Dear AMBER community,
I am having some difficulties with resp. I want to do a second-stage resp
fitting in which atoms 1-20 are restrained to have a net charge of 0.
However, once I've put the resp charges in a prep file and loaded it into
xleap, the charge of these atoms comes out to be 0.1230, not 0.
I created the constraints in my resp2 input file based on the peptoid
example in /opt/local/amber8/examples/resp_charge_fit/. The &cntrl namelist
is the same as what is automatically created by respgen (I've discovered
that ioutopt needs to equal 1 in order for AMBER to go through all the steps
to make a working prep file).
Here are the first and second stage resp input files:
First stage input file:
First resp fitting for methylated histidine, following Duan et al.
procedure.
&cntrl
nmol = 1,
ihfree = 1,
ioutopt = 1,
&end
1.0
Resp charges
0 26
7 0
1 0
6 0
6 0
8 0
1 0
6 0
1 0
1 0
6 0
7 0
6 0
1 0
7 0
6 0
1 0
1 0
1 0
6 0
1 0
6 0
8 0
1 0
7 0
1 0
1 0
Second stage input file:
Second fitting for methylated histidine, following Duan et al. procedure
except
restraining the non-blocking atoms to a total zero charge.
&cntrl
nmol = 1,
ihfree = 1,
ioutopt = 1,
iqopt = 2,
qwt = 0.001,
&end
1.0
resp charges
0 26
7 -99
1 0
6 -99
6 -99
8 -99
1 0
6 -99
1 0
1 8
6 -99
7 -99
6 -99
1 0
7 -99
6 -99
1 0
1 16
1 16
6 -99
1 0
6 -99
8 -99
1 -99
7 -99
1 -99
1 -99
20 0.0
1 1 1 2 1 3 1 4 1 5 1 6 1 7
1 8 1 9 1 10 1 11 1 12 1 13 1 14 1
15 1 16 1 17 1 18 1 19 1 20
Here is the -t output of the second stage fitting:
-0.030630 0.030630 0.002225 0.457386 -0.567234 0.115050 -0.136863
0.094573 0.094573 0.173194 -0.449827 0.022620 0.156302 0.161476 -
0.180110 0.099700 0.099700 0.099700 -0.302310 0.181925 0.335545 -
0.538195 0.053203 -0.593932 0.360673 0.260624
Strangely, if you add up the charges of atoms 1-20, the net charge is
actually 0.12208 rather than 0.1230--is this kind of difference normal after
reading information into XLeap? But regardless of whether the charge is
0.12208 or .1230, I can't use this--I need to find a way to make the charges
of atoms 1-20 equal 0.
I would be very grateful for any suggestions. Thank you in advance for your
help.
Sincerely,
Kenley
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Received on Sun Apr 02 2006 - 06:10:13 PDT
