[gmx-users] problem with fullerene simulations

[jampani srinivas]

Hi Justin,

Thanks for your reply, i have no particular choice i was using it for my
other work and just started with it.

Now i tried it again with spc model,

I still get the following error.
++++++++++++++++++++++++++++++++++++++++++++++
Program grompp, VERSION 4.5.4
Source code file: toppush.c, line: 1166

Fatal error:
Atomtype OWT3 not found
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
++++++++++++++++++++++++++++++++++++++++++++++

I could see these atoms are defined in .itp file of gromos force filed, but
i suspect some thing is going wrong with atom types in .atp file.

any suggestions?

Thanks
Srinivs.

On Fri, Jul 22, 2011 at 5:11 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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<http://tfy.tkk.fi/soft/downloads/files/c70_G53a6.itp>
>> >**" file downloaded  from http://tfy.tkk.fi/soft/**downloads/<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<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
>
> --
> ==============================**==========
>
> 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<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
> ==============================**==========
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-- 
*********************************************
*J. Srinivasa Rao
Post-doctoral Research Associate
Computational Biophysics Group
Department of Physics, Drexel University
3141 Chestnut St, Philadelphia, PA 19104
Ph:  215-895-1989
Web:http://jsrao.web.officelive.com/default.aspx*
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