[gmx-users] grompp atomtype problem

[Mitchell Stanton-Cook]

This may be the case. However if not, I suggest you use the PRODRG beta 
server (top right hand corner on the main page) to produce output files 
for a more appropriate forcefield.

I have generated and used files successfully using the beta server in 
the ff43a1.

Cheers
Mitch

John E. Kerrigan wrote:
> 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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