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

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From: JiYuan Liu <liujiyuan.nwsuaf.edu.cn>
Date: Tue, 29 Nov 2011 01:34:26 +0800

   Hi Benï¼
      Could you suggest me to change the torsion value in 93 line(addFragment
   terminal/CH3 bd /NAME/CLR/AN1-6/.CB. ag /NAME/CLR/AN1-6/.CG. tr
   /NAME/CLR/AN1-6/.ND2 131.0),the torsion 131.0 is not reasonable in this
   line?Please give me the detail.

     Best Regards

     JiYuan
   -------- åå§é®ä»¶ --------
   åä»¶äºº: Ben Roberts <ben.roberts.geek.nz>
   åéæ¶é´: 2011-11-28 23:57
   æ¶ä»¶äºº: AMBER Mailing List <amber.ambermd.org>
   ä¸»ãé¢: Re:Re: [AMBER] How MCPB add ligand with
   asmallmoleculein*_siderchain.bcl
   Hi JiYuan,
   On 28/11/2011, at 7:26 a.m., JiYuan Liu wrote:
> I have upload my current BCL script and the original PDB to my attachment,
   please have a look for them. Thank you.
   I see them.
   In my previous email, I suggested that you try adjusting the values of your
   torsional angles, that is the eighth argument to the addFragment command
   (you can recognise this because it's a number). Have you had a chance to do
   so?
   Regards,
   Ben
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Received on Mon Nov 28 2011 - 10:00:02 PST