[gmx-users] fatal error [using pdb2gmx]

Erik Lindahl lindahl at sbc.su.se
Mon Oct 24 20:28:32 CEST 2005


> Fatal error: Atom H1 in risidue GLY 2 not found in rtp entry with 7  
> atoms while sorting atoms. maybe different protonation state.  
> remove this hydrogen or choose a different protonation state.  
> Option -ignh will ignore all hydrogens in the input.
> I used force field # 3. Could you please explain to me how can I  
> solve this?

GROMOS96 45a3 is a united-atom force field, i.e. nonpolar hydrogens  
are merged with the carbons. Use the option "-ignh" to ignore the  
hydrogens in the input coordinate file, or choose an all-atom force  
field like OPLS-AA/L instead.



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

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