On Fri, Oct 09, 2015, Jim Wu wrote:
>
> I tried to load the .frcmod and .lib files and the pdb file for rhodopsin
> with retinal. However, I am still finding that missing parameters. Looking
> closer, I realized that these were exactly the parameters for the retinal
> molecule. Furthermore, there were some strange bonds and it did not look
> like retinal at all.
For the missing parameters: double check the parmchk2 inputs and outputs:
are the atom types that are being looked for there the same as the "missing"
ones you encounter later? It sounds like somehow what you are finally
building does not match what parmchk2 had looked for.
As for "strange bonds/did not look like retinal": this sounds like a problem
with the coordinates in the input pdb file: LEaP just uses whatever structures
you give it: if it doesn't "look like retinal", check how you created the
input pdb file. (It is possible that the coordinates are OK but the list of
bonds is not; I don't have enough information to comment very much about
that.)
> Can someone please explain to me the general method for correctly creating
> the .prmtop and .inpcrd files for a protein-ligand complex? Am I going
> along the right track?
Tutorial B5 seems like it should be very close to what you are doing (GFP
rather than retinal, but the ideas are the same).
....dac
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Received on Sat Oct 10 2015 - 07:30:03 PDT
