[gmx-users] Membrane Proteins & pdb2gmx

[Anirban Ghosh]

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 <pcl at 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
> pcl at uab.edu                     | Birmingham AL 35294-4461
> (205) 690-0808                  |
> ==================================================================
>
> --
> gmx-users mailing list    gmx-users at 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-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20111208/55cea7b5/attachment.html>