> <A0><A0><A0> We are going to built a protein model in which one amino acid
> was modified to non-standard residue experimentally.<A0> After
> obtaining the prepin and frcmod files by ANTECHAMBER, what else
> should be done to make this resdiue correctly bond to the next and
> previous residues?
Assigning connect0 and connect1 and head and tail after loading the
prepin will set up the residue to bond when it is loaded in a pdb
file. Best to set the atoms like this then saveoff the residue and
thenceforward loadoff the result, rather than always loadamberprep.
There used to be setup scripts for generating the residue libs, and
these would exemplify how it's done. Possibly also there is a demo
or more showing it.
Bill
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri May 14 2010 - 10:00:05 PDT
