AMBER Archive (2006)

Subject: Re: AMBER: Xleap woes

From: M. L. Dodson (mldodson_at_houston.rr.com)
Date: Thu Nov 16 2006 - 14:14:07 CST

On Thursday 16 November 2006 12:39, David A. Case wrote:
> 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
>

Or use the command loadPdbUsingSeq with a sequence specification
using only "DG", "DC", etc residue names.

Bud Dodson 

-- 
M. L. Dodson
Email:	mldodson-at-houston-dot-rr-dot-com
Phone:	eight_three_two-56_three-386_one

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