Modelling POPC lipids with gromos54a7.ff

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GROMACS version: gromacs/2023-cuda11.6.2-cpu-nompi
GROMACS modification: Yes/No
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Hello, I am trying to build a system of gramicidin A (containing Formyl-valine and ethanolamine as residues) in a POPC lipid bilayer. I’d like to use the G54A7 force field for modeling my system. The G54A7.ff folder contains a popc.itp file that I tried to “#include” as suggested here, but I’m still getting an error saying:

Fatal error:
Residue ‘POPC’ not found in residue topology database

I could only find a lipid.rtp file in the CHARMM forcefield folder. However, I wish to stick to the G54A7 ff due to other reasons. Is there anyway I can model my system by using the popc.itp file alone? Where can I find/ How can I build the right lipid.rtp file for my system?

Thank you.

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Hi,
Do you get the error when you run gmx pdb2gmx ? or ?
\Alessandra

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Yes. That is where I am running into this error. Apologies for not specifying it earlier.

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Hi,
The reason of the error (Residue ‘POPC’ not found in residue topology database) is that POPC is not defined in the rtp database.
An option is to create the top file for gramicidin A (using pdb2gmx and only on a structural file of gramicidin A). Then include POPC.itp into the topology in the correct position (PS GROMACS topology is hierarchical ) manually most likely before the water itp file and adjust the number of POPC molecules at the end of topol file.
\Alessandra