I want to make a model of a GPCR inserted into lipid bilayer. I obtained the structure file for a solvated POPC bilayer from the CHARMM-GUI site. I used CHARMM27 force field to model the bilayer and *pdb2gmx *had no problem generating the *.gro, *.top, and posre.itp files. When I perform *grompp* I receive the following warning and error;
"WARNING 1 [file ffnonbonded.itp, line 130]: Overriding atomtype HOL" "ERROR 1 [file bilayer.top, line 271489]: No default U-B types" I though that the issue with creating Urey-Bradley interactions using *pdb2gmx *had been corrected in Gromacs-4.5.4. Please give me some advice on how to proceed further. Thank you, Jackson Chief Elk
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