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Corina,<br><br>
<blockquote type=cite class=cite cite>"Fatal error: Residue '' not
found in residue topology database."<br>
I kind of expected it, I imagine that these ff do not have defined at
least one<br>
atomtype that I need for my molecule.</blockquote><br>
It isn't the atomtype, more the fact that it doesn't know the
residue.<br><br>
<blockquote type=cite class=cite cite> <br>
Where from to start fixing the problem? </blockquote><br>
You need to generate your own topology for the molecule. So you
need to define atom types, partial charges, bond length and constant,
dihedrals etc. The manual goes through the format needs for
topologies and there are quite a few discussions here on the list.
First you need to settle on the forcefield to use, then use that to build
the molecule.<br><br>
The error you are encountering is using pdb2gmx, which when you build
your own topologies you don't need to do. That step is to build the
topology of a protein that is built out of different residues quickly and
easily.<br><br>
<blockquote type=cite class=cite cite>Does one really need the residue
topology database? </blockquote><br>
No. It is just a handy tool to use with long proteins that are made
up of residues that fit together. Helps to automate the generation
of the topology.<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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