Re: modifying a nucleobase

From: Peter Freddolino (
Date: Sat Mar 28 2009 - 10:59:48 CDT

Hi John, wrote:
> Dear all,
> 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?

psfgen itself has no concept of where to put in chain breaks (it does it
 wherever you tell it to), so I assume here you're using autopsf and
finding that a chain break is inserted. Autopsf only recognizes the
canonical nucleotides as being part of a nucleic acid chain. For your
case you will either need to edit the chains in the autopsf gui (as you
suggest), write your own psfgen script, or modify your copy of autopsf
to recognize your residue (you would need to edit the function

> 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.

Well, if your new residue is at the 5' or 3' end, you'll need to alter
the charges of the patch to end up with the appropriate total charge.
Why, however, do you have changes to your backbone charges? In CHARMM
parameterization everything is divided into groups with integer charge,
and for most modifications you should only recalculate the charges in
the same group (and possibly tightly coupled neighboring groups -- in
your case I could see redoing the charges for the entire ring system.
Since you modified only the base, you should probably leave the backbone
charges intact during the parameterization.


> Kindest regards,
> John

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