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
--
========================================
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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