AMBER Archive (2006)

Subject: AMBER: Xleap woes

From: Shozeb Haider (
Date: Thu Nov 16 2006 - 17:07:01 CST


I have a prmtop file of single stranded DNA containing 10 bases. I wish
to extract bases 4,5 and 6 and create a prmtop for them. For some
strange reason, I am unable to generate it from the original prmtop
file. I have also tried to make a pdb and then generate the prmtop, but
then xleap sees base 4 and 6 as terminal bases and caps them. Then the
atoms in the trajectory does not correlate with the prmtop file. Can any
one suggest me how to make a prmtop file for these bases?

Secondly, how can one delete multiple residues in xleap ?
remove <unit> <unit.residue_number> deletes only one residue at a time.

Any suggestions shall be much appreciated.

Many thanks

Shozeb Haider
The London School of Pharmacy.
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