It seems to work :). Thank you! 2015-09-04 9:52 GMT+01:00 Dawid das <[email protected]>:
> > 2015-09-03 13:06 GMT+01:00 Justin Lemkul <[email protected]>: > >> FYI, CHARMM22 has no CMAP. CHARMM22/CMAP (what GROMACS somewhat >> misleadingly calls "charmm27.ff") does. >> > Yes, I was aware of that, just forgot to write CHARM22/CMAP. > > >> >> My question is, whether there is a way to use CMAP parameters only for >>> connection between standard a.a. and omit them for connection between my >>> chromophore and standard a.a.? >>> >>> >> You'd probably have to modify the topology after the fact, but the >> connection between the chromophore and the next residue is easily omitted >> by not having a [cmap] directive in the chromophore .rtp file. If the >> backbone of the chromophore has standard amino acid atom names, there's no >> way to tell pdb2gmx to not write a CMAP entry from the previous residue. >> You can comment out or remove that line later. >> > > Well, to be honest I defined my chromophore residue (let's call it CH6) in > aminoacids.rtp file along with all other amino acids but in fact I do not > use [cmap] directive under CH6 definition. I use only [atoms], [bonds], > [angles], [dihedrals] and [impropers] directives. > > Only the C and N atoms have standard amino acid atom names, because I did > not know how to define the proper connection between CH6 and natural amino > acids the other way around. > I will try to find those lines and comment them out. > > > > > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to [email protected].
