[gmx-users] Joining groups for simultaneous analysis in DSSP
Justin A. Lemkul
jalemkul at vt.edu
Wed Oct 13 20:00:10 CEST 2010
Ali Naqvi wrote:
> Hi all,
> I have a 25 amino acid peptide that contains 4 phosphoserines. The
> forcefield that I have been using is the ff43ap which was modified to
> include these groups. So during pdb2gmx I have the rtp and itp files for
> the forcefield in the folder in order for the software to find the
> appropriate charges. Anyway, simulation is all honkey dory but the
> problem is in DSSP analysis which separates the SEP from the protein.
> So the entire protein is 252 atoms but when I run the do_dssp program it
> is separated into two:
> Protein 208 atoms &
> SEP is 44 atoms
> I can run the dssp separately on the two groups, but since dssp uses
> information about adjacent sequence of amino acids, I would say
> separating the analysis in the SEP region 16-19 would be wrong as
> secondary structure would not be additive like lets say dihedral angles
> or rmsf.
> For results, in the SEP region I am getting the random coil (white as
> coloured by xpm2ps) which is equivalent to no secondary structure.
> Although I don't have a hard time believing this, just to be a devils
> advocate of my own results, I would like to process them together
> instead of separately. So my question is how to I join atoms into one
> group instead of having them separated?
In order to have a custom residue recognized as being part of the protein, you
need to add this residue to aminoacids.dat (in Gromacs version prior to 4.5) or
residuetypes.dat (4.5 and onward).
Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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