Re: [AMBER] xLeap

From: Jio M <>
Date: Fri, 27 Dec 2013 17:45:57 -0800 (PST)


Another thing I can think is, though not tried: add extra any terminal residue and save that topology. Then you can use by Jason to remove that extra terminal residues? 
Hope it works!
e.g. Desired DNA: 

Fake DNA: save topology 
now use 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? 


On Friday, December 27, 2013 2:23 PM, case <> 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

But generally, the behavior in the default files is what you want.  So be
careful with modifications.


AMBER mailing list
AMBER mailing list
Received on Fri Dec 27 2013 - 18:00:02 PST
Custom Search