[gmx-users] error with grompp

Shima Arasteh shima_arasteh2001 at yahoo.com
Fri Jun 29 15:04:40 CEST 2012


Check out the order of sections which you have included in your .top file. I always got this error because of the wrong orders of sections.


From: "reisingere at rostlab.informatik.tu-muenchen.de" <reisingere at rostlab.informatik.tu-muenchen.de>
To: gmx-users at gromacs.org 
Sent: Friday, June 29, 2012 5:24 PM
Subject: [gmx-users] error with grompp

Hi everybody,
I added ions to the solvent around my structure with the command:

genion -s 3m71_minim.tpr -o 3m71_minim_ion.gro -p 3m71.top -conc 0.1
-neutral -pname NA+ -nname CL-

and then I select the 13 (SOL)

Now I have in my topology file

[ molecules ]
; Compound        #mols
Protein_chain_A     1
DUM             30066
SOL         14305
NA+              32
CL-              32

which is correct in my opinion.

But now when I want to run grompp:

grompp -v -f minim_solv.mdp -c 3m71_minim_ion.gro -p 3m71.top -o
3m71_minim_ion.tpr 2>>logErr 1>>logOut

I always get the error:

No such moleculetype NA+

although I already included the ion topology file:

; Include topology for ions
#include "amber03.ff/ions.itp"

What is wrong here?

Best Eva

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