Hello Peter, Thanks a lot for clarifying my doubt! I have got it right now.
Thanks, Anirban On Thu, Dec 8, 2011 at 3:34 PM, Peter C. Lai <p...@uab.edu> wrote: > On 2011-12-08 02:43:13AM -0600, Anirban Ghosh wrote: > > Hello Justin, > > > > In your membrane protein simulation tutorial after making the topology, > you have mentioned that "Placing the new gromos53a6_lipid.ff directory in > $GMXLIB will allow you to use this force field system-wide." I suppose this > is valid only for the proteins (and not membranes) to be processed through > pdb2gmx using gromos53a6_lipid force-field, right? And to process a > membrane using pdb2gmx we need to change the aminoacids.rtp file with the > relevent POPC/DSPC/DPPC etc. entries. Right? Or can we somehow make pdb2gmx > use the POPC/DPPC/DSPC.itp file? > > Yes because in that tutorial, you are not adding an rtp with the lipid > residue names to generate lipid topologies "from scratch". The tutorial > uses pregenerated lipid topologies from Tieleman. You are certainly > able to add your own rtp files; pdb2gmx searches all validly formatted > rtp files in $GMXLIB/forcefield.ff/ for topology information by residue > name. For example, when I converted parts of CGenFF to gromacs, I added > my own library of residue types for the small molecules I am modeling as > its own .rtp file. (Basically what I mean is, there is no need to hack > aminoacids.rtp to add new residues, just add your own .rtp file). > > However you obtain a topology of a moleculetype (either using pdb2gmx or > from someone else e.g. Tieleman) with a given forcefield, you do not need > to > run pdb2gmx again to generate another topology using that forcefield for > subsequent tasks. Just include the relevant .itp file in the .top file > you specify to grompp. For example, I generated POPC.itp once and have been > using the same file for all my simulations involving POPC. > > Here is an entire membrane protein+lipid+water+ligand .top ready for > grompp -p (I use charmm36 with cgenff added - this is analogous to Justin's > gromos53a6_lipid modification): > > ---- > #include "charmm36cgen.ff/forcefield.itp" > #include "gpcr.itp" > #include "popc.itp" > #include "charmm36cgen.ff/tips3p.itp" > #include "charmm36cgen.ff/ions.itp" > #include "ligand.itp" > > [ system ] > ; Name > GPCR in POPC with LIGAND > > [ molecules ] > GPCR 1 > ; the gpcr.itp file starts with: > ; [ moleculetype ] > ; ; Name nrexcl > ; GPCR 3 > POPC 230 > SOL 21468 > NA 2 > LIGAND 1 > ---- > > gpcr.itp, popc.itp, and ligand.itp were all originally generated by me > using > pdb2gmx on the relevant molecules coordinate files at one point or another. > Again, these individual .itp files are reusable for other simulations > involving the same molecule types, protonation states, and charmm36cgen.ff. > > Hope that helps. > > -- > ================================================================== > Peter C. Lai | University of Alabama-Birmingham > Programmer/Analyst | KAUL 752A > Genetics, Div. of Research | 705 South 20th Street > p...@uab.edu | Birmingham AL 35294-4461 > (205) 690-0808 | > ================================================================== > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >
-- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists