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<blockquote type=cite class=cite cite>Therefore it gets correct where all
the bonds are, angles etc. However, it has left out the details of
how long they are, force constants etc. As I said in the previous
email, I assumed that these would all be inserted into the .top file to
then be subsequently used by the rest of the software. If this
isn't the case, then I don't actually have a problem at all then, was
just expecting something else.</blockquote><br>
Well, I got to the stage today (having sorted out the force field,
residues etc) to start to use the .top file generated by pdb2gmx using
the new residues I had defined. However, grompp comes up with a
warning that there are no default angles suppled in .top, and has to use
zeros. That comes up 10 times then it halts, since 10 warnings is
where it is meant to.<br><br>
Therefore, from this I assume that pdb2gmx should be putting the bond
details, not just which atoms are involved, into the .top file.<br><br>
Are there any suggestions on why it may be the case that it isn't putting
those into the .top?<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<br>
Monash University<br>
381 Royal Parade<br>
Parkville VIC 3010<br>
<font color="#0000FF"><u>dallas.warren@vcp.monash.edu.au<br>
</u></font>+61 3 9903 9076</html>