Hi,<br><br>in 4.0.3 (from cvs) charmm is included. Sorry for not mentioning the version. Generating the hydrogens works. What does not work, is using existing hydrogens.<br><br>Roland<br><br><div class="gmail_quote">On Fri, Jan 16, 2009 at 10:18 PM, Mark Abraham <span dir="ltr"><<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div class="Ih2E3d">Roland Schulz wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Hi,<br>
<br>
there seems to be something wrong with the sorting and identification of hydrogens in pdb2gmx when using CHARMM FF.<br>
<br>
It does not identify the hydrogen atoms correctly if they are already present, even if the names all match.<br>
<br>
To reproduce: Generate pdb with hydrogens using pdb2gmx. Then use this pdb as input of pdb2gmx again.<br>
<br>
Result e.g.:<br>
Atom H in residue VAL 2 not found in rtp entry with 16 atoms<br>
<br>
This does not happen with GROMOS or OPLS FF.<br>
</blockquote>
<br></div>
Sure. AFAIK nobody has written a functional ffcharmm.hdb file, so generation will not work. If someone has a need for one, they can write one. I'll be happy to include it in my GROMACS-CHARMM package.<br>
<br>
Mark<br>
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</blockquote></div><br><br clear="all"><br>-- <br>ORNL/UT Center for Molecular Biophysics <a href="http://cmb.ornl.gov">cmb.ornl.gov</a><br>