AMBER Archive (2006)

Subject: Re: AMBER: Xleap woes

From: Fenghui Fan (fenghui_fan_at_yahoo.com)
Date: Thu Nov 16 2006 - 13:22:59 CST

Firs you get the PDB file of4,5 residue and 6 with
TER following residue 6. Remember change the
corresponding residue number from 4, 5, 6 to resiodue
number 1,2,3. If you do not chnage the residue number,
then your results coour. Using the correct modified
PDB file, you get the promtop file and mdcrd file.
After you run the sander, the trajectory file residue
and atom types should be in agreement with the those
in the prmtop file.

Best regards.

Fenghui Fan

--- Shozeb Haider <shozeb.haider_at_pharmacy.ac.uk>
wrote:

> Hi
>
> 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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