[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).


> Cordially,
> Ali


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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