<html><head><style type="text/css"><!-- DIV {margin:0px;} --></style></head><body><div style="font-family:times new roman,new york,times,serif;font-size:12pt"><div>Why not use CHARMM36 FF? It is available in gromacs user contribution website.<br></div><div style="font-family:times new roman, new york, times, serif;font-size:12pt">If I remember correctly, charmm27 cannot yield correct area/lipid, you need to apply surface tension.<br><br>Cheeers,<br>Jianguo<br><div style="font-family:times new roman, new york, times, serif;font-size:12pt"><font face="Tahoma" size="2"><hr size="1"><b><span style="font-weight: bold;">From:</span></b> Jackson Chief <jchiefelk@gmail.com><br><b><span style="font-weight: bold;">To:</span></b> gmx-users@gromacs.org<br><b><span style="font-weight: bold;">Sent:</span></b> Monday, 5 September 2011 21:20:48<br><b><span style="font-weight: bold;">Subject:</span></b> [gmx-users] Error when performing grompp on lipid bilayer
modeled with CHARMM27<br></font><br><meta http-equiv="x-dns-prefetch-control" content="off">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>
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