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 <[email protected]> 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 <[email protected]> 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 <[email protected]> > > 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 <[email protected]> > >> 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 > >> > -- > >> > Gromacs Users mailing list > >> > > >> > * Please search the archive at > >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > >> posting! > >> > > >> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > >> > > >> > * For (un)subscribe requests visit > >> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > >> send a mail to [email protected]. > >> -- > >> Gromacs Users mailing list > >> > >> * Please search the archive at > >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > >> posting! > >> > >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > >> > >> * For (un)subscribe requests visit > >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > >> send a mail to [email protected]. > >> > > > > > > > > -- > > With Best Wishes > > Venkat Reddy Chirasani > > PhD student > > Laboratory of Computational Biophysics > > Department of Biotechnology > > IIT Madras > > Chennai > > INDIA-600036 > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to [email protected]. > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to [email protected]. > -- With Best Wishes Venkat Reddy Chirasani PhD student Laboratory of Computational Biophysics Department of Biotechnology IIT Madras Chennai INDIA-600036 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to [email protected].
