[gmx-users] pdb2gmx error H atoms not found in rtb Database

p.keymer at student.qut.edu.au p.keymer at student.qut.edu.au
Wed May 19 05:06:01 CEST 2004

Hi All

This is my first time using Gromacs.  I have been trying to
gonerate a topology for a few protiens however every time I
run pdd2gmx I encounter this (or a similar) fatal eror.

Fatal error: Atom HB1 in residue ARG 1 not found in rtp
database 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 have managed to overcome this problem by editing the pdb
file and removing the H atoms as the output sugests. However i
am concerned that this will affect the results.

Please can someome help me 
Have I Done the right thing or is there another way to do

Thank you 

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