DNA terminal Patch / How could I retain the primes in DNA

From: raghav singh (raghavbioinfo_at_gmail.com)
Date: Tue Jul 05 2011 - 03:23:21 CDT

Hi Users,

I am working on MD of an artificial DNA system , basically in the
polymerization of the segments so I have to use the terminal prime ... so
that if i will place two units in close contact they can make contacts with
each other.
but... the problem is that .. when I prepare psf file for my molecules it
automatically patches the terminal thymine nucleotide and the prime
disappears in the resulting autopsf.pdb and the psf file is also wrong.

Can anyone tell me how to avoid this problem... as well as if possible put
some light on Chain splitting too :)



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