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

[Justin A. Lemkul]

Hassan Shallal wrote:
> 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
> 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

Atom types (in the force field files and topology) and atom names (in the 
coordinate file) are different.  Your error has nothing to do with your 
C-terminal carboxylate.  Apparently, you're trying to use a heavy water model, 
since line 68 of ffnonbonded is:

66 OT  8   15.999400   -0.834  A   0.315057422683  0.6363864
67 #ifdef HEAVY_H
68 OT  8   9.951400    -0.834  A   0.315057422683  0.6363864 ; CHARMM TIP3p O
69 #endif

The normal OT type is on line 66, but is being overridden by a define statement.

-Justin

>  
> Great regards
> Hassan Shallal
> University of the Pacific, CA
>  
>  
> 

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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