Dear Rejwan,
> 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)
I think you should read what these IOP means; in particular iop(6/42=6).
iop(6/33=2) is not documented but means 'print the MEP'.
See
http://www.gaussian.com/g_tech/g_iops/ov6.htm
iop(6/42=6) is not the default algorithm defined by Singh & Kollman.
See: http://q4md-forcefieldtools.org/RED/
& in particular: http://q4md-forcefieldtools.org/RED/popup/net.php
regards, Francois
> --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
> > >
> >
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Received on Fri Jun 21 2013 - 00:30:03 PDT
