[gmx-users] error_in topology

Justin A. Lemkul jalemkul at vt.edu
Mon Oct 10 13:02:04 CEST 2011

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.


> 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
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


More information about the gromacs.org_gmx-users mailing list