Hi JiYuan,
On 23/11/2011, at 12:00 PM, JiYuan Liu wrote:
>
> Hi Ben,
> I have added the ligand in the side chain model,but the torsion of a H
> atom of the ligand is located the wrong place,I have taken n times to try to
> solve this problem,but I failed finally.I have uploaded the XML file of the
> ligand and the pdb of the side chain model to the attachment,please help
> me,thank you.
It would have been useful for us to also see your current BCL script and the original PDB you used as its input. However, my response would probably still have been the same, namely:
Did you try different values for the torsional angles when adding methyl groups and other fragments in your BCL script? I have found by experience that a strange value (i.e., something that's not a multiple of 60 degrees) is often needed to produce chemically reasonable geometries.
Regards,
Ben
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Received on Fri Nov 25 2011 - 07:30:05 PST
