VMD-L Mailing List

From: genie lfs (lfs.use_at_gmail.com)
Date: Mon Apr 24 2006 - 05:06:32 CDT

hello all..
i had to model a protein using different templates.
this protein was to be simulated to study interactions .when i ran a
energy minimisation of the structure , namd breaks down saying " bad
global count error , bad dihedrals , bad bond angels"..
can i correct the bad dihedrals using VMD ? or should i increase the
cutoff and go with the simulation(as mentioned, but am not for this
idea)

can any one suggest me what to do?
please.
ps; i have done a what if check on this protein and found a few
errors. can i correct them using VMD or is there any protein structure
corrrection server which i can submit.