My goal is to turn this PDB file (a non-standard organic molecule with
Iron): http://pastebin.com/raw.php?i=G06ajgSw
Into a prmtop and inpcrd file so that i can simulate it with OpenMM.
Before I would just convert the pdb with antechamber, create the .frcmod
with parmchk, then use tleap to create periodic box conditions and save as
inpcrd and prmtop files.
Now it seems to me that I will have to only use mtkpp, but the example in
MTKpp.pdf section 15.10 is kind of confusing for me. The example is for a
protein, how about for organic molecules?
Would I have to make the pdb file without iron, make the Oxygens a negative
charge, load the pdb, load iron, and connect them together?
Kind of like this (I know most of this probably doesn't make sense, but
this is close to the logic of it?): http://pastebin.com/raw.php?i=yStACxAS
Also I am confused on how to output to AMBER Prem and frcmod files (section
15.10.14). It says to do this "MCPB -i 1AMP_OH_toAmberFormats_sem.bcl -l
1AMP_OH_toAmberFormats_sem.bcl.log" but that is the command prompt, not the
script, does it recognize from the file name to output in AMBER files?
Thanks for your help!!
-Jonathan
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Received on Fri Apr 19 2013 - 14:00:02 PDT
