[AMBER] difference in amino94.xml (MCPB) and all_amino94.lib (leap) for CYM

From: Sangeetha B <sangeetha.bicpu.edu.in>
Date: Tue, 9 Oct 2012 16:29:19 +0530

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).

Also I have attached my chg2.prep file obtained after final resp run from
MCPB. Please check the charges in the file and suggest if they are fine to
use in simulations.

Thank you,
With regards,
B. Sangeetha

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Received on Tue Oct 09 2012 - 04:00:03 PDT
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