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Hi Ben,
I have produced the XML file for the ligand of small molecule,you could
have a look in my attachment.
How can I use the ca.XML within bcl scripts,would you like to tell me the
detail procedure,thank you very much.
Best Regards
JiYuan
-------- åå§é®ä»¶ --------
å件人: JiYuan Liu<liujiyuan.nwsuaf.edu.cn>
åéæ¶é´: 2011-11-20 11:55
æ¶ä»¶äºº: ben<ben.roberts.geek.nz>;amber
主ãé¢: Re:Re: [AMBER]How MCPB add ligand with a small molecule
in*_siderchain.bcl
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?
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>
主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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