[gmx-users] pdb2gmx

[Luciano Tavares]

 Hi gmx's,

 I was trying to convert a peptide structure in *.pdb to *.gro using
pdb2gmx and it showed:


Using ffoplsaa force field
Opening library file /usr/local/gromacs/share/top/ffoplsaa.atp
Atomtype 696
Reading residue database... (ffoplsaa)
Opening library file /usr/local/gromacs/share/top/ffoplsaa.rtp
Residue 50
Sorting it all out...
Opening library file /usr/local/gromacs/share/top/ffoplsaa.hdb
Opening library file /usr/local/gromacs/share/top/ffoplsaa-n.tdb
Opening library file /usr/local/gromacs/share/top/ffoplsaa-c.tdb
Processing chain 1 (1623 atoms, 160 residues)
Opening library file /usr/local/gromacs/share/top/specbond.dat
5 out of 5 lines of specbond.dat converted succesfully
There are 240 donors and 241 acceptors
There are 1211 hydrogen bonds
Fatal error: Atom H in residue PRO 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.


What is the better option?  My structure was generated by Sybyl. Before, I
had choose the option -ignh, but I have been problem with EM.

Thanks in advance...

Luciano


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