[gmx-users] Fwd: CNT Water and DNA protein, Not working

[Abhishek Agrawal]

---------- Forwarded message ----------
From: Abhishek Agrawal <aintabhishek at gmail.com>
Date: Tue, Mar 21, 2017 at 2:25 PM
Subject: CNT Water and DNA protein, Not working
To: gmx-users at gromacs.org


Hare Krishna Everyone!

OBJECITVE:
See I am aiming to make a system having
CNT
Water
DNA
to study the interaction of DNA with the CNT, when CNT has some charged
molecule attached to it or any one C be have some charge.

SPECIFICATIONS:
GROMACS 5.0.7
fftw
Python
VMD
i3 5005 2.0 GHz 4GB Ubuntu 16.04 LTS

PROBLEM:
Going through many tutorials, gromacs mailing list and Andre tutorial for
CNT on Gromacs site, I found that whatever I do, by making custom
forcefield or going by default forcefield with the GROMACS nothing is
working for me.
It gives error that residue "UNL" or whatever the PDB has, is not found in
the topolgy database,, this is for the default forcefield.
I make custom one, then CNT is accepted but then on solvating the Water is
not. Going forward DNA shall also be not accepted as it is not available in
the custom forcefield.

SUMMARY:
What to do to make a system having:
CNT Water and DNA, the FORCEFIELD is the major issue.
Please guide.

Regards,
Abhishek Agrawal
AMITY UNIVERSITY
Research Associate @ NIT Patna
NOIDA, INDIA