Amber Archive Oct 2013: by messages with attachments

Re: [AMBER] RED-VIII.52 Problem--cannot find scratch file and punch file Dongshan Wei (Mon Sep 30 2013 - 19:05:43 PDT)
1. rungms (32932 bytes)
[AMBER] Ambiguity in PMF calculated from umbrella sampling of a dihedral angle Mohan Pradhan (Tue Oct 01 2013 - 04:11:32 PDT)
1. 180_pmf.png (7785 bytes)
2. 0_pmf.png (7107 bytes)
Re: [AMBER] Ambiguity in PMF calculated from umbrella sampling of a dihedral angle Mohan Pradhan (Tue Oct 01 2013 - 06:11:22 PDT)
1. 180_all_dihedrals.png (43729 bytes)
2. 0_all_dihedrals.png (44022 bytes)
[AMBER] about error with "Must have more residues than processors!" Biao Ma (Tue Oct 01 2013 - 09:00:20 PDT)
1. 1ag2.equil.mdout.bak (6378 bytes)
2. 1ag2.heat.mdout.bak (7549 bytes)
3. blog.7458 (20251 bytes)
Re: [AMBER] Fwd: DMPC GAFF lipid membrane is freezing at 303 K. Subbarao Kanchi (Tue Oct 01 2013 - 19:25:11 PDT)
1. md.in (226 bytes)
[AMBER] Questions about VDW process of thermodynamic integration method 袁丹丹 (Thu Oct 03 2013 - 05:57:43 PDT)
1. 0and1.png (58536 bytes)
[AMBER] Questions about VDW process of thermodynamic integration method‏ 袁丹丹 (Thu Oct 03 2013 - 06:06:54 PDT)
1. 0and1.png (58536 bytes)
Re: [AMBER] The Error when I run MdoutAnalysizer.py Jason Swails (Thu Oct 03 2013 - 07:36:21 PDT)
1. mdoutanalyzer.patch (979 bytes)
Re: [AMBER] QM/MM MMPBSA Jason Swails (Fri Oct 04 2013 - 04:07:07 PDT)
1. mmpbsa.patch (3191 bytes)
Re: [AMBER] QM/MM MMPBSA Jason Swails (Fri Oct 04 2013 - 06:59:18 PDT)
1. mmpbsa.patch2 (1269 bytes)
Re: [AMBER] MPI install with openmpi Makoto Chikira (Sat Oct 05 2013 - 08:37:08 PDT)
1. config.h (5027 bytes)
Re: [AMBER] MPI install with openmpi Makoto Chikira (Sun Oct 06 2013 - 06:36:27 PDT)
1. 10-06_11-20-16.diff (174146 bytes)
2. 10-06_11-20-16.log (92554 bytes)
[AMBER] Soft-core questions for TI method yuandandan (Mon Oct 07 2013 - 00:43:29 PDT)
1. question.doc (89088 bytes)
2. three_cav-1.zip (593580 bytes)
Re: [AMBER] problem in creating .mol2 and .frcmod files Vijayalaxmi Sahoo (Mon Oct 07 2013 - 08:33:16 PDT)
1. bmim.pdb (1949 bytes)
2. bmim.mol2 (2627 bytes)
3. frcmod.bmim (222 bytes)
Re: [AMBER] Problem in creating .mol2 and .frcmod files Vijayalaxmi Sahoo (Wed Oct 09 2013 - 06:38:28 PDT)
1. bmim.pdb (1949 bytes)
2. bmim.mol2 (2627 bytes)
3. frcmod.bmim (222 bytes)
Re: [AMBER] RED-VIII.52 Problem--cannot find scratch file and punch file FyD (Thu Oct 10 2013 - 01:04:30 PDT)
1. Dongshan.txt (1510 bytes)
[AMBER] How to run npt simulation if IFBOX=0 in .prmtop file? Dongshan Wei (Thu Oct 10 2013 - 05:43:30 PDT)
1. nvt_vacuum.rst (70255 bytes)
2. supercell.prmtop (586525 bytes)
[AMBER] Fwd: Shifting molecules by a box length Heribert Reis (Thu Oct 10 2013 - 07:41:11 PDT)
1. fr.tbz (692285 bytes)
[AMBER] solvate box Rasha Alqus (Thu Oct 10 2013 - 08:35:50 PDT)
1. PAINT1.png (8818 bytes)
2. PAINT2.png (9412 bytes)
[AMBER] I/O errors while using CHARMM psf with CHAMBER Debayan Chakraborty (Thu Oct 10 2013 - 16:23:01 PDT)
1. rna_charmm.crd (18133 bytes)
2. rna.psf (72573 bytes)
[AMBER] tleap cannot handle dummies in the middle? Hannes Loeffler (Fri Oct 11 2013 - 09:18:43 PDT)
1. pert.tar.gz (1471 bytes)
[AMBER] Problem in deriving RESP charges with RED-3.52 tools Sajeewa Pemasinghe (Sat Oct 12 2013 - 23:12:39 PDT)
1. Mol_red1.log (128459 bytes)
2. Mol_red1.p2n (570 bytes)
Re: [AMBER] inquiry Vaibhav Dixit (Mon Oct 14 2013 - 02:43:03 PDT)
1. mdread.F90 (127271 bytes)
[AMBER] about rms atomic fluctuation for protein crystal .thank you very much! Yongxiu Li (Mon Oct 14 2013 - 04:36:06 PDT)
1. figure9.png (342484 bytes)
2. figure8.png (374882 bytes)
3. 3-3-3.png (29922 bytes)
[AMBER] Exceed character limit in bellyrestraint mask selection Mike Limb (Tue Oct 15 2013 - 08:29:18 PDT)
1. optimised_resid_mask.dat (859 bytes)
[AMBER] CYM residue problem(MCPB) houcemeddine (Thu Oct 17 2013 - 08:29:17 PDT)
1. 1CK7_fixed.pdb (275812 bytes)
2. 1CK7_settings.bcl (603 bytes)
3. 1CK7_sidechain.bcl (2877 bytes)
4. 1CK7_sidechain.mol (5076 bytes)
Re: [AMBER] Exceed character limit in bellyrestraint mask selection Mike Limb (Fri Oct 18 2013 - 10:35:44 PDT)
1. optimised_resid_mask.dat (859 bytes)
[AMBER] High Temperature at NSTEP = 0 Alessandra Lacetera (Tue Oct 22 2013 - 08:41:12 PDT)
1. solvate_complex_md1.outmd (19544 bytes)
[AMBER] Script? Beale, John (Tue Oct 22 2013 - 10:30:30 PDT)
1. image001.jpg (23871 bytes)
[AMBER] Regarding radial distribution function MOHD HOMAIDUR RAHMAN (Thu Oct 24 2013 - 04:46:48 PDT)
1. ts20_W_O_W_O_carnal.jpg (24253 bytes)
Re: [AMBER] MMPBSA.py error Rasha Alqus (Thu Oct 24 2013 - 06:02:32 PDT)
1. _MMPBSA_normal_traj_cpptraj.out (27786 bytes)
2. _MMPBSA_receptor.pdb (58327 bytes)
3. _MMPBSA_receptor_gb.mdout.0 (662 bytes)
Re: [AMBER] why are pres_X, pres_Y, and pres_Z different? Jose Borreguero (Mon Oct 28 2013 - 08:07:57 PDT)
1. crystal.png (236103 bytes)
Re: [AMBER] about rms atomic fluctuation for protein crystal .thank you very much! Yongxiu Li (Tue Oct 29 2013 - 01:03:39 PDT)
1. arf.dat (1025 bytes)

Amber Archive Oct 2013 by messages with attachments