Thanks Ben.
timestep dihedral are not in the zeta.dat files, I added them for
explanation.
I have just found out that there was a mismatch between any units for force
constants and the that of the restrained dihedral ( kcalmol/rad versus
degrees) so now I am getting some results.
Short of contacting the group that wrote the WHAM code, I do not know of
any mailing specifically dedicated to WHAM so I decided to ask on the
amberlist first. Let me know if there is!
Thanks,
Lekpa.
On Wed, May 5, 2010 at 3:04 PM, Ben Roberts <roberts.qtp.ufl.edu> wrote:
> Hi Lekpa,
>
> On 5/5/2010, at 3:32 p.m., Lekpa Duukori wrote:
>
> > Hello Ben,
> >
> > My zeta.dat files was generated by ptraj
> >
> > It looks like this
> >
> > timestep dihedral
> >
> > 5001.00 61.634403
> > 5002.00 73.807835
> > 5003.00 68.285963
> > 5004.00 69.185732
> > 5005.00 77.925740
> > 5006.00 67.384091
> > 5007.00 67.790124
> > 5008.00 68.074948
> > 5009.00 62.289917
> > 5010.00 65.399225
> >
> > One is attached ( for r2=r3=70 degrees)
>
> Try taking the decimal point and places (".00") off the end of your
> timestep. It may be that the WHAM code expects timesteps to be integral
> (which is, after all, not a stupid assumption). Also,try removing the header
> lines (in your case, "timestep dihedral" and the succeeding blank line), so
> that all lines have a "<timestep> <value>" entry on them.
>
> If those two things don't work, you may wish to ask for help in a forum or
> mailing list dedicated to WHAM, since the WHAM code is maintained and
> supported by a separate group of people.
>
> Regards,
>
> Ben
>
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Received on Wed May 05 2010 - 14:30:04 PDT
