Thanks Tsjerk .... [?]
Regards Lovika On Fri, May 23, 2014 at 4:17 PM, Tsjerk Wassenaar <tsje...@gmail.com> wrote: > Hi Lovika, > > Yes, you can > > #include "gold.itp" > > or something along those lines. > > Cheers, > > Tsjerk > > > On Fri, May 23, 2014 at 12:44 PM, Lovika Moudgil <lovikamoud...@gmail.com > >wrote: > > > Thanks for reply Abhijit... .I will definitely try this . > > > > Hey Tsjerk ... Is it possible , if I define all this in a different .itp > > and than define that .itp file in .top file ????? > > > > > > On Fri, May 23, 2014 at 3:45 PM, Tsjerk Wassenaar <tsje...@gmail.com> > > wrote: > > > > > Hi Lovika, > > > > > > IIRC your gold is frozen, right? So you have a moleculetype definition > > for > > > one gold atom (atomtype, mass, charge). You can just put it in the .top > > > file after the #includes of the force field, like > > > > > > #include "forcefield.itp" > > > #include "protein.itp" > > > > > > [ moleculetype ] > > > AU 1 > > > > > > [ atoms ] > > > 1 AU 1 UA UA 1 0 196.96655 > > > > > > [ system ] > > > Protein with gold > > > > > > [ molecules ] > > > ... > > > > > > > > > Hmm, I wonder, should one account for the gravitational effects of > gold. > > > Pretty heavy stuff :p > > > > > > Cheers, > > > > > > Tsjerk > > > > > > > > > > > > On Fri, May 23, 2014 at 11:39 AM, Lovika Moudgil < > > lovikamoud...@gmail.com > > > >wrote: > > > > > > > Hi everyone.. > > > > I have a .pdb file with protein and gold slab .Problem is I can > > generate > > > > .top file for my protein with pdb2gmx but I want my slab in the same > > > > system .I can generate .gro file for both but what about .top file . > > Can > > > > any body help me with this issue .Thanks in advance. > > > > > > > > Regards > > > > Lovika > > > > -- > > > > 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-usersor > > > > send a mail to gmx-users-requ...@gromacs.org. > > > > > > > > > > > > > > > > -- > > > Tsjerk A. Wassenaar, Ph.D. > > > -- > > > 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 gmx-users-requ...@gromacs.org. > > > > > -- > > 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 gmx-users-requ...@gromacs.org. > > > > > > -- > Tsjerk A. Wassenaar, Ph.D. > -- > 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 gmx-users-requ...@gromacs.org. >
-- 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 gmx-users-requ...@gromacs.org.