Hi Sven,<br>
<br>
The pdb file contains all hydrogens, while you chose a united-atom force field probably. Use the option -ignh.<br>
<br>
Cheers,<br>
<br>
Tsjerk<br><br><div><span class="gmail_quote">On 10/16/05, <b class="gmail_sendername">Sven Huttenhouse</b> <<a href="mailto:mdsimulation@hotmail.com">mdsimulation@hotmail.com</a>> wrote:</span><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
dear GROMACS users.<br><br>I'm a new gromacs user from Illinois Institute of Technology (IIT).<br><br>I'm trying to get the pdb file of Glycine to study glycine crystallization.<br>I found an online pdb file for it. but when I used pdb2gmx to convert it to
<br>a .gro file I got the following error message:<br><br>fatal error: atom H9 in risidue GLY 1 not found in rtp enrty with 7 atoms<br>while sorting atoms. maybe different protonation state. remove this hydrogen<br>or chose a different protonation state.
<br>option -ignh will ignore all hydrogen in the input.<br><br>I got the glycine pdb file from the following link<br><br><a href="http://wbiomed.curtin.edu.au/teach/biochem/tutorials/pdb/">http://wbiomed.curtin.edu.au/teach/biochem/tutorials/pdb/
</a><br><br>can any one help me please. and is there any other way to construct my .pdb<br>file for any molecule.<br>kind regards<br>Sven Huttenhouse.<br><br>_________________________________________________________________
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