AMBER Archive (2006)

Subject: Re: AMBER: Xleap woes

From: David A. Case (case_at_scripps.edu)
Date: Thu Nov 16 2006 - 12:39:39 CST

On Thu, Nov 16, 2006, Shozeb Haider wrote:
>
> 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.

This doesn't seem "strange" to me. I don't know what you tried, but
direct conversions from one prmtop file to another is generally supported only
for removing entire molecules (such as stripping waters and ions).

> 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?

You have to edit the leaprc file that you use, removing the commands that
substitute capped residues for regular ones at the chain ends. For example,
a line like this:

    { 0 "G" "DG5" } { 1 "G" "DG3" } { "G" "DG" } { "GN" "DGN" }

instructs LEaP to substitute DG5 for G at the 5' end, and DG3 for G at the 3'
end. If you remove those commands, the substitutions will not be made.

...good luck...dac

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