On Tue, Oct 9, 2012 at 12:59 PM, Sangeetha B <sangeetha.bicpu.edu.in> wrote:
> Dear Amber users,
>
> I have already posted it a few days back. Since I did not get any replies
> yet and my query lies unsolved, I am reposting this. Sorry for the repost.
>
> I am using MCPB to generate prep and frcmod files for my protein with Zn2+
> atom coordinated by HieHieCymCym motif.
> I have successfully generated the prep and frcmod files with restraints on
> all the backbone atoms (CA, H, HA, N, HN, C, O) to the AMBER parm99.dat
> force field values (ChgModC).
> When I check the charges generated finally, it is different from the ones
> seen in $AMBERHOME/dat/leap/lib/all_amino94.lib.
> When I compare the charges for CYM from
> $AMBERHOME/dat/leap/lib/all_amino94.lib and
> file:///usr/local/amber11/dat/mtkpp/amino94.xml, it is completely
> different.
>
> amino94.xml (MCPB) all_amino94.lib (leap)
>
> N -0.46300 -0.415700
> HN 0.25200 0.271900
> CA 0.03500 -0.035100
> HA 0.04800 0.050800
> CB 0.73600 -0.241300
> HB3 0.24400 0.112200
> HB2 0.24400 0.112200
> SG -0.73600 -0.884400
> C 0.61600 0.597300
> O -0.50400 -0.567900
>
>
> Why is this difference observed? Someone suggest me which values should be
> used for the CYM backbone atoms (including Hs).
>
The LEaP versions are 'defined' to be correct. I would use those. I don't
know how or when the MTK++ versions were generated (or if they were even
supposed to be the same as FF94, although I think they should be).
HTH,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Tue Oct 09 2012 - 05:00:03 PDT
