Re: [AMBER] obtain a .pdb file from a .prepin/.frcmod file

From: Alessandro Nascimento <>
Date: Sat, 31 Jul 2010 16:56:27 -0300

There should be an easier way, but what I would do is:

load the prepin/frcmod in leap (using the same ff as before):

If its a small molecule (i.e., using gaff):

cat > leaprc << EOF
source leaprc.gaff
loadamberprep file.prein
loadamberparams file.frcmod
list // here
look for your molecule name listed in leap. Assuming <0>
saveamberparm <0> file.prmtop file.inpcrd

then load the prmtop/inpcrd files in ambpdb:

ambpdb -p file.prmtop <file.inpcrd> file.pdb

Hope that helps!!!


On Sat, Jul 31, 2010 at 4:42 PM, Ehsan Habibi <> wrote:
> Hi Amber users,
> Can we obtain a .pdb file from a .prepin/.frcmod file in Amber? if yes,
> what's the command line?
> Regards,
> Ehsan
> _______________________________________________
> AMBER mailing list

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Received on Sat Jul 31 2010 - 13:00:06 PDT
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