On Wed, Nov 16, 2011, Qinghua Liao wrote:
>
> I have one problem in leap. When I load a pdb file of a protein into tleap
> with ff99SB, and check it, there are some missing parameters like these:
>
> Could not find bond parameter for: CT - O
Looks to me like the conect records in rec1.pdb are causing problems. Try
deleting them. Since you have three disulfide bonds, you should change the
corresponding CYS residues to CYX, then use the "bond" command in LEaP to
construct them. See the example on p. 17 of the Amber Users' Manual.
...dac
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Nov 16 2011 - 06:30:05 PST
