You can't minimize a pdb file directly. Normally you would use leap to
convert to prmtop and restart file. But if you already built this system,
there is no need for that. When you do your clustering, just don't use pdb
format to save it. If you did it in cpptraj, just save to restart format,
not pdb, and then use it with your original prmtop to minimize. Check the
cpptraj manual for info on how to select the format when saving the
coordinates.
Or, use cpptraj to read in your pdb and save a restart format.
There are many ways to solve this.
On Thu, Oct 28, 2021, 8:36 AM Hector A. Baldoni <hbaldoni.unsl.edu.ar>
wrote:
> Hi,
>
> This may help you: http://archive.ambermd.org/201506/0097.html
>
> Greeting,
> Hector
>
>
> El 2021-10-28 01:52, priya murugan escribió:
> > Hello researchers,
> >
> > Can some suggest to me how to minimize the PDB format file in Amber 16?
> > Before this, I've used Amber 16 to minimize my .CRD format file. But
> > when I
> > tried to minimize my representative structure in PDB format which I got
> > from clustering analysis, but unable to run minimization.
> >
> > Kindly let me your thoughts and if there is any other option other than
> > AMBER kindly let me know.
> >
> > Thanks & Regards
> >
> > *PRIYA MURUGAN *
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
> --
> --------------------------------------
> Dr. Hector A. Baldoni
> Profesor Titular (FQByF-UNSL)
> Investigador Adjunto (IMASL-CONICET)
> Area de Quimica General e Inorganica
> Universidad Nacional de San Luis
> Chacabuco 917 (D5700BWS)
> San Luis - Argentina
> hbaldoni at unsl dot edu dot ar
> Tel.:+54-(0)266-4520300 ext. 6157
> --------------------------------------
> First things first. But not necessarily in such order.
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Thu Oct 28 2021 - 06:00:03 PDT
