On Thu, Jun 14, 2012, Asmita Gupta wrote:
>
> I want to generate force field library files for an N3-protonated cytosine.
> For that, i used RED server (AnteRed for P2N file), gaussian 09 for
> goemetry optimization and finally RED tools for mol2 file generation. I
> created a .lib file on the lines of script given here :
> http://q4md-forcefieldtools.org/REDDB/projects/F-60/script1.ff. But after
> loading the resulting .lib file, tleap still is unable to recognize the
> modified residue in the PDB file and i get an error like this :
>
> Creating new UNIT for residue: PC sequence: 6
This indicates that your library file didn't load a unit named "PC". Use
the "list" command to see what units you have (after loading the .off file,
but before running loadPdb). Look at the off file to see if you can figure
out what is going on.
Your script to convert mol2 to off looks like you are confusing atom names
and atom types. You will be far better off to hand edit the mol2 file so that
the atom names match those in your PDB file, and the atom types match those
(as much as possible) for a regular cytosine residue. Then you won't need to
make the off file at all.
...good luck...dac
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Received on Thu Jun 14 2012 - 13:30:03 PDT
