On Mon, Nov 23, 2015, Ayesha Kanwal wrote:
> i put -ek flag to the below command and it generates sqm.in , sqm.out and mol2 file
Sounds like it worked...did you take a look at the sqm.out file, and compare
it to what happened before you added the -ek flag?
> and when i test the parameters through parmchk command
> parmchk -i sustiva.mol2 -f mol2 -o sustiva.frcmod
> the frcmod shows no angles the results of my frcmod file are:
There is no indication of any error here: all the angles that your molecule
needs are already in gaff.dat, so parmchk (you should really usd parmchk2)
doesn't put them into the frcmod file.
If you want to see all the parameters (including the ones in the gaff.dat
file) add '-a Y' to the parmchk2 command line.
Bottom line: it sounds like everything worked, at least from what you have
written.
....dac
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Received on Mon Nov 23 2015 - 05:30:06 PST
