[gmx-users] Problem with position restraints

[David]

On Tue, 2002-09-10 at 04:53, Ben Tehan wrote:
> To fellow gromacs users,
> 	I am having some unexpected problems when trying to setup initial
> dynamics with restraints, has anyone seen this before?
> 
> >grompp -f pr.mdp -c post_min.gro -p 1a1v.top -o pr.tpr
> 
> Warning: as of GMX v 2.0 unit of compressibility is truly 1/bar
> checking input for internal consistency...
> calling /lib/cpp...
> processing topology...
> Generated 135 of the 1081 non-bonded parameter combinations
> Cleaning up temporary file gromppdOxKKF
> Fatal error: [ file "posre.itp", line 9 ]:
>              Atom index (4) in position_restraints out of bounds (1-1)
Yes, you probably included the ions.itp before the position restraints
or the other way around. You are trying to restrain atom 4 in a molecule
that has only one atom. Move the posre.itp up (or down)

> 
> 
> 
> >>posre.itp
> ; In this topology include file, you will find position restraint
> ; entries for all the heavy atoms in your original pdb file.
> ; This means that all the protons which were added by pdb2gmx are
> ; not restrained.
> 
> [ position_restraints ]
> ; atom  type      fx      fy      fz
>      1     1  1000  1000  1000
>      4     1  1000  1000  1000
>      5     1  1000  1000  1000
> etc...
> 
> >>post_min.gro
> Hepatitis B
> 53648
>     1PRO      N    1   4.430   5.708   1.998
>     1PRO     H1    2   4.468   5.630   2.049
>     1PRO     H2    3   4.449   5.694   1.900
>     1PRO     CA    4   4.286   5.719   2.026
>     1PRO     CB    5   4.266   5.854   2.095
>     1PRO     CG    6   4.404   5.885   2.150
>     1PRO     CD    7   4.499   5.829   2.045
>     1PRO      C    8   4.204   5.725   1.896
> etc...
> 
> 
> I appreciate any insights that anyone is able to give me with this
> problem.
> The posre.itp file is the one generated when first running pdb2gmx and I
> can't see anything wrong with it. 
> Thanks in advance,
> Ben.
> 
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-- 
Groeten, David.
________________________________________________________________________
Dr. David van der Spoel, 	Biomedical center, Dept. of Biochemistry
Husargatan 3, Box 576,  	75123 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://zorn.bmc.uu.se/~spoel
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