[gmx-users] gbsa.itp problem

[Justin A. Lemkul]

Yao Yao wrote:
> Hi All,
> 
> when I grompp for energy minimization, I met the error like,
> 
> --------------------------------------------------------------
> Back Off! I just backed up mdout.mdp to ./#mdout.mdp.1#
> checking input for internal consistency...
> processing topology...
> Opening library file /share/apps/gromacs407/share/gromacs/top/ffamber03.itp
> Opening library file 
> /share/apps/gromacs407/share/gromacs/top/ffnonbonded.itp
> 
> WARNING 1 [file ffnonbonded.itp, line 38]:
>   Overriding atomtype NA
> 
> Opening library file /share/apps/gromacs407/share/gromacs/top/ffbonded.itp
> Opening library file /share/apps/gromacs407/share/gromacs/top/gbsa.itp
> 
> ERROR 1 [file gbsa.itp, line 1]:
>   Invalid directive implicit_genborn_params
> 
> 
> -------------------------------------------------------
> Program grompp, VERSION 4.0.7
> Source code file: toppush.c, line: 756
> 
> Fatal error:
> Unknown bond_atomtype 0.172
> -------------------------------------------------------
> 
> Since in the version 4.0.7 there is no gbsa.itp, I simply copied the 
> file with the same name from gmx 4.5-4 and introduced ffamber03 force 
> field into 4.0.7.
> I understand updating to 4.5.X will solve this problem, but for testing 
> my QMMM semi-empirical implementation, I have to use gmx version 4.0.7, 
> at least for now.
> So I am wondering if there is any way I can solve it in 4.0.7.
> 

You can't do implicit solvent simulations with a version < 4.5.

-Justin

-- 
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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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