From: ramya narasimhan (ramya_jln_at_yahoo.co.in)
Date: Fri Feb 22 2008 - 04:41:23 CST
I have minimized 100 structures (8 residues) using NAMD minimization. But when I checked that structures in VMD ramaplot, nearly 12% of the structures are in disallowed region. I checked one structure (which has secondary structure out of 100 structures) in ramaplot, even for that,it showed one residue in disallowed region. I minimized the structure in InsightII using Discover (amberff) and viewed the minimized structure in molprobity, it showed 100% of residues in allowed region. And there is difference in the allowed regions in both ramaplot and molprobity. Now I have two questions
1. Is it possible to minimize the structure by making any reasonable changes in the minimization routine? If yes, how ?
2. (Actually it should not be posted in NAMD, but to know from NAMD experts)
Is it possible to minimize NAMD pdb file in CHARMM?
I did it to test for minimization, but charmm is stating error.
Thanks in advance.
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