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 <jalem...@vt.edu>
*To:* Discussion list for GROMACS users <gmx-users@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 <jalem...@vt.edu <mailto:jalem...@vt.edu>>
> *To:* Yao Yao <ya...@ymail.com <mailto:ya...@ymail.com>>; Discussion
list for GROMACS users <gmx-users@gromacs.org
<mailto:gmx-users@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
========================================
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