AMBER Archive (2008)

Subject: Re: AMBER: running minimisation on cis-azobenzene

From: David A. Case (case_at_scripps.edu)
Date: Mon Apr 07 2008 - 10:39:24 CDT

On Sun, Apr 06, 2008, Chih-Ying Lin wrote:
>
> And, what those :1_at_C3 :1_at_C4 :1_at_N1 :1_at_N2 means???
> And, what the cordinate (1,11,12,13) means?
>
> dihedral pk phase pn atoms
> 45: 0.000 3.14 3.0 :1_at_C3 :1_at_C4 :1_at_N1 :1_at_N2 (1,11,12,13)
> 52: 0.000 3.14 3.0 :1_at_C5 :1_at_C4 :1_at_N1 :1_at_N2 (9,11,12,13)
> 54: 0.000 3.14 3.0 :1_at_N1 :1_at_N2 :1_at_C7 :1_at_C8 (12,13,14,15)
> 55: 0.000 3.14 3.0 :1_at_N1 :1_at_N2 :1_at_C7 :1_at_C12 (12,13,14,23)

As the heading above those phrases indicates, these are atoms. The first
set of four strings is ":residue-number_at_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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