Re: [AMBER] Problems with tleap when generating gib structures

From: Jason Swails <>
Date: Tue, 5 Jan 2016 11:57:39 -0500

On Tue, Jan 5, 2016 at 11:51 AM, Levan Tsereteli <> wrote:

> No it did not work. When I am generating 123 units its all ok. If I am
> adding just one unit more everything breaks.
> with the following error. Have no idea what to do next. Any help will be
> appreciated.

​I don't think it's that common to use the sequence command like this (I
certainly don't build anything more than ~10 residues with it). One idea
is to build up 120-residue chunks:

chunk1 = sequence {RES1 RES2 RES3 ... RES120}
chunk2 = sequence {RES121 RES122 ... RES​

system = sequence {chunk1 chunk2 ...}

This can recurse as long as is necessary to build the whole system. I'm
not sure if the resulting chunk# units remember their "head" and "tail"
designation (i.e., if tleap will know how to connect chunk1 and chunk2, for
instance), but it's at least worth a shot.

If that doesn't work, my next idea would be to grep for the 124 limit that
you found in the .m4 file and see if it appears to be hard-coded in other
places as well.


Jason M. Swails
Rutgers University
Postdoctoral Researcher
AMBER mailing list
Received on Tue Jan 05 2016 - 09:00:04 PST
Custom Search