[gmx-users] berger-oplsaa combination for DPC micelle

Low Soo Mei lowsm at bii.a-star.edu.sg
Wed Jun 4 14:04:01 CEST 2008

Hi Gromacs users,

I am trying to simulate a protein with a micelle, and have used dpc.itp 
from Dr. Tieleman's site.  I have also introduced parts of lipid.itp 
into ffoplsaanb.itp and ffoplsaabon.itp in accordance with Chris Neale's 
half-epsilon double-pairlist method.  But when I issue a grompp command 
for minimization, grompp gives a fatal error that the "Bonded/nonbonded 
atom type 'CH3' not found!".  This atom type CH3 is present in dpc.itp.  
I am now wondering if I can match this to some existing atom in the 
oplsaa and how I might go about choosing which atom. 

I would be grateful for your advice, and am happy to attach files if needed.

Soo Mei

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