Re: [AMBER] problem in leap

From: Qinghua Liao <fantasticqhl.gmail.com>
Date: Wed, 16 Nov 2011 21:17:34 +0100

Dear Prof. Case,

Thanks very much for your explanations. Finally I figured it out, I guess
it's resulted from diffenert methods of different softwares on handling
molecules. Thanks.

-- 
Best Regards,
Qinghua
Ph.D. student
Juelich Research Center
On Wed, Nov 16, 2011 at 3:26 PM, David A Case <case.biomaps.rutgers.edu>wrote:
> 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
>
>
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Received on Wed Nov 16 2011 - 12:30:04 PST