AMBER Archive (2002)

Subject: Re: carnal

From: Stéphane Teletchéa (steletch_at_biomedicale.univ-paris5.fr)
Date: Mon Nov 04 2002 - 04:09:10 CST

You forgot to declare what are the residues you want a fit from :

Stef

DECLARE
  GROUP gALL (RES 1-20);
  RMS t1 FIT gALL s1;

Le Jeudi 31 Octobre 2002 19:30, Ioana Cozmuta a écrit :
> Hi amber users,
>
> I am trying to do a rmsd calculation between my initial non-minimized
> structure of the protein and the subsequent minimized structures (at
> different steps in the minimization procedure). I am trying to use carnal
> for this just to learn how to use it but I keep on getting an error
> message. I did try to build the input file for carnal according to the
> example in the amber manual (those files are also pdb). The pdb files I am
> refering to in the input file are obtained from restart files using the
> ambPdb command.
>
> Here is my input file:
>
> FILES_IN
> PARM p1 polyAT_vac_Hmin.prmtop;
> STREAM s1
> min_gb.pdb
> fixit.pdb;
> FILES_OUT
> TABLE tab1 rms_to_start;
> DECLARE
> RMS r1 FIT gALL s1;
> OUTPUT
> TABLE tab1 r1;
> END
>
> And the error message:
>
> input stdin
>
> > FILES_IN
> > PARM p1 polyAT_vac_Hmin.prmtop;
>
> Reading parm file (polyAT_vac_Hmin.prmtop) parm: opening
> polyAT_vac_Hmin.prmtop
>
> > STREAM s1
> > min_gb.pdb
>
> Using default parm (polyAT_vac_Hmin.prmtop) for STREAM s1
>
> > fixit.pdb;
>
> stream: opening fixit.pdb
> Error: fixit.pdb: full pdb format not supported
> Only ATOM records in amber order allowed
>
> However, if I replace the pdb files with the original .restrt carnal
> works.
>
> My question is what is the way to do this calculation using .pdb files?
> For the record, I am using amber7.
>
> Thank you,
> Ioana