Francesco,
I think using "N*" in a leap script (instead of N*) is only for
reading the atom types; obviously leap internally uses N*...
impropers are not mandatory FF parameters...
regards, Francois
> Renaming N* atom type as "N*", following yesterday suggestions here, leap
> loads my pdb, which includes new residue MOL (ambertools14 parm10 verbosity
> 2). bond commands are included in the leap script, linking all parts
> between MOL and the protein. However, leap crashes after loading the
> impropers of MOL. I would appreciate suggestions as to which kind of side
> investigation I could carry out in order to fix the problem. See also last
> part below, please.
>
>> saveamberparm MOL MOL.parm7 MOL.rsd7
> Checking Unit.
> WARNING: The unperturbed charge of the unit: -1.000000 is not zero.
>
> -- ignoring the warning.
>
> Building topology.
> Building atom parameters.
> Building bond parameters.
> Building angle parameters.
> Building proper torsion parameters.
> Building improper torsion parameters.
> --Impropers:
> 1 C11<MOL> - H21<MOL> - C12<MOL> - N2<MOL>
> 1 C12<MOL> - C13<MOL> - N2<MOL> - HE2<MOL>
> 1 C16<MOL> - O5<MOL> - C17<MOL> - O6<MOL>
> 1 C20<MOL> - OE1<MOL> - CD<MOL> - OE2<MOL>
> 1 C3<MOL> - O1<MOL> - C4<MOL> - O2<MOL>
> 1 C7<MOL> - O3<MOL> - C8<MOL> - O4<MOL>
> 1 C9<MOL> - N1<MOL> - C11<MOL> - C12<MOL>
> 1 CB<MOL> - ND1<MOL> - CG<MOL> - CD2<MOL>
> 1 CG<MOL> - HD1<MOL> - ND1<MOL> - CE1<MOL>
> 1 CG<MOL> - HD2<MOL> - CD2<MOL> - NE2<MOL>
> 1 CH3<MOL> - O<MOL> - C<MOL> - OXT<MOL>
> 1 N1<MOL> - H22<MOL> - C13<MOL> - N2<MOL>
> 1 ND1<MOL> - HE1<MOL> - CE1<MOL> - NE2<MOL>
> total 13 improper torsions applied
> Building H-Bond parameters.
> Incorporating Non-Bonded adjustments.
> Not Marking per-residue atom chain types.
> Marking per-residue atom chain types.
>
> To the extent that it might be relevant, notice that even though leap does
> not complain any more about atom type N* in the syntax "N*", impropers
> involving "N*" were not built.
>
> I wonder whether N* should be rewritten as "N*" also in the frcmod file,
> other that (as I did) in the script to leap, for example ipropers
>
>
> H5-N*-CR-NA -> H5-"N*"-CR-NA
>
> and similarly for bond, angles and dih
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Received on Fri Dec 19 2014 - 03:00:02 PST
