On Thu, Jan 26, 2017, Paul Meister wrote:
> Sorry for not being specific. The tRNA isn't bound through the phosphate
> group, but is instead held to the protein through many hydrogen bonds. The
> 5' terminal phosphate is supposed to participate in the reaction. The PDB
> ID for this protein is 2DXI. Running the files through LEaP, it tells me
> that there are no parameters for OP3, a phosphate oxygen. The mol2 file
> from RED shows me that it is there and bound. I'm just not sure why there
> are parameters for the other two oxygen atoms, but not for OP3.
You can see why we really like to see *exact* error messages:
earlier you wrote that the atom was "not recognized"; now you are saying
that it has "no parameters". To me (as an Amber developer) these are very
different types of problems. Not recognizing an atom usually involves
problems with the residue or atom names; not finding parameters usually has to
do with the atom *type* and parameters that are loaded.
Try this: At the beginning of the tRNA, your PDB file looks like this:
ATOM 1 OP3 G C 501 19.050 87.190 73.029 1.00 73.49 O
ATOM 2 P G C 501 18.499 87.676 71.706 1.00 75.79 P
ATOM 3 OP1 G C 501 16.984 87.888 71.715 1.00 73.44 O
ATOM 4 OP2 G C 501 18.979 86.828 70.515 1.00 77.51 O
ATOM 5 O5' G C 501 19.153 89.150 71.502 1.00 63.81 O
ATOM 6 C5' G C 501 18.729 90.260 72.301 1.00 48.63 C
Change this to this:
ATOM 1 O OHE C 500 19.050 87.190 73.029 1.00 73.49 O
ATOM 2 P G C 501 18.499 87.676 71.706 1.00 75.79 P
ATOM 3 OP1 G C 501 16.984 87.888 71.715 1.00 73.44 O
ATOM 4 OP2 G C 501 18.979 86.828 70.515 1.00 77.51 O
ATOM 5 O5' G C 501 19.153 89.150 71.502 1.00 63.81 O
ATOM 6 C5' G C 501 18.729 90.260 72.301 1.00 48.63 C
This uses the standard Amber libraries, rather than those from RED, and you
should check the charges closely: they might not sum exactly to an integer.
If you'd rather use the RED mol2 file, you might ask Francois for help;
if asking for help here, you should post both the mol2 file you are using and
the exact inputs and outputs that are causing the problem.
...dac
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Received on Thu Jan 26 2017 - 19:30:02 PST
