[gmx-users] topology_for_3 point model

[balaji nagarajan]

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.


> 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
 		 	   		  
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20111010/cfa0431b/attachment.html>