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<DIV><FONT color=#000000 size=2 face=Arial>Dear Gromacs society,</FONT></DIV>
<DIV><FONT size=2 face=Arial></FONT> </DIV>
<DIV><FONT size=2 face=Arial>I was running a simulation using CHARMM27/TIP3P/virtual sites.</FONT></DIV>
<DIV><FONT size=2 face=Arial>Gromacs version: 4.5.2</FONT></DIV>
<DIV><FONT size=2 face=Arial></FONT> </DIV>
<DIV><FONT size=2 face=Arial>I had only one warning which says <STRONG>(file ffnonbonded.itp, line 68): overriding atomtype OT</STRONG></FONT></DIV>
<DIV><FONT size=2 face=Arial></FONT> </DIV>
<DIV><FONT size=2 face=Arial>In the .gro and .top files produced by pdb2gmx, the only atoms that are described as OT are the two oxygen atoms of the C-terminal carboxylic acid group (neutral in my system), they are assigned as OT1 and OT2...No other oxygen atom is described as OT</FONT></DIV>
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<DIV><FONT size=2 face=Arial>First questions: How harmful this warning could be to the integrity of my simulation? I would assume it shouldn't be that harmful because my system has a fairly big, well folded protein (331 residues) and the C-terminus is far far away from the area I am interested in, besides the overriding itself imply a corrective action by gromacs!!!</FONT></DIV>
<DIV><FONT size=2 face=Arial></FONT> </DIV>
<DIV><FONT size=2 face=Arial>Second issue: while I am searching the web for the above issue, I camE across this website:</FONT></DIV>
<DIV><A href="http://towhee.sourceforge.net/forcefields/charmm27.html"><FONT size=2 face=Arial>http://towhee.sourceforge.net/forcefields/charmm27.html</FONT></A></DIV>
<DIV><FONT size=2 face=Arial>If you go all the way down to the section of Oxygen atom descriptions, you will find that <STRONG>OT</STRONG> has the description of (<STRONG> Water oxygen, modified TIP3P model).</STRONG> Well, this is weird because the carboxylate oxygens in the C-terminal COOH group were assigned as OT1 and OT2 whereas thay should have been assigned as OC1 and OC2 (<STRONG>OC is Carboxylate oxygen non-lipid version</STRONG> as mentioned in the same website)...</FONT></DIV>
<DIV><FONT size=2 face=Arial></FONT> </DIV>
<DIV><FONT size=2 face=Arial>I changed the OT1 and OT2 designations in the .top and .gro files to OC1 and OC2 and repeat the simulation, I unexpectedly still get the above warning message... now it is really confusing and that's why I decided to seek help from the gromacs mailist</FONT></DIV>
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<DIV><FONT size=2 face=Arial>Any help, feedback, clarification is very much appreciated</FONT></DIV>
<DIV><FONT size=2 face=Arial></FONT> </DIV>
<DIV><FONT size=2 face=Arial>Great regards</FONT></DIV>
<DIV><FONT size=2 face=Arial>Hassan Shallal</FONT></DIV>
<DIV><FONT size=2 face=Arial>University of the Pacific, CA</FONT></DIV>
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