Hi Justin. I am now trying to generate all the missing files (.rtp, .hdb, .tdb, .atp). I will present the monomeres as aminoacids. Since the polymer will be simulated along with a lipid membrane (CHARMM36 force field), I won't actually need the aminoacids.
I have five different monomers (3 + 2 terminal ones), that are quite similar so after importing one I should be OK. Best, Jernej On Wed, Dec 14, 2011 at 12:17, <gmx-users-requ...@gromacs.org> wrote: > Jernej Zidar wrote: >> Hi Mark. >>>> How will pdb2gmx "know" it has to parse the monomeres.rtp file? >>> It can't. You must add to an existing .rtp file. >> >> That's a problem (and a negative surprise), because I can't just add a >> new residue to the aminoacids.rtp in Charmm27.ff folder. Charmm27 and >> CGenFF are two different things, though they can be used together. >> > > The CGenFF files can be found on the Gromacs website: > > http://www.gromacs.org/Downloads/User_contributions/Force_fields > > To make them fully functional and capable of using pdb2gmx, you would have to > add several files - .rtp, .hdb, .atp, and probably a few others. > >>> I will add that you will also have to add the residue to aminoacids.dat >>> file, so that the polymer repeat unit is recognized. for your small >>> polymer molecule you can just generate from the swissparam website >> >> That could well work in the case of the smallest polymer that is >> composed of just five monomers, but it is absolutely out of the >> question in the case of experimentally-relevant polymers that are >> composed of at least 40 units. >> > > How many different monomers are involved? Repeat units and polymeric > assemblies > are precisely what pdb2gmx is for (consider the trivial example of a protein). > For further polymer-related tips, see the following: > > http://www.gromacs.org/Documentation/How-tos/Polymers > > -Justin -- Windows: Re-Boot, Linux: Be-Root. -- 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
