[gmx-users] 1-4 Scaling problem of ASN-NAG from GLYCAM

[Rashmi]

Dear All,

The protein on which I am working, have few ASN residues which are N-linked
with the N-acetyl-glucosamine (NAG). I have taken the parameters of the NAG
and  N-linked ASN from the GLYCAM_06. I have added this N-linked ASN as a
new residue in aminoacids.rtp file and accordingly all the parametrs are
added in respective files. After this both pdb2gmx and grompp are working
without any error.

But the problem I am facing is related to 1-4 scaling. For the GLYCAM,
fudgeLJ and fudgeQQ should be 1. I have read the following mailing post
that how one can mix the fudgeLJ and fudgeQQ in GROMACS.

http://lists.gromacs.org/pipermail/gmx-users/2011-April/060839.html

In the manual, I have come across with two type of pairs function. In
function type 1, two parameters are needed and is used as default. But,
in function type 2, five parameters are needed: fudgeQQ, q_i, q_j, V(cr)
and W(cr).

So can I replace function type 1 with 2 in the pdb2gmx generated topology
for only those pairs belong to the NAG and side chains of N-linked ASN. So
that, I can use fudgeQQ of 1.0, q_i / q_j from the rtp/topology and V(cr) /
W(cr) (calculated from the sigma and epsilon using combination rule) for
those pairs. Will this give No Scaling for 1-4 pair belong to NAG and side
chains of N-linked ASN.

Or another which I found “those 1-4 pairs belong to side chains of N-linked
ASN and NAG, so I could remove them from [ pairs ] section and put into the
[ pairs_nb ] section.” Then these pairs will be treated as normal
non-bonded pairs.

Please suggest me, what I can do in this regard and which is the correct
way.

Thank you in advance.


-- 
With Regards,

Rashmi Kumari
Research Scholar
School of Computational and Integrative Sciences
Jawaharlal Nehru University
New Delhi- 110067.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20120113/922d86d7/attachment.html>