[gmx-users] How to create an rtp file for a lipid?
Justin A. Lemkul
jalemkul at vt.edu
Thu Jan 20 19:22:56 CET 2011
Dr. Ramón Garduño-Juárez wrote:
> Dear All:
> I am trying to build a lipid bilayer made of DMPC
> (Dimyristoylphosphatidylcholine) surrounding a putative membrane
> channel. Everything goes well until I come across with the use of
> pdb2gmx and further on to the use of gromp, where I realized that I need
> to add some information about DMPC, information that is supposed to be
> in the rtp format.
Using an .rtp is an unnecessarily laborious (and indirect) way to add a lipid
topology. Simply #include an .itp file. You haven't said what force field
you're trying to use, but for Gromos force fields, you can use the topology from
There are probably topologies out there for CHARMM, as well, but I don't have
the link handy.
> I have no idea how to build such rtp file for DMPC. I have read and
> practiced with all tutorials about the construction of lipid bilayer
> with GROMACS. I have also read the relevant information about rtp files
> in the GROMACS Manual. However, I still cannot figure out how to do this.
The procedure you're looking for is nearly identical to the membrane protein
topology. The only difference is the lipid :)
> I will appreciate very much any help provided. I am stuck and would like
> to learn how to create an rtp file from scratch, which I am sure I need
> to do more than once during this project...
Investing time in an .rtp file is probably not useful here, but if you're intent
on doing it, simply read through the .rtp file for your force field and see how
the existing building blocks are built. If I were you, I would not waste my
time doing so.
> Much obliged,
> Ramon Garduno
Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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