Re: [AMBER] How MCPB add ligand withasmallmoleculein*_siderchain.bcl

From: Ben Roberts <>
Date: Fri, 2 Dec 2011 10:23:19 -0500

Hi JiYuan,

On 29/11/2011, at 12:03 p.m., JiYuan Liu wrote:

> Hi Ben,
> My e-mail client seems to be creating new threads all the time?It may be
> misunderstanded me,I still reply my the email since you reminded me at the
> first time.No more than I would like to delete the first "Re:" and only
> remain one "Re:"in the title of every reply´╝it could cause to create new
> threads?If yes,I am so sorry.

Yes, that could be it. Some e-mail clients interpret every change to the subject line, no matter how small, as an indication that a new thread should be started. Whatever you did differently this time, it worked.

> I have found that the H3 torsion or angle is not correct in the small
> molecule when I runed *_addHs.bcl.I tried to change the torsion of H3 in the
> lib XML of the small molecule,in fact nothing has improved.Could I need
> toadd fragments like CH3 to my small molecule?

I'm not sure without seeing your BCL scripts. So I'll keep a lookout for them.


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Received on Fri Dec 02 2011 - 07:30:05 PST
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