[gmx-users] Regarding lipid topology

Venkat Reddy venkat4bt at gmail.com
Wed Jul 2 19:33:04 CEST 2014


Thank you Sir. Sorry for the late reply. So, the changes like dihedral
angle for C8-C9=C10-C11 should be 180 instead of 0 in trans state. Are
there any other adjustments I should make to build the trans lipid isomer
topology from cis? Thank you for your valuable time and concern.


On Mon, Jun 16, 2014 at 4:44 PM, Dr. Vitaly Chaban <vvchaban at gmail.com>
wrote:

> Of course, no. You need to adjust your topology (force field?) to
> distinguish between cis- and trans- states.
>
>
> Dr. Vitaly V. Chaban
>
>
> On Mon, Jun 16, 2014 at 11:03 AM, Venkat Reddy <venkat4bt at gmail.com>
> wrote:
> > Dear all,
> > I want to simulate a membrane protein system. My membrane is composed of
> > DOPC (cis isomer) and DEPC (trans isomer). I have downloaded DOPC
> topology
> > from lipidbook website. Since DOPC and DEPC are isomers, can I use the
> > topology of DOPC for DEPC also?
> >
> > Thank and regards
> >
> > Venkat Reddy Chirasani
> > PhD student
> > Laboratory of Computational Biophysics
> > Department of Biotechnology
> > IIT Madras
> > Chennai
> > INDIA-600036
> > --
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-- 
With Best Wishes
Venkat Reddy Chirasani
PhD student
Laboratory of Computational Biophysics
Department of Biotechnology
IIT Madras
Chennai
INDIA-600036


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