[gmx-users] (no subject)

Asmaa Elsheshiny pyaaea at leeds.ac.uk
Wed Sep 30 18:15:39 CEST 2009

Hi, everybody,
I tried to use pdb2gmx program to obtain .top& .gro files  but I eceived the following error message 
Fatal error:
Atom HB3 in residue ARG 1 not found in rtp entry with 24 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.
even when i add a n&c termials to the peptide, I find that there is no difference in the error message
also I checked .rtp file and if find there is no HB3 ( there is no 3 in any of the atomic numbering in any of the aminoacids residues), so I modified the .pdb file by changing thr numbering.
But this affects dramatically the shape of the the molecule ( cause distruction of certain portions of it). I do not want to use the flag -ignh because when i made this the molecule has changed greatly and affects my results badly. So what do you think that I could do?

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