Hi
Another thing I can think is, though not tried: add extra any terminal residue and save that topology. Then you can use parmed.py by Jason to remove that extra terminal residues?
Hope it works!
e.g. Desired DNA:
AGAG
TCTC
Fake DNA: save topology
AAGAGA
TTCTCT
now use parmed.py and shed off last terminal base pairs, you get desired new DNA topology (AGAG). Just wondering why would you require incomplete DNA topology without terminal residues?
regards
On Friday, December 27, 2013 2:23 PM, case <case.biomaps.rutgers.edu> wrote:
On Fri, Dec 27, 2013, Himanshu Joshi wrote:
>
> I am trying to get a new topology of DNA in xLeap.
> But xLeap is adding and removing some atoms to residues
> treating them as terminal residues. Is there a way to prevent
> xLeap doing this automated manipulating ?
It's hard to be helpful with such a vague description. You don't say what you
did, or what the problem was.
The way LEaP handles terminal residues is determined by the "addPdbResMap"
section of your leaprc file. So you could make a copy of that file, edit
(or remove) the addPdbResMap section, and use your new file as input to
LEaP.
But generally, the behavior in the default files is what you want. So be
careful with modifications.
...dac
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Dec 27 2013 - 18:00:02 PST
