Oh, I didn't knew I could do that in VMD. Thanks a lot!!
On Mon, Nov 21, 2016 at 2:39 PM, Amy Rice <arice3.hawk.iit.edu> wrote:
> 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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>
>
>
> --
> Amy Rice
> Ph.D. Student
> Physics Department
> Illinois Institute of Technology
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Received on Mon Nov 21 2016 - 12:00:04 PST
