[gmx-users] Regarding lipid topology

[Venkat Reddy]

Dear Sir,
I have measured the dihedral angles for both cis and trans conformations
using VMD. As expected, for cis isomer the dihedral angle was 0 and for
trans = 180. Expect this, I couldn't find any change between these isomers.


On Thu, Jul 3, 2014 at 3:07 PM, Dr. Vitaly Chaban <vvchaban at gmail.com>
wrote:

> Unlikely anything on top of dihedrals.
>
> Try to use VMD to see if the lipid molecules look as you like.
>
> I do not have to handle lipid isomer simulations, fortunately.
>
>
> Dr. Vitaly V. Chaban
>
>
> On Wed, Jul 2, 2014 at 7:33 PM, Venkat Reddy <venkat4bt at gmail.com> wrote:
> > 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
> > --
> > Gromacs Users mailing list
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-- 
With Best Wishes
Venkat Reddy Chirasani
PhD student
Laboratory of Computational Biophysics
Department of Biotechnology
IIT Madras
Chennai
INDIA-600036