[gmx-users] Fatal Error

[David van der Spoel]

Dhananjay joshi wrote:
>  
> Dear all ,
> 
> I got following error while using pdb2gmx.
> 
> 
> Fatal error:
> Atom HD1 in residue HISB 61 not found in rtp entry with 12 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.
> 
> Which one is preferable removal of hydrogen or choise of different 
> protonation state ?
> 
> I have not yet tried any one....
Since HE1 is the default unless there are HBonds you may want to run 
interactively (-inter) or use -ignh and check where pdb2gmx puts the 
proton (where there is an HB  acceptor nearby).
> 
> Dhananjay
> 
> 
> 
> <http://adworks.rediff.com/cgi-bin/AdWorks/sigclick.cgi/www.rediff.com/signature-home.htm/1507191490@Middle5?PARTNER=3> 
> 
> 
> 
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-- 
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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