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
Cordially,
Ali
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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