Hi
Thanks for your input. The G09 input file I used to extract RESP via Antechamber reads as following. Should I make changes and re-run Gaussian in the following line?
#HF/6-31G* SCF=tight Test Pop=MK iop(6/33=2) iop(6/42=6) opt iop(6/50=1)
Thanks for your suggestions.
//Rejwan
--Link1--
%chk=molecule
#HF/6-31G* SCF=tight Test Pop=MK iop(6/33=2) iop(6/42=6) opt iop(6/50=1)
remark line goes here
0 1
C 6.6215000000 5.1461000000 0.1163000000
C 5.7259000000 4.2389000000 -0.3176000000
C 6.2373000000 6.3368000000 0.9704000000
--------------------------------
H 11.0017000000 6.8296000000 2.6926000000
H 10.5984000000 6.6920000000 -1.6004000000
H 11.7998000000 9.1604000000 2.5323000000
H 11.3920000000 9.0243000000 -1.7406000000
H 11.9987000000 10.2632000000 0.3195000000
g09.gesp
g09.gesp
--- On Tue, 6/18/13, Rejwan wrote:
> From: Rejwan
> Subject: Re: [AMBER] problem with tleap
> To: "AMBER Mailing List"
> Cc: jason.swails.gmail.com
> Date: Tuesday, June 18, 2013, 9:46 PM
> --- 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
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> >
http://lists.ambermd.org/mailman/listinfo/amber
> >
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Jun 19 2013 - 08:30:02 PDT
