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
