[gmx-users] gbsa.itp problem

[Justin A. Lemkul]

Yao Yao wrote:
> Hi Justin,
> 
> Thanks for your reply. Is there a way I can use explicit water to get 
> rid of the error?
> 

Solvate as you would any normal system and don't try to use force field files 
from newer versions.

-Justin

> Thanks,
> 
> Yao
> 
> ------------------------------------------------------------------------
> *From:* Justin A. Lemkul <jalemkul at vt.edu>
> *To:* Yao Yao <yao0o at ymail.com>; Discussion list for GROMACS users 
> <gmx-users at gromacs.org>
> *Sent:* Tuesday, September 6, 2011 2:42 PM
> *Subject:* Re: [gmx-users] gbsa.itp problem
> 
> 
> 
> 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
> 
> -- ========================================
> 
> 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
> 
> ========================================
> 
> 

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

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

========================================