I am trying to run a minimisation for actinomycin D and this error cam up. We checked the .itp file of actinomycin D and the CH3 shows as follows:
nr type resnr resid atom cgnr charge mass
1 CH3 1 UNK C43 1 0.000 15.0350
We don't think there is anything wrong with the above, and yet the error is still popping up. What could we do?
Giancarlos Ortega: Whichever force field you're using doesn't seem to have the "CH3" Atomtype for POPC's terminal methyl group. That said, it's very unlikely that your force field doesn't have parameters for a carbon in a methyl group. It's probably just named something else. For instance, in the CHARMM-36m force field, the atomtype for the carbon of a terminal methyl group on POPC's acyl chain is named "CTL3". For reference, I've included that POPC.itp.
The solution here is to either:
a) use the force field your popc.itp is made for,
b) switch to the CHARMM36m force field and use the POPC.itp I've included,
c) modify your popc.itp to reflect the naming for your desired force field, OR
d) set up your system with CHARMM-GUI which will create membrane and give you the proper *.itp files for your system.
CHARMM-GUI link: http://www.charmm-gui.org/?doc=input/membrane.bilayer
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