[AMBER] problem with charge on iron in heme cysteine system

From: pancham lal gupta <panchamlalgupta.gmail.com>
Date: Fri, 23 Dec 2011 13:27:26 +0530

Hi.....
         I have done charge calculation of cysteine bound heme through this
command
         line----> #p hf/6-31g scf=tight pop=(mk,readradii) iop(6/33=2) in
gaussian 03.
         we got log file (i have attached this log file)

Through all these command in amber i have calculated charge which is in
file
resp_at.ac.

line=$1
antechamber -i $line."log" -fi gout -o $line."ac" -fo ac
espgen -i $line."log" -o $line".esp"
respgen -i $line".ac" -o $line".respin1" -f resp1
respgen -i $line".ac" -o $line".respin2" -f resp2
resp -O -i $line".respin1" -o $line".respout1" -e $line".esp" -t qout_stage1
resp -O -i $line".respin2" -o $line".respout2" -e $line".esp" -q
qout_stage1 -t qout_stage2
antechamber -i $line".ac" -fi ac -o $line"_resp.ac" -fo ac -c rc -cf
qout_stage2
atomtype -i $line"_resp.ac" -o $line"_resp_at.ac" -f ac -p amber
prepgen -i $line"_resp_at.ac" -o $line"_int.prep" -f int -rn SUS -rf SUS.res

i have charges of all atoms of heme cysteine system but surprisingly charge
on iron is
only 0.217647 but the formal charge on iron is +2.but in calculation i have
got very less charge.

is it right? or
Something wrong i have made in this charge calculation.?
please help me.....


Pancham lal
IIT DELHI


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Received on Fri Dec 23 2011 - 00:00:03 PST
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