[gmx-users] Re: DMF topology file

Vitaly V. Chaban vvchaban at gmail.com
Sat Sep 5 15:34:58 CEST 2009

Hi Abhishek,

I know two possible ways. The first is to find PBD file of DMF (one
molecule) and then use x2top program of the gromacs package. When asked for
a FF, OPLS/AA can be pointed out. DMF contains only common atoms, so I guess
there will be no problems to generate the topology automatically. The second
way is to make topology by hand. If one has enough experience it can be of
some pleasure. :)

Good luck!

Vitaly V. Chaban, Ph.D. (ABD)
School of Chemistry
V.N. Karazin Kharkiv National University
Svoboda sq.,4, Kharkiv 61077, Ukraine
email: chaban at univer.kharkov.ua,vvchaban at gmail.com
skype: vvchaban, cell.: +38-097-8259698
!!! Looking for a postdoctoral position !!!

On Sat, Sep 5, 2009 at 3:20 PM, Abhishek Banerjee <a.banerjee at ymail.com>wrote:

> hi Vitaly,
>                 Thanks for your help. I have created a DMF box. Now I want
> to do NTP and NVT on that. For that I want to use OPLS/AA force field. I got
> some reference paper on that. How can I go to create a itp or top for DMF.
> If you give me some hints about the steps to crate a topology file for
> DMF(OPLS/AA), will be greate help for me.
> thanks
> abhishek
> ------------------------------
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