[gmx-users] membrane protein simulation - errors

[Yunlong Liu]

Hi,


I am trying to use Gromacs 5.0 to run membrane protein simulation. I built my membrane protein system with POPC membrane and TIP3P water in VMD. Then I used gmx pdb2gmx to build gromacs topology files.


My force field is charmm22* and it contains a lipids.rtp entry. It can successfully recognize the POPC molecules in my pdb and the water. But it keeps complaining something like this :


Processing chain 7 'L' (5360 atoms, 40 residues)
Warning: Starting residue POPC1 in chain not identified as Protein/RNA/DNA.
Warning: Starting residue POPC2 in chain not identified as Protein/RNA/DNA.
Warning: Starting residue POPC3 in chain not identified as Protein/RNA/DNA.
Warning: Starting residue POPC7 in chain not identified as Protein/RNA/DNA.
Warning: Starting residue POPC8 in chain not identified as Protein/RNA/DNA.
More than 5 unidentified residues at start of chain - disabling further warnings.
Problem with chain definition, or missing terminal residues.
This chain does not appear to contain a recognized chain molecule.
If this is incorrect, you can edit residuetypes.dat to modify the behavior.

Then I modified the residuestypes.dat to add POPC and TIP3 into the file but it still keeps complaining.

I tried to ignore this and run grompp -f minim.mdp -c my.gro .. to generate the tpr file but I got an error like this:

-------------------------------------------------------
Program gmx, VERSION 5.0-rc1
Source code file: /home/yunlong/Downloads/gromacs-5.0-rc1/src/gromacs/gmxpreprocess/toppush.c, line: 2393

Fatal error:
Invalid Atomnr j: 5, b2->nr: 3

For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------?


I am wondering whether I can do membrane protein simulation in Gromacs without building the system in Gromacs.

Thanks.
Yunlong


Davis Yunlong Liu

BCMB - First Year PhD Candidate

School of Medicine

The Johns Hopkins University

E-mail: yliu120 at jhmi.edu<mailto:yliu120 at jhmi.edu>