I tried to apply charmm36 forcefield to my mixed lipid bilayer in two software different software (gromacs, accelrys). But in gromacs, error coming up with: POPE1 could not be recognized as protein/DNA/RNA ... and in accelrys says that could not be typed POP1, TIP3 and ...
Anyone can help me to pass through this ?
The GROMACS message is not an error; it is merely noting that it is detecting a residue that is not protein, DNA, or RNA (typically what pdb2gmx is used for). Since POPE is a lipid, this is correct. If pdb2gmx is failing, it must be due to a different reason.
For mixed membranes, a very easy method for setting the system up is to use the CHARMM-GUI. It will provide a GROMACS topology and all necessary input files.
Dear Justin,
would you please name some of reasons ? maybe I could figure something out.
(Like removing ResNum or InsCode, or changing the MEMB to Lipid)
I have tried CHARMM-GUI to, but it comes out with same massage !
Without a specific error, there's nothing for me to suggest because I don't know what problem I'm trying to solve.
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