--- On Tue, 6/18/13, Jason Swails wrote:
> From: Jason Swails
> Subject: Re: [AMBER] problem with tleap
> To: "AMBER Mailing List"
> Date: Tuesday, June 18, 2013, 5:09 PM
> On Tue, Jun 18, 2013 at 4:06 PM,
> Rejwan
> 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]?
I LOOKED AT FRCMOD FILE. IT DOES NOT HAVE ANY WARNING AT ALL.
>
>
> > 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?)
PARMCHK DID NOT HAVE ANY COMPLAIN AND OF COURSE I DID IMPORT FRCMOD INTO TLEAP VIA loadAmberParams
>
__________________
IF YOU WANT TO HAVE A LOOK AT THOSE FILES I CAN SEND THEM. HOWEVER, WHAT ELSE COULD BE THE PITFALL ? INTERESTINGLY I RUN LIGEAND-PROTEIN MD BEFORE BY SAME ANTECHAMBER PROTOCOL WITHOUT PROBLEM. THANKS.
-rejwan
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
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Received on Tue Jun 18 2013 - 19:00:02 PDT
