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.
Chris.
-- 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.
Cheers,
Soo Mei
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