On Tue, 2014-03-25 at 20:08 +0530, DEBOSTUTI GHOSHDASTIDAR wrote:
> Dear Amber Users
>
> Could anyone suggest if there is a way to generate frc and prep files for
> an organic molecule, say X, from the topology file of a system containing
> large number of X in a box of water? It would be kind of going backward.
Check out ParmEd.
There is the "writeOFF" and "writeFrcmod" commands that will write a
frcmod and library file with all of the parameters and residues present
in the system, respectively.
If you want JUST the library/frcmod for X, you can strip everything
except X. Note that for writeOFF you need to load a restart file. So a
ParmEd script like this will work:
parm /path/to/my/prmtop
loadRestrt /path/to/my/inpcrd
writeOFF my.lib
writeFrcmod my.frcmod
You can then run it with
parmed.py -i <File>
Alternatively, you can just run "xparmed.py" and use the point-and-click
interface in the GUI.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Tue Mar 25 2014 - 10:30:03 PDT
