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
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--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Sat Sep 24 2011 - 17:30:04 PDT
