[gmx-users] grompp atomtype problem

[John E. Kerrigan]

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.

John

> 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. Then
> 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 the
> .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
> FATAL ERROR: ATOMTYPE 'CH3' NOT FOUND

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