AMBER: RESP charge fitting problems with capping group

From: hayden <s0237717.sms.ed.ac.uk>
Date: Thu, 22 Jun 2006 10:51:52 +0100

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

 



-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Sun Jun 25 2006 - 06:07:11 PDT
Custom Search