[gmx-users] problem pdb2gmx and dummy

gerph at correo.unam.mx gerph at correo.unam.mx
Thu May 13 20:16:40 CEST 2004

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. 

Gerardo Perez Hernandez

UNAMonos Comunicándonos

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