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?
Cheers,
Pyaaea _______________________________________________
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