AMBER Archive (2006)

Subject: AMBER: charge constraints in resp

From: Kenley Barrett (kenley.barrett_at_gmail.com)
Date: Thu Mar 30 2006 - 10:22:36 CST

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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