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<DIV><FONT face=Arial size=2>thank you for help :)</FONT></DIV>
<DIV><FONT face=Arial size=2>michal </FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
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<DIV>There is no Gromacs tool to do this (yet), but there are some scripts
<BR>floating<BR>around to merge .top or .itp files.<BR>I'll attach one I have
written a long time ago, so don't laugh about the<BR>style. It still works fine
for me. You also need to merge the coordinate<BR>files (.pdb or .gro or
whatever). I also have a script for this somewhere.<BR>Let me know if you need
it.<BR><BR>Regards,<BR>Uwe<BR><BR>Michal Kolinski wrote:<BR><BR>><I> Thank
you for advice. In my case I have receptor protein with a <BR></I>><I>
ligand inside the active site of the receptor.
<BR></I>><I><BR></I>><I> I need to constrain distance between one of the
receptors atom and one <BR></I>><I> of the ligands atom
to<BR></I>><I><BR></I>><I> force a proper orientation of the ligand during
the simulation. As I <BR></I>><I> understand I have
to<BR></I>><I><BR></I>><I> combine both topologies (for receptor and
ligand) and then put it in a <BR></I>><I> single *.tip file.
<BR></I>><I><BR></I>><I> Is there a simple way to
rewrite/renumber all the atoms of the ligand?<BR></I>><I><BR></I>><I>
Michal<BR></I>><I><BR></I>><I>------------------------------------------------------------------------<BR></I></DIV></BODY></HTML>