[gmx-users] topology_for_3 point model

[Justin A. Lemkul]

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: jalemkul at vt.edu
>  > To: gmx-users at 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
>  >
>  > ========================================
>  > --
>  > gmx-users mailing list gmx-users at gromacs.org
>  > http://lists.gromacs.org/mailman/listinfo/gmx-users
>  > Please search the archive at 
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>  > Please don't post (un)subscribe requests to the list. Use the
>  > www interface or send it to gmx-users-request at gromacs.org.
>  > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> 

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

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

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