GROMACS version: 2019
GROMACS modification: Yes with plumed
I would like to simulate a protein containing a Zn ion bound to 4 Cys. After reading the
pdb2gmx input files section in the gromacs documentation and looking for similar cases in the gromacs mailing list/forum I tried the following approach:
- Separate the protein residues and the Zn residue in pdb file with a TER line, so that termini are correctly identified.
- Merge the 2 chains with the
-merge interactiveoption of pdb2gmx.
- Add a line
residuetypes.datin the force field folder.
- add a line
CYS SG 2 ZN ZN2 4 0.234 CYN ZN2to
specbond.datin the current folder, where the pdb file also resides (the documentation is not clear about where specbond.dat file should reside.)
There are a couple of things (probably related) that don’t work as expected.
First, when running pdb2gmx I get this warning:
Warning: No residues in chain starting at ZN21201 identified as Protein/RNA/DNA. This makes it impossible to link them into a molecule, which could either be correct or a catastrophic error. Please check your structure, and add all necessary residue names to residuetypes.dat if this was not correct.
But ZN2 is defined in residuetypes.dat. So why does this appear?
Second, when pdb2gmx prints the
Special Atom Distance matrix: ZN is not shown (only CYS-CYS distances), and when checking
topol.top, no bond has been created between ZN and the CYS residues, and the latter have not been renamed as CYN.
I’ve checked, and in the pdb file, the ZN–SG distances are: 0.225, 0.253, 0.211 and 0.247 nm. So they are within 10% of the distance specified in the
specbond.dat. Why aren’t these bonds created then and how should I define them or format the pdb so that they are created?
Thanks for your time.