I forgot to add were leap crashes;
....................
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.
Impropers that add been set with N* were not applied.
I have set all bonds to the metal, while those between metal ligands and
the protein were not set (i.e.-CH2 free valencies)
fp
---------- Forwarded message ----------
From: Francesco Pietra <chiendarret.gmail.com>
Date: Wed, Dec 17, 2014 at 10:52 PM
Subject: leap crashes and set: Improper number of arguments!
To: AMBER Mailing List <amber.ambermd.org>
As before I forgot the subject, here again:
Using ambertools14, with a protein incorporating a tm complex (MOL), leap
crashed at generating .parm7/rsc7 for this residue. When loading the
residue, leap warns
> set MOL.1.C11 type CC
> set MOL.1.N1 type N*
set: Improper number of arguments!
usage: set <container> <parameter> <object>
or: set default <parameter> <value>
> set MOL.1.C12 type CW
> set MOL.1.H21 type H4
> set MOL.1.HE1 type H5
> set MOL.1.NE2 type N*
set: Improper number of arguments!
usage: set <container> <parameter> <object>
or: set default <parameter> <value>
when N* type is encountered.
Params for N* were provided in frcmod
N* 14.010 0.530 (and bonds angles dih)
and in leaprc:
{ "N*" "N" "sp2" }
set MOL.1.N1 type N*
set MOL.1.NE2 type N*
Is that a question of names?
thanks
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Received on Wed Dec 17 2014 - 14:30:02 PST
