Ok lets see if I get any luck after stripping water. I am absolutely sure
about the topology files as we get converged result in all previous
calculation. May be some minor issues.
Thanks for your help. I appreciate it a lot.
On Fri, May 23, 2014 at 8:49 PM, Asaminew Haile <ashaethio.gmail.com> wrote:
> Hi Soumendranath Bhakat
>
> I'm using both molsurf and surf in cpptraj
> and working fine
> but I've water and ions striped trajectory and prmtop files.
> *I use autoimage*
>
>
> *May be you have some corrrupted snapshot in your trajectories*
> *"*WARNING in dispatchToken: Token string "surf" not found in tokenlist"
> means
> surf is not in ptraj
>
>
> hope this helps
>
>
>
>
>
> On Fri, May 23, 2014 at 9:31 AM, Soumendranath Bhakat <
> bhakatsoumendranath.gmail.com> wrote:
>
> > Hii All;
> >
> > During calculation of SASA with CPPTRAJ and PTRAj encountered some error
> >
> > sasa input
> >
> > trajin md50.mdcrd
> > molsurf R1 :1-560 out sasa.dat
> >
> > Execution in cpptraj ~/amber12/bin/cpptraj com_solvated.top sasa.ptrj
> >
> > Error: reroute(): cusp edge mismatch
> >
> > Execution in PTRAJ input same.
> >
> > error :
> >
> > WARNING in dispatchToken: Token string "surf" not found in tokenlist
> >
> >
> > WARNING in dispatchToken: Token string "r1" not found in tokenlist
> >
> >
> > WARNING in dispatchToken: Token string ":1-560" not found in tokenlist
> >
> >
> > WARNING in dispatchToken: Token string "out" not found in tokenlist
> >
> >
> > WARNING in dispatchToken: Token string "sasa.dat" not found in tokenlist
> >
> > md50.mdcrd contains water and counterions.
> >
> > Help will be highly appreciated.
> >
> > Best;
> >
> > S.B
> > --
> > Thanks & Regards;
> > Soumendranath Bhakat
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Asaminew H. Aytenfisu, Grad Student
> David Mathews' group
> Department of Biochemistry and Biophysics
> University of Rochester Medical Center
> Office: 3-8807
> 601 Elmwood Avenue, Box 712
> Rochester, NY 14642
> (585) 275-1748
> _______________________________________________
> AMBER mailing list
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> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Thanks & Regards;
Soumendranath Bhakat
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Received on Fri May 23 2014 - 09:00:03 PDT
