Dear gromacs users, I would like to perform simulations of a protein embedded in popc, using a force field of the gromos series and I downloaded popc.pdb, popc.itp, lipid.itpa and the force field ffG43a2x extended for lipids. Looking throughout the archive I found different suggestions, but none of them help me to successfully perform my simulations:
- Using the ffG43a2x* force field, when I run pdb2gmx on the popc.pdb, I get this error: Fatal error: Error in hdb file ffG43a2x.hdb: Wrong number of control atoms (2 iso 3) on line: 1 1 N -C CA - If I manually write a topology file for the ffG43a2x force field and submit it to grompp to write a .tpr, I get this error: Fatal error: Atomtype 'CA' not found! In the topology file I included both lipid.itp and popc.itp, and I commented the following lines in the lipid.itp file as suggested: [ defaults ] 1 1 - I also tried to add the different sections [ atomtypes ], [ pairtypes ], etc... of the lipid.itp files to ffG53a5* files, but I still get the error: Atomtype 'CA' not found! Does anybody know what I miss? Is there a way to resolve this problem and use popc with ffG53a5 or ffG43a2x? All comments are very appreciated! Thanks in advance! Chiara
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