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<DIV><FONT face="Courier New">Hi GMX users,</FONT></DIV>
<DIV><FONT face="Courier New"></FONT> </DIV>
<DIV><FONT face="Courier New">I am dealing with a system which has a
Molybdenum-containing cofactor in it. I have written a "itp" file for this
cofactor, and included that in my top file and tried to use it, but I am
getting error, saying that it can't find the atom type 'MO' for the grompp
command.</FONT></DIV>
<DIV><FONT face="Courier New">Here is the few last line of the
message:</FONT></DIV>
<DIV><FONT face="Courier New"></FONT> </DIV>
<DIV>
<P class=MsoNormal style="MARGIN: 0in 0in 0pt"><FONT
face="Courier New">Processing topology …</FONT></P>
<P class=MsoNormal style="MARGIN: 0in 0in 0pt"><FONT
face="Courier New">Generated 1125 of the 1326 nonbonded parameter
combination</FONT></P>
<P class=MsoNormal style="MARGIN: 0in 0in 0pt"><FONT face="Courier New">Cleaning
up temporarily file grompp001302</FONT></P>
<P class=MsoNormal style="MARGIN: 0in 0in 0pt"><FONT face="Courier New">Fatal
error: atom type ‘MO’ not found! </FONT></P>
<P class=MsoNormal style="MARGIN: 0in 0in 0pt"><FONT
face="Courier New"></FONT> </P></DIV>
<DIV><FONT face="Courier New">I have named the molybdenum atom MO and have
added the following line into atommass.dat files:</FONT></DIV>
<DIV><FONT face="Courier New">??? MO 95.9400</FONT></DIV>
<DIV><FONT face="Courier New">I have also added a line into ffgmx.atp
file:</FONT></DIV>
<DIV><FONT face="Courier New">MO 95.94000 ; molybdenum</FONT></DIV>
<DIV><FONT face="Courier New">At the end of email I have put the content of
the itp file for the cofactor called MOS.</FONT></DIV>
<DIV><FONT face="Courier New"></FONT> </DIV>
<DIV><FONT face="Courier New">1) Would you please let me know if the itp file is
OK? I didn't add any values for bonds, angles and dihedrals. Are those info
necessary?</FONT></DIV>
<DIV><FONT face="Courier New"></FONT> </DIV>
<DIV><FONT face="Courier New">2) Is there any further changes that I need to do?
i.e. to add a necessary info into a particular file.</FONT></DIV>
<DIV><FONT face="Courier New"></FONT> </DIV>
<DIV> </DIV>
<DIV><FONT face="Courier New">Many thanks for your help.</FONT></DIV>
<DIV><FONT face="Courier New"></FONT> </DIV>
<DIV><FONT face="Courier New">Cheers, Saivoush</FONT></DIV>
<DIV><FONT face="Courier New"></FONT> </DIV>
<DIV><FONT face="Courier New"></FONT> </DIV>
<DIV><FONT face="Courier New"></FONT> </DIV>
<DIV><FONT face="Courier New">[ moleculetype ]</FONT></DIV>
<DIV><FONT face="Courier New">;name nrexcl</FONT></DIV>
<DIV><FONT face="Courier New">MOS 3</FONT></DIV>
<DIV><FONT face="Courier New">[ atoms ]</FONT></DIV>
<DIV><FONT face="Courier New">; nr type resnr resid atom cgnr
charge</FONT></DIV>
<DIV><FONT face="Courier New">1 MO 1 MOS MO 1 0.474</FONT></DIV>
<DIV><FONT face="Courier New">2 S 1 MOS S 1
-0.125</FONT></DIV>
<DIV><FONT face="Courier New">3 OA 1 MOS O1 1 -0.397</FONT></DIV>
<DIV><FONT face="Courier New">4 OA 1 MOS O2 1 -0.372</FONT></DIV>
<DIV><FONT face="Courier New">5 HS 1 MOS HAA 1 0.199</FONT></DIV>
<DIV><FONT face="Courier New">6 HS 1 MOS HAB 1 0.221</FONT></DIV>
<DIV><FONT face="Courier New">[ bonds ]</FONT></DIV>
<DIV><FONT face="Courier New">;ai aj fu </FONT></DIV>
<DIV><FONT face="Courier New">1 2 1 </FONT></DIV>
<DIV><FONT face="Courier New">1 3 1</FONT></DIV>
<DIV><FONT face="Courier New">1 4 1 </FONT></DIV>
<DIV><FONT face="Courier New">3 5 1 </FONT></DIV>
<DIV><FONT face="Courier New">4 6 1</FONT></DIV>
<DIV><FONT face="Courier New">[ angles ]</FONT></DIV>
<DIV><FONT face="Courier New">;ai aj ak fu </FONT></DIV>
<DIV><FONT face="Courier New">2 1 3 1 </FONT></DIV>
<DIV><FONT face="Courier New">2 1 4 1 </FONT></DIV>
<DIV><FONT face="Courier New">1 3 5 1 </FONT></DIV>
<DIV><FONT face="Courier New">1 4 6 1 </FONT></DIV>
<DIV><FONT face="Courier New">3 1 4 1 </FONT></DIV>
<DIV><FONT face="Courier New">[ dihedrals ]</FONT></DIV>
<DIV><FONT face="Courier New">;ai aj ak al fu </FONT></DIV>
<DIV><FONT face="Courier New">2 1 3 5 1 </FONT></DIV>
<DIV><FONT face="Courier New">2 1 4 6 1 </FONT></DIV>
<DIV><FONT face="Courier New">5 3 1 4 1 </FONT></DIV>
<DIV><FONT face="Courier New">6 4 1 3 1 </FONT></DIV></BODY></HTML>