[gmx-users] gbsa.itp problem

[Justin A. Lemkul]

Yao Yao wrote:
> I mean if I still want to use the introduced amber03 ff, when I solvate 
> it as normal, it asks for gbsa.itp,
> 
> ----------
> Fatal error:
> Library file gbsa.itp not found in current dir nor in default directories.
> (You can set the directories to search with the GMXLIB path variable)
> 
> ----------
> 
> So is there any other file I need to change?
> 

You're still using 4.5 force field files.  You need to be using the ones that 
came with 4.0.7 if you're using 4.0.7.

-Justin

> thanks,
> 
> yao
> 
> 
> ------------------------------------------------------------------------
> *From:* Justin A. Lemkul <jalemkul at vt.edu>
> *To:* Discussion list for GROMACS users <gmx-users at gromacs.org>
> *Sent:* Tuesday, September 6, 2011 3:21 PM
> *Subject:* Re: [gmx-users] gbsa.itp problem
> 
> 
> 
> 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 <mailto:jalemkul at vt.edu>>
>  > *To:* Yao Yao <yao0o at ymail.com <mailto:yao0o at ymail.com>>; Discussion 
> list for GROMACS users <gmx-users at gromacs.org 
> <mailto: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
> 
> ========================================
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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

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