I created topology file in xleap in the usual procedure
x=loadmol2 molecule
loadamberparams frcmod
saveamberparm x molecule.prmtop molecule.inpcrd
I did check x
this says unit is ok
and I am running the simulations in implicit solvent so my topology file has
no box information .
Yes I have inorganic atoms in cluster where I have specified dihedral
information in the frcmod file .Is this error related to the dihedral
information in my frcmod flle.I ran mmpbsa binding energy calculation
between the cluster and my polymer which works only while I calculate the
entropy this fails.
In my frcmod file the periodicity of torsional barrier is zero,(PN is zero)
What information do I need to give ,for solving this .
Thanks
kirtana
On Sat, Sep 24, 2011 at 8:17 PM, Jason Swails <jason.swails.gmail.com>wrote:
> On Fri, Sep 23, 2011 at 5:52 PM, kirtana S <skirtana4.gmail.com> wrote:
>
> > I want to calculate the change in entropy due to binding of my polymer
> > with
> > the cluster , here I am using nmode analysis.
> > Is there anyway I can specify my complex which consist of the two (these
> > are
> > not bonded and I am running implicit solvent) of them during entropy
> > calculations .
> >
> > I am calculating this change through the entropy after this polymer binds
> > to
> > my cluster .
> >
> > I am using Amber tools 1.5 .My input file
> >
> > &general
> > startframe=1,endframe=10,keep_files=2,
> > /
> > &nmode
> > nmstartframe=1,nmendframe=10,
> > nminterval=5,nmode_igb=1,
> > /
> >
> >
> > MMPBSA -O -i nmode.in -o final_results.dat -cp complex.prmtop -y mdcrd
> > I get an error as
> > Found an invalid periodicity in the prmtop file: 0
> >
>
> This suggests a weird dihedral definition. How did you create your
> topology
> file? Did you specify any parameters yourself? Where would you have
> gotten
> such a periodicity?
>
> We need more information to help diagnose this problem.
>
> HTH,
> Jason
>
>
> > Error:error during mmpbsa_py_nabnmode calculations!
> >
> > Thanks
> > Kirtana
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
> _______________________________________________
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> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Sun Sep 25 2011 - 10:00:03 PDT
