The *.prm files are really only needed for running the simulation and are
not necessary for visualization or saving the pdb. Any simulation that your
colleague did in NAMD should have an associated *.psf file, which
essentially defines the atom types and bonds/angles/dihedrals. Both VMD and
cpptraj are capable of reading a psf; if you load the psf along with the
dcd files you will be able to save the final frame as a PDB directly
without having to generate a prmtop.
Hope this helps,
- Amy
On Mon, Nov 21, 2016 at 1:29 PM, Hai Nguyen <nhai.qn.gmail.com> wrote:
> you can use a pdb file that match the atoms in your prm file and use that
> pdb for topology
>
> ambpdb -p your.pdb < your.rst > your_new.pdb
>
> Hai
>
> On Mon, Nov 21, 2016 at 2:21 PM, The Cromicus Productions <
> thecromicusproductions.gmail.com> wrote:
>
> > Hi everyone,
> >
> > Is there any way of converting prm files into prmtop?
> > A colleague of mine works in NAMD and he gave me a bunch
> > of simulations of which I want to get the pdb file associated to the
> > final screenshot. I have the dcd files (Which I convert to mdcrd and
> > then I save the final screenshot as a .rst file) and then the prm files
> > (which I guess I should convert to prmtop).
> > My idea was to use a command as in the tutorial:
> > $AMBERHOME/bin/ambpdb -p polyAT_vac.prmtop < polyAT_gb_init_min.rst >
> > polyAT_gb_init_min.pdb
> >
> > but I have a bunch of prm files
> > par_all36_carb.prm
> > par_all36_cgenff.prm
> > par_all36_lipid.prm
> > par_all36_na.prm
> > par_all36_prot.prm
> >
> > Is there any way to work with this?
> > Thanks a lot!
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> >
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>
--
Amy Rice
Ph.D. Student
Physics Department
Illinois Institute of Technology
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Received on Mon Nov 21 2016 - 12:00:03 PST
