Re: AMBER: loading DNA-RNA hybrid in xleap

From: Ilyas Yildirim <>
Date: Sun, 3 Jul 2005 07:23:56 -0400 (EDT)

> thanks for the suggestion. actually i didnt not construct the structure
> in nucgen. it is reported in pdb and it is an nmr structure. kindly tell
> me how to overcome this problem for such structures.

If its in a .pdb file, you have to change the residue names. The residue
names are probably the same in the DNA and RNA strand (like C for cytosine
in DNA and RNA). If you change the residue names to RC, RG, RU, RA; xleap
will recognize them as RNA residues. If you change the residue names to
DC, DT, DA, DG; xleap will recognize them as DNA residues. So, you have to
be careful on the residue names given in the .pdb file. The Brookhaven
pdb format does not have these naming. So, you have to change it by
yourself if you want xleap to recognize them as the way u want.

Note also that there are 3' and 5' end naming for all these residues
(A,C,G,U,T). So, be careful on that too. Run xleap, load a force field and
give the 'list' command. It will show you which residues are defined for
this particular force field. Examine the D... and R... named residues.
Hope this helps.


  Ilyas Yildirim
  - Department of Chemisty       -				-
  - University of Rochester      -				-
  - Hutchison Hall, # B10        -				-
  - Rochester, NY 14627-0216     - Ph.:(585) 275 67 66 (Office)	-
  -			-
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Received on Sun Jul 03 2005 - 12:53:00 PDT
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