Dear Jonathan,
To generate non-standard residues with (or without) a metal center,
you could also use R.E.D. Server or R.E.D. Server Developement: See
the q4md-forcefieldtools.org web site...
To start you just provide a PDB file for the active site; Ante_R.E.D.
2.0 will generate a P2N file that is used in a second step by the
R.E.D. IV program.
regards, Francois
> 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?
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Received on Sun Apr 21 2013 - 08:00:03 PDT
