OTOMSHOME/tools/convertatomnames.py -p protein.pdb -o protein_pms.pdb -s amber -c $PROTOMSHOME/data/atomnamesmap.dat</pre>
<p> 
The converted structure will be in <code>protein_pms.pdb</code>. This execution assumes that the Amber naming convention is used in <code>protein.pdb</code>. 
<p> 
<li>We have crystallographic waters in the protein structure and we need to convert them to the water model we will be using in the simulation (TIP4P). This can be done by 
<p> 
<pre>python $PROTOMSHOME/tools/convertwate