[gmx-users] R: grompp atomtype problem

Anna Marabotti anna.marabotti at isa.cnr.it
Thu May 10 17:23:25 CEST 2007

Dear John,
you are right, that's what happened! I set up the protein with the Gromos96
ff as I use to do, but I followed the tutorial for the ligand, and so I used
the gromacs forcefield.
I will use the prodrg_beta site to obtain Gromos96 itp files. 
Many thanks for your help and best regards

-----Messaggio originale-----
Da: John E. Kerrigan [mailto:kerrigje at umdnj.edu] 
Inviato: giovedì 10 maggio 2007 16.41
A: amarabotti at isa.cnr.it; gmx-users at gromacs.org
Oggetto: grompp atomtype problem

Hi Anna,

Your input files did not come through.  However, it might be possible
you are using two different forcefields unintentionally?  In the
tutorial, we use the gromacs forcefield (ffgmx or pdb2gmx -ff gmx).
Perhaps you have used a different forcefield?  The prodrg site creates
ffgmx itp files.  The prodrg beta site creates Gromos96 itp files.  It's
easy to mix these up because the output is so similar.


> Hi all,
> I'm trying to simulate the MD of a protein with a ligand. Since it is the
> first time, I followed exactly (at least, I think so!) suggestions from
> "GROMACS tutorial for drug-enzyme complex" by J. Kerrigan. I started from
> the PDB coordinates of the complex, I extracted the coordinates of the
> ligand and created a .itp file for the ligand using the PRODRG server.
> I submitted the protein alone to pdb2gmx, and then I manually edited the
> .pdb and the .top files in order to re-introduce the coordinates of the
> ligand into the protein. Therefore, I opened the .pdb file of the protein
> created by pdb2gmx, and pasted the coordinates of the ligand obtained by
> PRODRG (changing the n. of residue to continue numbering), and I edited
> .top file by adding #include "lig.itp" in the ff statement, LIG in the [
> molecules ] section etc. Then I created the box with editconf, solvated it
> with genbox and started grompp before neutralizing the -5 charge of the
> protein with genion.
> The grompp output gave me a fatal error:
> Source code file: toputil.c, line 61

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