[gmx-users] problem with fullerene simulations

Justin A. Lemkul jalemkul at vt.edu
Fri Jul 22 23:11:33 CEST 2011

jampani srinivas wrote:
> Hi Gromacs users,
> I am trying to run a fullerene simulaton in TIP4P water model, i am 
> using the "c70_G53a6.itp 
> <http://tfy.tkk.fi/soft/downloads/files/c70_G53a6.itp>" file downloaded 
>  from http://tfy.tkk.fi/soft/downloads/. i have added TIP4P water model 
> using genbox command, later when i am trying to generate .tpr file for 
> energy minimization it gives me the following error. 
> -------------------------------------------------------
> Program grompp, VERSION 4.5.4
> Source code file: toppush.c, line: 1166
> Fatal error:
> Atomtype OWT4 not found
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> -------------------------------------------------------
> I looked up in the mailing list and found many helpful comments but i 
> could not resolve the problem, i searched in the tip4p.itp file of 
> gromos force field and i could see that tip4p water model is defined in 
> that file, but i could not find the atom types defined in atomtypes.atp 
> file. when i try to enter the atom types for some reason it does not 
> read my entries. 

This may or may not be related to a bug that has been fixed in the development 
version of the code.  Simply adding OWT4 into atomtypes.atp is insufficient; you 
need to add nonbonded parameters in ffnonbonded.itp as well.  Without seeing the 
actual error message(s) you're getting, I don't dare guess further.

> here is my .top file
> ; The force field files to be included
> #include "ffG53a6.itp"
> [ moleculetype ]
> #include "fullerene.itp"
> ; Include water topology
> #include "tip4p.itp"
> [ system ]
> Fullerene in Water
> [ molecule ]
> FUL                   1
> SOL              1696
> Can anybody help me?

Is there a particular reason you need to use TIP4P?  The Gromos force fields 
were parameterized with SPC water, so that's what is expected to work.  In 
principle, you should be able to use any water model you want, but you still 
have to demonstrate that it's a valid approach.



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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