Re: [AMBER] How MCPB add ligand with a small molecule in*_siderchain.bcl

From: Ben Roberts <ben.roberts.geek.nz>
Date: Tue, 22 Nov 2011 23:00:42 -0500

Hi JiYuan,

> Whether add fragment with Methyl terminating groups is a necessory procedure in create *_sidechain.bcl?If not add the fragment,could the *_sidechain.bcl be generate the accurate results?

(I thought I had answered this question; if I have duplicated it, my apologies.)

Yes, the methyl groups are necessary. Without them, your cluster will have several dangling bonds.

Regards,
Ben
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Received on Tue Nov 22 2011 - 20:30:03 PST
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