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
thanks
francesco pietra
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Received on Thu Dec 18 2014 - 11:00:03 PST
