[gmx-users] Re: Problems prior to running lipid-protein simulation

Bruce Milne bfmilne at ff.up.pt
Wed Oct 10 17:49:23 CEST 2007

Dear Adak,

gmx-users-request at gromacs.org wrote:
> Dear All;
> when I try to run pdb2gmx command for making .top file of POPC+Protein, an error appears: Residue 'POPC' not found in residue topology database.
> I have copied all necessary .itp files in share folder and also in the path where it is run.
>   what could be the problem and how to solve it? (I have passed these steps long time ago but now I am not able to reproduce the procedure!)
> thanks;
> Adak Nasiripour.
I think the process you might be wanting to perform is to run pdb2gmx 
for your protein only (with suitably adjusted coordinates so that it 
matches your bilayer coordinates) and then add #include lines to the 
resulting topology to add in the POPC part *after* the force field 
#include statement:

#include "ffgmx.itp"
#include "lipids.itp"
#include "popc.itp"

 - assuming that these are your .itp file names. Then adjust the [ 
molecules ] section to list the number and type of your components and 
you should have a working .top file.

You don't have to run pdb2gmx for the whole system at any point (it's 
not going to work anyway unless you add the POPC parameters to all the 
force field files and then add the POPC residue to the  .rtp file so 
that  pdb2gmx can recognize it).



"Hamewith - the road that's never dreary"

Dr. Bruce F. Milne
Faculdade de Farmácia
Universidade do Porto
Rua Aníbal Cunha - 164

email: bfmilne at ff.up.pt

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