Dear Valentina,
You could use R.E.D. Server Dev. at
http://q4md-forcefieldtools.org/REDServer-Development/
to develop force field libraries for the non-protonated and protonated
phosphate groups.
In the F-90 REDDB project you can find examples of non-protonated and
protonated phosphate groups as examples:
http://q4md-forcefieldtools.org/REDDB/projects/F-90/
http://q4md-forcefieldtools.org/REDDB/projects/F-91/
R-OH Me-OPO3(2-) ---> R-OPO3(2-)
Me-OPO3H(-) R-OPO3H(-)
You use two inter-mcc between the OH group of the 'R-OH' building
block and the Me group of 'Me-OPO3(2-)' and 'Me-OPO3H(-)'
R.E.D. Server Dev. performs charge dervation, force field library
building and force field parameter generation; key points here are
atom typing for molecular fragments and fragment fusion between the 3
elementary building blocks.
force field parameters are in the frcmod.* files
all should be done automatically.
See the documentation:
http://q4md-forcefieldtools.org/REDServer-Development/Documentation/
http://q4md-forcefieldtools.org/Tutorial/Tutorial-4.php
regards, Francois
> 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?
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Received on Sun May 04 2014 - 22:30:03 PDT
