[gmx-users] problem pdb2gmx and dummy

David spoel at xray.bmc.uu.se
Thu May 13 23:32:03 CEST 2004

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 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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