[gmx-users] problem pdb2gmx and dummy

[David]

On Thu, 2004-05-13 at 20:16, gerph at correo.unam.mx wrote:
> Dear gromacs user, 
> Until now I have simulations of my protein using default atoms definition for
> aromatics residues,  
> but when I tried to use "-dummy aromatics" option I have a consistent error (I
> tried whit differents proteins) 
> for the first residue, 
>  
> WARNING: atom H is missing in residue SER 1 in the pdb file 
>          You might need to add atom H to the hydrogen database of residue SER 
>          in the file ff???.hdb (see the manual) 
>  
> There were 1 missing atoms in molecule Protein_B 
> Number of bonds was 7439, now 7439 
> Opening library file /usr/share/gromacs/top/ffgmx2.ddb 
> Fatal error: Invalid directive NH3 in dummy database ffgmx2.ddb 
>  
> I tried with -ter -missing  to modify the NH3 if this corresponding to the
> termini residue and  
> include only one H missing, but it does not work. Before try modified the ddb
> file I want to know if  
> there some alternative to fix this problem. I use gromacs 3.2.1. 

With -dummy aromatics you should use the gromos96 force field.
With -dummy h you can also use the OPLS force field (if you need all
atoms). ffgmx2 is deprecated.


-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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