Re: [AMBER] leap: adding a residue to a unit

From: David A Case <>
Date: Fri, 8 May 2015 08:19:37 -0400

On Thu, May 07, 2015, Hannes Loeffler wrote:
> I am trying to figure out why the following doesn't work:
> source leaprc.ff14SB
> source leaprc.gaff
> loadAmberParams frcmod.ionsjc_tip3p
> # define the BNZ unit
> loadoff benz.lib
> # create unit l containing one BNZ residue
> l = loadpdb bnz.pdb
> X = createUnit X
> bnz = copy l.BNZ
> add X bnz
> #or:
> # add X l.BNZ

I agree that this can be confusing. The origin is that very little testing is
done using the createUnit, copy or add commands in the way you are doing. Lachele may be
of some help here, although they may have also moved to using their own
internal tools for this.

My strategy is generally to create a pdb file that has all the needed
components, then use a single loadpdb command to create the final unit.
But this might not fit your desired workflow....

Apolgies for a non-answer here...I've filed a bugzilla entry. (Please contact
me off-line if you'd like to be able to post bugzilla bugs yourself.)


> The add results either in a segfault when run with tleap -f or,
> interactively, I get an error message:
> add: The object bnz is already contained within
> There should be a string following the "within" according to the code.
> I guess I am just being naive about what I can do with leap.

AMBER mailing list
Received on Fri May 08 2015 - 05:30:04 PDT
Custom Search