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

From: JiYuan Liu <liujiyuan.nwsuaf.edu.cn>
Date: Tue, 22 Nov 2011 10:20:11 +0800

   Hi Ben,
       I have received your reply email with the attachment,but I cant open the
   your email with the attachment.

                                 Best Regards

                                 JiYuan
   -------- 转åé®ä»¶ä¿¡æ¯ --------
   å件人: JiYuan Liu<liujiyuan.nwsuaf.edu.cn>
   åéæ¶é´: 2011-11-21 21:12
   æ¶ä»¶äºº: ben<ben.roberts.geek.nz>;amber
   ä¸»ãé¢: Fw:Re: [AMBER] How MCPB add ligand with a small molecule
   in*_siderchain.bcl
   Hi Ben
         I have obtain the *.xml file of ligand with a small molecule,it is so
   simple like below:
   ---------------------ca.xml-------------------------------------------------
   ----
   <?xml version='1.0' ?>
   <parms name='ca'>
       <types />
       <bondLengths />
       <bondAngles />
       <bondTorsions />
       <bondImpropers>
           <entry t1='c3' t2='o' t3='c' t4='o' Nt='2' Vn='1.1' gamma='180'
   groupName='ca' />
       </bondImpropers>
   </parms>
   but I don't understand add ca.xml in which file,for example in
   *_sidechain.bcl,which Syntax could I use to build the ligand with a small
   molecule,please guide me,thank you.

   Best Regards

   JiYuan
   -------- åå§é®ä»¶ --------
   å件人: Ben Roberts <ben.roberts.geek.nz>
   åéæ¶é´: 2011-11-19 01:03
   æ¶ä»¶äºº: JiYuan Liu <liujiyuan.nwsuaf.edu.cn>
   ä¸»ãé¢: Re:Re: [AMBER] How MCPB add ligand with a small molecule
   in*_siderchain.bcl
   Hi JiYuan,
   On 18/11/2011, at 1:17 a.m., JiYuan Liu wrote:
> Hi Ben,
> 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?
> You told me add ligand parameters with a small molecule based on the
   GAFF force field parameters. I have looked at the files 'atomtypes_gaff.xml'
   and 'parm_gaff.xml' under $AMBERHOME/dat/mtkpp,unfortunately I dont know how
   to use these files to write the ligand code in the *_sidechain.bcl,could you
   give me an example,thank you.
   Start by preparing a mol2 file of your ligand (without the metals) and
   running it through Antechamber producing a prepi file as output. See the
   Antechamber section of the AmberTools manual for instructions on how to do
   the latter step. Once you have your prepi file, run it through prep2xml (an
   MTK++ program) to produce an XML file that you can then use within bcl
   scripts.
   Regards,
   Ben
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Received on Mon Nov 21 2011 - 18:30:03 PST
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