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

chris.neale at utoronto.ca chris.neale at utoronto.ca
Wed Jun 4 18:01:33 CEST 2008

In general, you should always post your relevant files with your  
question. It makes it easier for us to answer you. That said, I happen  
to have already used DPC and here is what I have done. I made a new  
dpc_rename.itp and it is quite different, but should simulate the  
exact same. Here is the beginning of the atoms section

;Chris Neale modified atomtype names here to follow popc.itp
; Atoms double checked vs. popc.itp by CN Oct5 2006
[ atoms ]
;   nr    type   resnr  residu    atom    cgnr        charge          mass
      1     LC3       1    DPC      C1       1         0.4       ; qtot: 0.248
      2     LC3       1    DPC      C2       1         0.4       ; qtot: 0.496
      3     LC3       1    DPC      C3       1         0.4       ; qtot: 0.744
      4     LNL       1    DPC      N4       1        -0.5       ; qtot: 0.752
      5     LH2       1    DPC      C5       1         0.3       ; qtot: 1

and then you need to make modifications to the other sections so that  
the parameters are found appropriately.


-- original message --

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

More information about the gromacs.org_gmx-users mailing list