[gmx-users] grompp error with gromacs-3.3

[Erik Lindahl]

Hi,

>
>
> I checked that line and it contains information for dihedrals (made  
> by prodrg webserver)
> [ dihedrals ]
> ; ai  aj  ak  al  fu    c0, c1, m, ...
>    3   1   4  13   2     35.3  334.8 0     35.3  334.8 0 ; imp    
> C2*  O2*  C3*  C1*
>
>    4   3   5  11   2     35.3  334.8 0     35.3  334.8 0 ; imp    
> C3*  C2*  O3*  C4*
>
> Could you give me some suggestions? Thanks.
This is due to better error control in grompp.

The torsion above is specified as harmonic function form (often  
called "improper" in Gromacs, for historical reasons). For this  
interaction type there should be two parameters per state - the  
equilibrium angle and force constant (Table 5.4 in the manual).

I would _guess_ you should remove the 0's, it might be good to check  
with Daan (prodrg author).


Cheers,

Erik


-----------------------------------------------------------
Erik Lindahl  <lindahl at sbc.su.se>
Assistant Professor, Stockholm Bioinformatics Center
Stockholm University, SE 106 91 Stockholm
Phone: +46 8 5537 8564     Fax: +46 8 5537 8214