VMD-L Mailing List

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Mon Apr 24 2006 - 10:15:42 CDT

(Apologies, sent to wrong address)


attached mail follows:

Hi,
you might want to submit this to NAMD-L and paste in the exact errors
you are getting, and possibly the config file as well. This kind of
error usually means there's something odd about your input.
Best,
Peter

genie lfs wrote:

>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.
>
>