Amber Archive Feb 2010: by messages with attachments

Re: [AMBER] errors in leap case (Mon Feb 01 2010 - 08:19:13 PST)
1. leaprc.ff03.r1 (4559 bytes)
[AMBER] Test log s. Bill (Mon Feb 01 2010 - 09:48:10 PST)
1. test.log (4382 bytes)
2. TEST_FAILURES.diff (279 bytes)
Re: [AMBER] Test log s. Bill (Mon Feb 01 2010 - 12:41:28 PST)
1. TEST_FAILURES.diff (184352 bytes)
[AMBER] Information regarding how to group atoms for ionic liquid dhilip kumar ramalingam (Wed Feb 03 2010 - 01:10:31 PST)
1. n-Butyl-3-methylimidazolium.pdf (136982 bytes)
[AMBER] Problem reading PDB residues in AmberTools-1.3 Hopkins, Robert (Thu Feb 04 2010 - 18:10:04 PST)
1. leap.log (281936 bytes)
[AMBER] load pdb into xleap Jim Miller (Fri Feb 05 2010 - 01:12:12 PST)
1. model.pdb (159075 bytes)
[AMBER] FW: Problem reading PDB residues in AmberTools-1.3 Hopkins, Robert (Fri Feb 05 2010 - 07:37:09 PST)
1. leap.log (281936 bytes)
2. IRxequ15ctr.pdb (992312 bytes)
[AMBER] Problem in Ptraj Kshatresh Dutta Dubey (Fri Feb 05 2010 - 22:41:12 PST)
1. ptraj_all.in (1564 bytes)
2. ptraj_all.in_out (14302 bytes)
[AMBER] Regarding restraints during minimisation stage 1 in explicit solvent Asfa Ali (Sun Feb 07 2010 - 21:23:12 PST)
1. w_wat_min1.out (18302 bytes)
[AMBER] sleap crash with single water molecule and amoeba Neil Henson (Mon Feb 08 2010 - 06:14:45 PST)
1. signature.asc_ (199 bytes)
[AMBER] Antechamber: imidazole=aromatic, imidazolium=not aromatic? Gabriel Rocklin (Mon Feb 08 2010 - 23:33:17 PST)
1. imidazole.mol2 (979 bytes)
2. imidazole_out.prepi (1100 bytes)
3. imidazolium.mol2 (1078 bytes)
4. imidazolium_out.prepi (1194 bytes)
[AMBER] Reducing RMS errors in TI calculation ET (Tue Feb 09 2010 - 13:02:48 PST)
1. DV_DL_step1_V0_complex.jpg (61641 bytes)
2. DV_DL_step2_V0_complex.jpg (73768 bytes)
3. DV_DL_step3_V0_complex.jpg (62073 bytes)
RE: [AMBER] QM/MM new parameters s. Bill (Tue Feb 09 2010 - 14:40:08 PST)
1. qm2_parameters.h (147004 bytes)
2. Data.out (18319 bytes)
[AMBER] strange behavior in QMMM simulation M. L. Dodson (Thu Feb 11 2010 - 12:35:25 PST)
1. CAB.in (891 bytes)
2. qmmm_region.pdb (1772 bytes)
Re: [AMBER] mm_pbsa statistics problem Marina Grabar (Fri Feb 12 2010 - 03:57:24 PST)
1. snapshot_DNA_TD22_2_com.all.out (199973 bytes)
2. snapshot_DNA_TD22_2_lig.all.out (178484 bytes)
3. snapshot_DNA_TD22_2_rec.all.out (178420 bytes)
Re: [AMBER] sleap crash with single water molecule and amoeba Neil Henson (Tue Feb 16 2010 - 08:20:22 PST)
1. signature.asc_ (199 bytes)
Re: [AMBER] relaxed PES Jason Swails (Wed Feb 17 2010 - 12:05:06 PST)
1. scan.sh (2705 bytes)
[AMBER] Segmentation fault with xleap while loading a leaprc Nicolas Sapay (Thu Feb 18 2010 - 05:48:00 PST)
1. nicolas_sapay.vcf (333 bytes)
Re: [AMBER] Segmentation fault with xleap while loading a leaprc Nicolas Sapay (Thu Feb 18 2010 - 06:29:54 PST)
1. nicolas_sapay.vcf (333 bytes)
Re: [AMBER] Segmentation fault with xleap while loading a leaprc Nicolas Sapay (Thu Feb 18 2010 - 08:42:59 PST)
1. nicolas_sapay.vcf (333 bytes)
[AMBER] chamber - psf/pdb from VMD Balazs Jojart (Thu Feb 18 2010 - 13:45:18 PST)
1. ala_ala_ala.pdb (2658 bytes)
2. ala_ala_ala.pdb.BAK (2747 bytes)
3. ala_ala_ala.psf.BAK (9205 bytes)
Re: [AMBER] Segmentation fault with xleap while loading a leaprc Nicolas Sapay (Fri Feb 19 2010 - 06:42:00 PST)
1. nicolas_sapay.vcf (333 bytes)
Re: [AMBER] Re: Antechamber: imidazole=aromatic, imidazolium=not aromatic? Gabriel Rocklin (Fri Feb 19 2010 - 15:51:24 PST)
1. ATOMTYPE_GFF.DEF (15774 bytes)
[AMBER] trajectory alignment to a reference frame Oliver Kuhn (Wed Feb 24 2010 - 07:17:39 PST)
1. traj_alignment.png (199536 bytes)
RE: [AMBER] Re: Antechamber: imidazole=aromatic, imidazolium=not aromatic? Niel Henriksen (Wed Feb 24 2010 - 17:42:36 PST)
1. amino-benzimidazole.mol2 (1012 bytes)
2. amino-benzimidazole.output (1371 bytes)
3. amino-1-methyl-benzimidazole.mol2 (1188 bytes)
4. amino-3H-1-methyl-benzimidazolium.mol2 (1246 bytes)
[AMBER] Simple question on EM Shaandar Nyamtulga (Wed Feb 24 2010 - 19:42:03 PST)
1. exam.min1.out (14755 bytes)
[AMBER] Query about xmin gunajyoti das (Wed Feb 24 2010 - 23:58:14 PST)
1. min1.out (11154 bytes)
[AMBER] Problem in MM-PBSA Hyma vathi (Thu Feb 25 2010 - 01:54:48 PST)
1. min.out (13933 bytes)
2. heat.out (119399 bytes)
Re: [AMBER] Question on applying restraints in absolute dG calculations with TI in Amber 10 steinbrt.rci.rutgers.edu (Thu Feb 25 2010 - 02:15:13 PST)
1. bugfix.31 (906 bytes)
[AMBER] Query about LMOD gunajyoti das (Thu Feb 25 2010 - 03:53:31 PST)
1. min1.out (196951 bytes)
[AMBER] msd calculation using ptraj diffusion Monika Sharma (Fri Feb 26 2010 - 22:05:39 PST)
1. time-ptraj.pdf (75195 bytes)
RE: [AMBER] msd calculation using ptraj diffusion hannes.loeffler.stfc.ac.uk (Sat Feb 27 2010 - 01:22:20 PST)
1. winmail.dat (0 bytes)
RE: [AMBER] msd calculation using ptraj diffusion hannes.loeffler.stfc.ac.uk (Sat Feb 27 2010 - 05:18:59 PST)
1. winmail.dat (0 bytes)
[AMBER] xmin_verbosity gunajyoti das (Sat Feb 27 2010 - 05:40:59 PST)
1. min1.out (73323 bytes)

Amber Archive Feb 2010 by messages with attachments