AMBER Archive (2008)

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

From: Chih-Ying Lin (chihying_at_usc.edu)
Date: Mon Apr 07 2008 - 12:10:43 CDT

HI

>From rdparm
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) => ca-ca-na-nh
       52: 0.000 3.14 3.0 :1_at_C5 :1_at_C4 :1_at_N1 :1_at_N2 (9,11,12,13) => ca-ca-na-nh
       54: 0.000 3.14 3.0 :1_at_N1 :1_at_N2 :1_at_C7 :1_at_C8 (12,13,14,15) => na-nh-ca-ca
       55: 0.000 3.14 3.0 :1_at_N1 :1_at_N2 :1_at_C7 :1_at_C12 (12,13,14,23) => na-nh-ca-ca

>From 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

They directed DIFFERENT Dihedrals.....
and I doubt that pk should NOT be ZERO for the case From rdparm....
How could I get the CORRECT diheral angle SOURCE?

Thanks
Lin

----- Original Message -----
From: "David A. Case" <case_at_scripps.edu>
Date: Monday, April 7, 2008 8:48 am
Subject: Re: AMBER: running minimisation on cis-azobenzene
To: amber_at_scripps.edu

> 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
> firstset 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
> parmchkdoesn'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
>
> --------------------------------------------------------------------
> ---
> The AMBER Mail Reflector
> To post, send mail to amber_at_scripps.edu
> To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu
>
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu