[gmx-users] problem with fullerene simulations
jampanis at gmail.com
Fri Jul 22 23:27:01 CEST 2011
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
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.
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/**
>> >**" 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
>> 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
>> 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 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
> gmx-users mailing list gmx-users at gromacs.org
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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
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