[gmx-users] Re: Creating topology for a small organic molecule

Vitaly V. Chaban vvchaban at gmail.com
Sun Oct 25 23:18:26 CET 2009

> Another question is, how difficult is it to create the topology for the
> molecule by hand for the amber99 force field. Could someone please get me
> started on that, if it would be easier. The molecule is a derivative of
> cytosine.
> I am using GROMACS 4 on Mac OS 10.5

I would advise to start with X2TOP and CHAPTER 5 of the manual.


Vitaly V. Chaban, Ph.D.
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 !!!

More information about the gromacs.org_gmx-users mailing list