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<blockquote type=cite class=cite cite>I 'd like your help to create a
input file (.pdb, .gro,etc..) from a gamess calculation result.<br>
I converted a xyz file from the z-matrix in gamess output to pdb with
openbabel,<br>
but when I run pdb2gmx, the result is:<br>
"Fatal error: Residue 'UNK' not found in residue topology
database"</blockquote><br>
You are getting that error because the molecule name within the pdb file
is "UNK", and that is not a residue present within the force
field that you are trying to generate the topology for. If the
molecule happens to be a residue in the force field you want to use, then
simply change the "UNK" to the correct residue name.
However, more than likely the molecule isn't one in the list of residues
available, therefore you will have to generate it all yourself (covered
in the manual) and/or using the PRODRG server to generate one for
you.<br><br>
Catch ya,<br>
<x-sigsep><p></x-sigsep>
<b>Dr. Dallas Warren<br>
</b><i>Research Fellow<br>
</i>Department of Pharmaceutical Biology and Pharmacology<br>
Victorian College of Pharmacy, Monash University<br>
381 Royal Parade, Parkville VIC 3010<br>
<font color="#0000FF"><u>dallas.warren@vcp.monash.edu.au<br>
</u></font>+61 3 9903 9083<br>
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