Hi Julia - See my comments below:
> Thank you very much for your quick reply and the advice about the atom
> names. I changed some of the atom names so that the protein's pdb and the
> residue's mol2 files matched well, and that fixed the problems regarding
> unknown residue types and many of the warnings I was receiving. Now when I
> view the protein in the graphical editor, there are no long bonds, and atom
> types/charges all seem to be defined. However, I am still having problems
> with some unknown parameters.
Let me first say that I do not use .mol2 file format, and prefer to create
residues in .off file format. When you say no long bond, what exactly do
you mean? When you created the .mol2 file format for this particular
residue, did you create all the necessary bonds in xleap before saving it
in .mol2 format? Also, did you use gaff or amber99 ff to create the .mol2
for this residue?
> Could not find bond parameter for: C - n3
> Could not find bond parameter for: c - N
> Checking for angle parameters.
> Could not find angle parameter: O2 - C - n3
> Could not find angle parameter: O2 - C - n3
> Could not find angle parameter: C - n3 - c3
> Could not find angle parameter: C - n3 - hn
> Could not find angle parameter: C - n3 - hn
> Could not find angle parameter: CT - C - n3
> Could not find angle parameter: h4 - c - N
> Could not find angle parameter: o - c - N
> Could not find angle parameter: c - N - H
> Could not find angle parameter: c - N - CT
> Could not find angle parameter: c3 - c - N
> There are missing parameters.
> check: Warnings: 10
> Unit is OK.
All the above messages mean that you are missing the explained parameters
to define the molecule. Lower letter atom types mean gaff parameters
while the capital letters mean atom types for parm94/99 and its variants.
You mix both force fields, I think, which is reasonable thing to do if you
want to represent one part of the molecule with amber99 and the
other part with gaff, but the boundary regions need to be defined. That
is the reason why you are getting the above messages. When I say boundary,
it is the covalent bond region of SRP with the protein. So, in your frcmod
file, create all these missing parameters by making analogy to the
already defined sets in either gaff or amber94/99/etc. Hope this helps.
Good luck,
Ilyas
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Received on Fri Jul 08 2011 - 11:00:05 PDT
