On Tue, Oct 11, 2016, shahab shariati wrote:
>
> I want to convert prmtop and inpcrd file (created using antechamber) to
> gromacs files using amb2gmx.pl.
>
> When I use command:./amb2gmx.pl --prmtop lig.prmtop -crd lig.inpcrd
> -outname lig, I encontered with:
> sh: rdparm: command not found
The amb2gmx.pl script (which is not a part of Amber) expects to find a program
called "rdparm". The latter used to be a part of Amber, but is no longer
distributed.
The best thing to do is to contact the authors of this script (Gromacs team?)
and see if they have an updated version.
Less good, but might work: you can cd to $AMBERHOME/AmberTools/src/ptraj and
type "make install"; this will put rdparm into $AMBERHOME/bin. It that is in
your PATH, then the amb2gmx script might work.
....dac
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Received on Tue Oct 11 2016 - 11:00:02 PDT
