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.
Best Regards
JiYuan
Hi Ji-Yuan,
On 14/11/2011, at 10:15 p.m., Áõ¼ªÔª wrote:
> Hi Ben,
> I am very luck and pleasure to get your instant reply.As you refered in
your first mail,van der Waals parameters of the Manganese I have obtained by
the website
http://www.pharmacy.manchester.ac.uk/bryce/amber(you may take a
look at the attachment).Although I have obtained the parameter with MN2+,I
don't know how to change these MN2+ parameters into metalparm.xml(like zn
<entry mass="65.40" name="ZN" vdwRadius="1.1" potentialWellDepth="0.0125"
element="Zn" hybridization="sp3" description="Zn(II), Merz, PAK,
JACS,113,8262"/>) and metals.xml(like zn </fragment>
> <fragment code="METSM ZN" identity="Zinc(II) Ion" symbol=" ZN"
type="m">
> <atom atNum="30" atmCharge="2.0" bond12="-1" bond13="-2" bond14="-3"
bondAngle="90.0" bondLength="1.0" bondTorsion="180.0" chain="M" identity="ZN
" index="1" type="ZN" symbol="Zn" kind="0"/>
> <alias alias=" ZN " original="ZN "/>
> <alias alias=" ZN" original="ZN "/>).
Please be specific here. What exact pieces of information are you missing,
that would allow you to create an appropriate parameter entry?
> I also would like to need your advises,because I encounter some new
problems:
> (1) when I created the side chain model by hand,I dont know how to add the
ligand with a small molecule that has three oxygen coordnated with two MN2+
in the *_sidechain.bcl.If I dont add the ligand information in that file.
See my earlier response to another of your queries.
> (2) I also runed successfully MCPB -i *_sidechain.bcl -l
*_sidechian.bcl.log.The log showed that MCPB Exited Normally,I can get the
two files with *_sidechain_fc.com and *_sidechain_opt.com,habe these two
files been optimised by gaussian?
No. They are Gaussian input files only. You will need to run the
*_sidechain_opt.com file first, and use its output to run
*_sidechain_fc.com.
Hope that helps,
Ben
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Received on Thu Nov 17 2011 - 22:30:03 PST
