On Tue, Jun 18, 2013 at 4:06 PM, Rejwan <rejwan_88.yahoo.com> wrote:
> I'm trying to make the topology file of a ligand-protein system.
>
> In tLeap suit of Amber I fed both .prepin and .frcmod of the ligand, I
> used RESP charge obtained via Gaussian 09 Geometry Optimization for PREPIN
> file. The .frcmod file was created by parmchk routine.
>
Did you look at the resulting frcmod file? Did you see any statements like
[ATTN: Needs Revision]?
> The tLeap error showed only 2 out of 10 torsion terms could be
> implemented. Could you please help how can I extract the missing Angle and
> Torsion terms ? Also where should I plug the terms (Is it in the .frmod
> file ?) to rerun Leap ? I'm copying the error screen.
>
You should put any missing parameters into the frcmod file. However,
parmchk should have done this for you (unless there were bonds between your
ligand and protein, for instance, but this seems unlikely given that all
missing parameters involve gaff atom types). Even if parmchk couldn't find
any parameters, it will put zeroes in for everything and indicate that it
needs revision. (You should always check the frcmod file after parmchk
creates it). Therefore, the fact that parameters are still missing
indicates that you've probably made some kind of error (did you remember
to load the frcmod into your tleap session via the [ loadAmberParams ]
command?)
Good luck,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Jun 18 2013 - 14:30:02 PDT
