balaji nagarajan wrote:
Dear Users !
Thanks for the mail , now i fixed it
i have a general doubt,
i saw the path of gromacs
/usr/local/gromacs-4.5.3/share/top
there for the three point water model only spc216.gro is there is this
common for
all , ie ., spc , spc/e and tip3p.
Please see FAQ #1 under:
http://www.gromacs.org/Documentation/FAQs#System_Preparation_and_Preprocessing
-Justin
> Date: Mon, 10 Oct 2011 07:02:04 -0400
> From: jalem...@vt.edu
> To: gmx-users@gromacs.org
> Subject: Re: [gmx-users] error_in topology
>
>
>
> balaji nagarajan wrote:
> > Dear Users !
> >
> > I have a problem in generating the topology of the attached
molecule as pdb.
> >
> > earlier i have done using the same pdb for solvating the structure
using
> > spc and spce water box ,
> >
> > there was no such error when i do for TIP4P and oplsaa force field
i got
> > the error
> >
> > as follows
> >
> > -------------------------------------------------------
> > Program grompp, VERSION 4.5.3
> > Source code file: grompp.c, line: 523
> >
> > Fatal error:
> > number of coordinates in coordinate file (1AKI_solv.gro, 4164)
> > does not match topology (topol.top, 5527)
> > --------------------------------------------------------------------
> >
> > I used the following lines to do that
> >
> > pdb2gmx -ignh -ff oplsaa -f 1AKI.pdb -o 1AKI_processed.gro -water tip4p
> > editconf -f 1AKI_processed.gro -o 1AKI_newbox.gro -c -d 0.9 -bt cubic
> > genbox -cp 1AKI_newbox.gro -cs spc216.gro -o 1AKI_solv.gro -p topol.top
>
> You told pdb2gmx to write the TIP4P topology into your .top, but then
you used a
> 3-point water model. You need to solvate with tip4p.gro.
>
> -Justin
>
> > grompp -f sub.mdp -c 1AKI_solv.gro -p topol.top -o em.tpr
> > mdrun -v -deffnm em
> >
> > in the grompp it says the error , how to solve this , and it comes
only
> > for tip4p not for other water models.
> >
> > thanks in advance
> >
>
> --
> ========================================
>
> 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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