[gmx-users] Error when performing grompp on lipid bilayer modeled with CHARMM27

Justin A. Lemkul jalemkul at vt.edu
Mon Sep 5 15:24:31 CEST 2011

Jackson Chief wrote:
> 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"

Here you have an atomtype defined twice somehow.

> "ERROR 1 [file bilayer.top, line 271489]:
>   No default U-B types"

This error suggests you've created a bonded interaction for which parameters do 
not exist, probably through use of incorrect atom 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.

To what issue are you referring?



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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