On Sun, Apr 06, 2008, Chih-Ying Lin wrote:
>
> And, what those :1.C3 :1.C4 :1.N1 :1.N2 means???
> And, what the cordinate (1,11,12,13) means?
>
> dihedral pk phase pn atoms
> 45: 0.000 3.14 3.0 :1.C3 :1.C4 :1.N1 :1.N2 (1,11,12,13)
> 52: 0.000 3.14 3.0 :1.C5 :1.C4 :1.N1 :1.N2 (9,11,12,13)
> 54: 0.000 3.14 3.0 :1.N1 :1.N2 :1.C7 :1.C8 (12,13,14,15)
> 55: 0.000 3.14 3.0 :1.N1 :1.N2 :1.C7 :1.C12 (12,13,14,23)
As the heading above those phrases indicates, these are atoms. The first
set of four strings is ":residue-number.atom-name", The numbers in
parentthese are atom numbers.
Did you look carefully at the output of parmchk?
> >
> > DIHE
> > ca-ha-ca-ca 1 0.000 0.000 0.000 ATTN,
> > need revision
^^^^^^^^^^^^^^
> > ca-ha-ca-ha 1 0.000 0.000 0.000 ATTN,
> > need revision
^^^^^^^^^^^^^^^^
When you get the "ATTN, need revision" statement, that means that parmchk
doesn't know how to assign the force constant, so it just puts in a
"placeholder". You will need to assign these torsions by hand.
...good luck...dac
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Received on Fri Apr 18 2008 - 21:17:38 PDT
