Hello all,
I read a paper which use AMBER MD simulations. Their analysis contain
the hydrophobic contacts. They define the hydrophobic contact for a
pair of the hydrophobic side chains of residues(Ala, Cys, Phe, Leu,
Met, Ile, Val) was considered to be formed when a minimal distance
between the center of mass of any pair of residues is less than 5.4A.
I read the Ambertools help and find a command "contacts". But it seems
that it could not do the analysis above. So would I ask a question
that how to do this analysis?
The other question is that if I want to constrain the residues with
mask. e.g. I just want to know the interaction among Ala, Cys, Phe.
Can I write like this: :Ala, Cys, Phe.CA?
Thanks!
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Mar 07 2012 - 19:30:02 PST
