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
quit
EOF
then load the prmtop/inpcrd files in ambpdb:
ambpdb -p file.prmtop <file.inpcrd> file.pdb
Hope that helps!!!
--Alessandro
On Sat, Jul 31, 2010 at 4:42 PM, Ehsan Habibi <EHabibi.ibb.ut.ac.ir> 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
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>
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Received on Sat Jul 31 2010 - 13:00:06 PDT
