VMD-L Mailing List

From: Stefan Franzen (Stefan_Franzen_at_ncsu.edu)
Date: Fri Aug 12 2011 - 13:46:24 CDT

Hi all,

     We are working with a 2'-O methyl modified nucleic acid that we wish to
incorporate in to DNA. In RNA, this works great, but in DNA the PSF builder
automatically replaces the O2' with a hydrogen by applying the DEO1 patch.
We have tried overriding the patch by changing the modified nucleotide to
RNA, but this deletes all of the other nucleotides in the chain.

QUESTIONS:
1. Is there some way to mix RNA and DNA in one chain?

2. Alternatively, is there a patch that would permit the addition of a
nucleotide in the middle of a chain? The patch for this must exist in the
PSF builder code since it automatically links the nucleotides. However, it
must be in the code since it is not present in the topology file.

Any help would be appreciated.

Stefan