modifying a nucleobase

Date: Sat Mar 28 2009 - 09:05:01 CDT

Dear all,

I'm running a simulation on an RNA/DNA heteroduplex where I modify a
uracil into a 5-halo-4-thiouridine. I have generated a force field force
the respective modification and made the respective changes to both my
topology and parameter files. However, when I try to generate a .psf the
modified uracil is not recognized as a part of the RNA strand, generated
as an other strand. How can I state in my topology file that this modified
nucleobase is a RNA residue?

I've noticed all atom labels in a RNA residue have an 'N' in the second
position, maybe as a recognition device. I've tried to implement this
pattern in the new residue, but to no avail. I know I can change the chain
in the auto-psf generator, but would like for the new residue to be
automatically recognized as an RNA residue.

Also, is there another modification I need to make in any patches
concerning my new charges on the phopsphate P and O3'? The P charge has
gone from 1.50 to 0.754, and the O3' charge from -0.570 to -0.591.

Kindest regards,

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