Dear Amber users
I am having problems with getting the correct charge for a saccharide unit
that I am making with the resp procedure. In short, I have done the
following:
1. Calculated single point energy with gaussian 03.
2. created an ac file using antechamber
3. run respgen for resp type 1 and type 2
4. run resp with each of the resp inputs.
5. created a prep file using antechamber and outputted charges from
resp (in which I used resp2 inputs)
My problem is this: I have several capping groups that need to be cleaved
off the main saccharide unit such that the net charge of the main unit
remains at -1. To test the ability of resp to hold some charges steady and
vary others I have attempted to restrain 4 atoms to sum to zero by adding
restraints at the end of the resp2.in input file as follows:
Resp2 input file
*****************************************
Resp charges for organic molecule
&cntrl
nmol = 1,
ihfree = 1,
ioutopt = 1,
iqopt = 2,
qwt = 0.001,
&end
1.0
Resp charges for organic molecule
-1 39
8 0
6 0
1 0
7 0
1 0
6 0
1 0
6 0
8 0
6 0
1 0
1 11
1 11
1 0
8 0
6 0
6 0
8 0
6 0
1 0
1 20
1 20
1 0
1 23
1 0
6 0
8 0
15 0
8 0
8 0
8 0
1 0
1 0
6 0
1 0
8 0
6 0
1 0
8 0
4 0.000000
1 19 1 20 1 21 1 22
*****************************************************
My problem is that, even when I allow all the atoms to vary (i.e. set there
values to 0 in second column), the restraints do not make the selected
charges sum to 0. Why is that? And how can I get my capping groups to sum to
zero so that when I cleave them I don't adversely affect the charge of the
main saccharide unit?
Many thanks to anyone who can prevent me from going completely bonkers over
this.
Hayden
______________________________________________
Hayden Eastwood
Perdita Barran Research Group
Joseph Black Building
Edinburgh University
West Mains Road
EH9 3JJ
Tel: 0131 650 4773
e-mail: s0237717.sms.ed.ac.uk
Research page:
http://homepages.ed.ac.uk/pbarran/PBRG/
"You have to be an academic to believe some things; no ordinary person would
be so stupid." -George Orwell
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Received on Sun Jun 25 2006 - 06:07:11 PDT
