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
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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