Dear all,
I have a DNA G-quadruplex with total net charge of -17. I would like to
protonate some phosphate groups of the guanines to reach the net charge
of -5 (in according with my experimental mass data), and then run a MD
simulation in gas phase.
I have found here
http://ambermd.org/antechamber/dna.html the prep file
for the protonated guanine and I have generated the frcmod file with
parmchk2. After that I have modified my pdb file to replace the residue
names of the guanines and then I have used leap to generate prmtop and
inpcrd files (leap.log attached).
Basically I have obtained the net charge of -5 that I wanted, but also
some "warnings" and improper torsions that I do not understand to what
they are due. prmtop and inpcrd seem fine but if I try to minimize the
structure, I end up with improper conformations of the protonated
guanines (NH2 of the base not in the plane), and then totally weird
conformations during the equilibration that ends with the unfolding of
the structure (restart file attached).
I guess that everything is related to what I have done in leap.
Please, could you help me to understand what is going wrong?
All the best,
Valentina D'Atri
Institut Européen de Chimie et Biologie
INSERM U869 - ARNA Lab
Postdoctoral Researcher
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Received on Wed Apr 30 2014 - 10:30:03 PDT
