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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Received on Mon Nov 21 2016 - 11:30:05 PST
