[Chimera-users] prmtop

Eric Pettersen pett at cgl.ucsf.edu
Mon May 24 13:37:29 PDT 2010

On May 20, 2010, at 11:46 PM, richardbonnet wrote:

> Dear,
> Is there a way to use writeprmtop with the command line?
> Is it a way to use chimera to write prmtop amd inpcrd files for a  
> ligand
> (gaff type + am1-bcc charge) + the corresponding protein (Gasteiger
> charges + ff99sb) with the command line? I have lot of problems with
> input format for antechmaber. It can intersting to use chimera with  
> the
> command line to solve this type of stuff.

Hi Richard,
	These Amber tools are being created in collaboration with an Amber  
developer and the collaboration has been slow going and therefore all  
of these tools are very much in an unfinished state, including the  
fact that none of them have command-line equivalents.
	Nonetheless you can workaround the lack of command-line versions by  
using a small Python script to call their Python API via Chimera's  
"runscript" command.  So if you had a Python script file (e.g. named  
"callWritePrmtop.py") that contained this:

from WritePrmtop import writePrmtop
from chimera.selection import currentMolecules
writePrmtop(currentMolecules()[0], arguments[0], "ff99SB")

then a Chimera script like this would call it:

addh # if needed
sel #0
runscript /path/to/callWritePrmtop.py output.prmtop

After execution, the file "output.prmtop" (in the same folder as the  
callWritePrmtop.py script) would contain the PRMTOP for the selected  
model (#0 in the example script).


                         Eric Pettersen
                         UCSF Computer Graphics Lab

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