Amber Archive Feb 2012 by messages with attachments

Re: [AMBER] MMPBSA problem Urszula Uciechowska (Wed Feb 01 2012 - 00:02:35 PST)
1. LIG.prmtop (80247 bytes)
2. L_lig.crd.1 (6329 bytes)
Re: [AMBER] NMODE list index out of range error Sangeetha B (Wed Feb 01 2012 - 20:18:27 PST)
1. MMPBSA_nm.zip (287072 bytes)
Re: [AMBER] Fwd: about using MMPBSA Tan and Luo method in AMBER 11: discrepancy in ECAVITY values Qin Cai (Thu Feb 02 2012 - 12:33:57 PST)
1. patch_ecavity (738 bytes)
[AMBER] Charge calculation using RESP: MCPB kanika singal (Mon Feb 06 2012 - 04:06:04 PST)
1. 1fx7_ms2_large_mk.log (373692 bytes)
2. 1fx7_ms2_chg1.xml (66707 bytes)
3. 1fx7_ms2_large_mk1.resp2.chg (932 bytes)
4. 1fx7_ms2_large.pdb (5067 bytes)
[AMBER] pmemd test failure when compiling with intel 12.1.2 Vlad Cojocaru (Mon Feb 06 2012 - 07:22:52 PST)
1. test_a_serial.log (100063 bytes)
[AMBER] Fwd: NMODE list index out of range error Sangeetha B (Tue Feb 07 2012 - 03:52:42 PST)
1. MMPBSA_nm.zip (287072 bytes)
[AMBER] error in tleap execution of loadpdb molguin.miners.utep.edu (Tue Feb 07 2012 - 22:09:48 PST)
1. NEWPDB.PDB (4951 bytes)
2. pyrolle.frcmod (1058 bytes)
3. pyrolle.prep (7621 bytes)
4. tleap.log (9054 bytes)
5. Test.pdb (4951 bytes)
Re: [AMBER] AMBER minimization Olena Dobrovolska (Wed Feb 08 2012 - 04:19:21 PST)
1. P1.min.out (117547 bytes)
2. RST.dist (28279 bytes)
Re: [AMBER] Force Field Parameterization -- Torsion Potentials Karl N. Kirschner (Wed Feb 08 2012 - 05:11:55 PST)
1. Relative_Energy_all.ps (23082 bytes)
[AMBER] Fwd: Residue Decomposition Sander Error Hirdesh Kumar (Thu Feb 09 2012 - 20:33:37 PST)
1. _MMPBSA_pb_decomp_com.mdin (352 bytes)
2. _MMPBSA_pb_decomp_lig.mdin (292 bytes)
3. _MMPBSA_pb_decomp_rec.mdin (298 bytes)
Re: [AMBER] Generating topology files for non standard amino acid residue Matthew D Antalek (Mon Feb 13 2012 - 20:55:34 PST)
1. 3fY_2.ac (2959 bytes)
2. mainchain.3fY (386 bytes)
Re: [AMBER] md stopping in TI calculation leila karami (Tue Feb 14 2012 - 01:12:08 PST)
1. free_tg_1_min_v0_0.1.out (18244 bytes)
2. free_tg_1_min_v1_0.1.out (18803 bytes)
Re: [AMBER] ptraj analysis Giachetti Andrea - CERM (Tue Feb 14 2012 - 07:40:06 PST)
1. distance.jpg (14587 bytes)
Re: [AMBER] Change the residue number in pdb file Jan-Philip Gehrcke (Wed Feb 15 2012 - 06:46:51 PST)
1. renumber_pdb_residues.py (5617 bytes)
Re: [AMBER] compiler-dependent error: "Invalid atom or grouping specified in restraint." David A Case (Thu Feb 16 2012 - 06:33:07 PST)
1. sander_restraint_parse_testcase.tar.gz (477420 bytes)
[AMBER] Ligands fly away from binding pocket tian zhu (Sun Feb 19 2012 - 15:30:35 PST)
1. min_sol.in (152 bytes)
2. min_all.in (99 bytes)
3. heat.in (340 bytes)
4. density.in (258 bytes)
5. equil.in (293 bytes)
6. prod.in (204 bytes)
[AMBER] Antechamber Beale, John (Mon Feb 20 2012 - 02:04:32 PST)
1. image001.jpg (23871 bytes)
Re: [AMBER] Problem building octahedral coordinated ligands in LEaP Jesper Sørensen (Mon Feb 20 2012 - 10:38:54 PST)
1. frcmod.dummymg (1212 bytes)
2. md6.off (1913 bytes)
3. example.tleap (344 bytes)
[AMBER] Charges Beale, John (Tue Feb 21 2012 - 02:11:32 PST)
1. image001.jpg (23871 bytes)
Re: [AMBER] Which method is the best way to solve metalloprotein?MCPB or Only consider Electrostatic and VDW JiYuan Liu (Tue Feb 28 2012 - 01:16:04 PST)
1. backbone_rmsd.png (35888 bytes)
2. density.png (23987 bytes)
3. temp.png (22902 bytes)
4. total_energy.png (24310 bytes)
5. backbone_rmsd.png (40437 bytes)
6. density.png (44535 bytes)
7. temp.png (50032 bytes)
8. total_energy.png (68785 bytes)
9. ca1.pdb (2133 bytes)
10. ca.pdb (1485 bytes)
Re: [AMBER] strip and use of distance-based mask Nanna Holmgaard List (Wed Feb 29 2012 - 08:32:48 PST)
1. distancemask.tar.gz (452868 bytes)

Last message date: Wed Feb 29 2012 - 14:30:02 PST
Archived on: Mon Dec 23 2024 - 05:54:25 PST

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