Dear Dr Case,
>> If you construct ATP from
>> http://q4md-forcefieldtools.org/REDDB/Project/F-90/ you will see that
>> the ATP mol2 file (FF lib) is composed of 4 residues; loading a FF lib
>> composed of >1 residue_s_ in the LEaP program can only be used if the
>> PDB file used to match the FF lib only contains ATP (i.e. not an
>> ATP-protein complex for instance). This is a strong limitation in
>> LEaP.
>
> I don't understand this, and I guess an example would help. We routinely
> load FF lib files that contain more than 1 residue, and use them to create
> protein-ligand files with no limitations that resemble the one your mention
> above. (For example, the standard protein libraries are lib files that
> contain many residues.)
Example: See the Java applet at http://q4md-forcefieldtools.org/REDS/
It loads UTP
http://q4md-forcefieldtools.org/REDS/mol2-Jmol/UTP2.mol2 composed of 4
residues.
And see the corresponding FF lib composed of a single residue:
http://q4md-forcefieldtools.org/REDS/mol2-Jmol/UTP2-2.mol2
[R.E.D. Python can generate a FF lib composed of the different
building blocks in a single FF lib composed of 4 residues, or composed
of a single residue (atom names are renamed if found identical in this
residue)].
I think the same append in the off file format:
less $AMBERHOME/dat/leap/lib/all_amino94.lib
Here the off file is just a juxtaposition of individual FF lib
composed of a single residue:
saveoff ALA all_amino94.lib
saveoff ARG all_amino94.lib
etc...
ALA contains a single residue; if ALA contains two residues (for the
backbone & side chain for instance) the match with the PDB file will
not occur (even if the residue & atom names are the same in the ALA FF
lib and in the PDB file, which contains a whole protein).
We already discussed about this problem...
regards, Francois
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Received on Wed Sep 18 2013 - 23:00:03 PDT
