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 <b>pdb2gmx </b>had no problem generating the *.gro, *.top, and posre.itp files. When I perform <b>grompp</b> I receive the following warning and error;<div>
<br></div><div><div><div style="text-align: center;">"WARNING 1 [file ffnonbonded.itp, line 130]:</div><div style="text-align: center;"> Overriding atomtype HOL"</div><div><br></div></div><div><div style="text-align: center;">
"ERROR 1 [file bilayer.top, line 271489]:</div><div style="text-align: center;"> No default U-B types"</div><div><br></div></div><div>I though that the issue with creating Urey-Bradley interactions using <b>pdb2gmx </b>had been corrected in Gromacs-4.5.4. Please give me some advice on how to proceed further.</div>
<div><br></div><div>Thank you,</div><div>Jackson Chief Elk</div><div><br></div></div><div><br></div>