bauß (Wed Jan 16 2013 - 00:23:47 PST)
1. anna_bauss.vcf (348 bytes)
Re: [AMBER] A link atoms between protein and sugar! john Kerk (Thu Jan 17 2013 - 00:40:13 PST)
1. FUL.mol2 (4637 bytes)
Re: [AMBER] problem starting amber Ayesha Fatima (Fri Jan 18 2013 - 06:53:54 PST)
1. 35D.gif (2012 bytes)
Re: [AMBER] Citrate ion (-3) parameters moitrayee.mbu.iisc.ernet.in (Sat Jan 19 2013 - 05:27:17 PST)
1. out.p2n (1731 bytes)
2. o1.mol2 (1619 bytes)
Re: [AMBER] [AMBER: gauche effect in OS-CT-CT-F Karl N. Kirschner (Mon Jan 21 2013 - 02:20:49 PST)
1. Figure_E.gaff.pdf (6590 bytes)
2. Figure_E.parm99SB.pdf (6573 bytes)
3. torsion_rotation.png (76048 bytes)
[AMBER] amber11 installation test files Mary Varughese (Mon Jan 21 2013 - 02:28:40 PST)
1. 10-29_11-50-30.diff (22168 bytes)
2. 10-29_11-50-30.log (71459 bytes)
[AMBER] Bug in amber12, pmemd ch2int function Ake Sandgren (Mon Jan 21 2013 - 03:50:35 PST)
1. fix-pmemd-ch2int-inner-loop-wrong-variable (1349 bytes)
Re: [AMBER] Citrate ion (-3) parameters moitrayee.mbu.iisc.ernet.in (Mon Jan 21 2013 - 09:39:00 PST)
1. CIT.mol2 (1901 bytes)
2. out.p2n (2103 bytes)
3. CIT.off (3191 bytes)
4. CIT.frcmod (2634 bytes)
Re: [AMBER] KCl crystals with Dang parameters ? Thomas Cheatham (Wed Jan 23 2013 - 16:41:00 PST)
1. tmp.pdf (9871 bytes)
[AMBER] TI alpha-beta glucose Glycam06h Kepa K. Burusco (Fri Jan 25 2013 - 05:42:45 PST)
1. gluTIallAtoms.tgz (84475 bytes)
[AMBER] Exiting due to the presence of inconsistent SHAKEH hydrogen clusters Sanjib Paul (Tue Jan 29 2013 - 04:22:28 PST)
1. wat.off (1362 bytes)
[AMBER] Fwd: Regarding the problem with ligand conformation aneesh cna (Tue Jan 29 2013 - 05:12:38 PST)
1. crystal.png (12028 bytes)
2. QM.png (17265 bytes)
3. simulation.png (16879 bytes)
Re: [AMBER] patching problem amber12 Vaibhav Dixit (Tue Jan 29 2013 - 21:27:54 PST)
1. patch_amber.py (42927 bytes)
Re: [AMBER] How to save secondary structure gnuplot as image Daniel Roe (Wed Jan 30 2013 - 10:03:25 PST)
1. Gnu2jpg.sh (729 bytes)
[AMBER] two fold difference between MMPBSA.py and NAMDenergy plugin in vmd 1.9.1 dbaogen (Wed Jan 30 2013 - 22:10:55 PST)
1. Catch.jpg (149254 bytes)
Re: [AMBER] Fwd: Regarding the problem with ligand conformation aneesh cna (Thu Jan 31 2013 - 03:35:56 PST)
1. MOL.prep (2895 bytes)
2. MOL.frcmod (10965 bytes)
Re: [AMBER] Fwd: Regarding the problem with ligand conformation Karl N. Kirschner (Thu Jan 31 2013 - 08:42:42 PST)
1. atom_labels.png (59193 bytes)
2. atom_types.png (55797 bytes)
3. rotation_QM.png (207483 bytes)
4. Energy_curves.png (6098 bytes)
5. partial_atomic_charges.png (88928 bytes)
Re: [AMBER] AMBER 4.1 Manual David A Case (Wed Jan 30 2013 - 15:02:52 PST)
1. amber4.1_manual.pdf (1062375 bytes)
[AMBER] mmPBSA and restraint energy decreasing psu4.uic.edu (Thu Jan 31 2013 - 15:37:29 PST)
1. mmPBSA_question_2.JPG (25722 bytes)

Last message date: Thu Jan 31 2013 - 21:00:02 PST
Archived on: Fri Dec 20 2024 - 05:54:44 PST

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