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>
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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Received on Mon Nov 21 2011 - 05:30:11 PST
