[gmx-users] A warning concerning file ffnonbonded.itp overriding atomtype OT

Hassan Shallal hshallal at PACIFIC.EDU
Tue Nov 30 20:44:07 CET 2010

Dear Gromacs society,
I was running a simulation using CHARMM27/TIP3P/virtual sites.
Gromacs version:  4.5.2
I had only one warning which says (file ffnonbonded.itp, line 68): overriding atomtype OT
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
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!!!
Second issue: while I am searching the web for the above issue, I camE across this website:
http://towhee.sourceforge.net/forcefields/charmm27.html <http://towhee.sourceforge.net/forcefields/charmm27.html> 
If you go all the way down to the section of Oxygen atom descriptions, you will find that OT has the description of ( Water oxygen, modified TIP3P model). 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 (OC is Carboxylate oxygen non-lipid version as mentioned in the same website)...
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
Any help, feedback, clarification is very much appreciated
Great regards
Hassan Shallal
University of the Pacific, CA
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