Problems with MD

Hi, I am doing MD with a protein which has a magnesium atom and I have problems in the step “create protein system topology”. The FATAL error said: “Atom .R<MG 305>.A<MG 1> does not have a type”, and I don’t know how can I solve this error.

Hi Jonathan,

I’m assuming you are using the BioBB MD setup workflow from our website, is that correct?

In that case, the pdb2gmx step is using the default value for the force-field parameter, which is “amber99sb-ildn” (see the pdb2gmx BioBB documentation). This force-field should recognize the Magnesium atom, as it is included in the parameters files. Please make sure that your PDB looks something like this:

ATOM   1417  OXT ALA A 181      14.104  17.472   1.698  1.00 94.14           O
TER
HETATM 1419 MG    MG B 550      10.849  31.802  25.007  1.00 29.34          MG

where the magnesium is tagged as HETATM and has a different chain id.

If you are using a different force-field, then you should ensure that the MG atom is included in the parameter files.

That said, please take special care with metal ions, as they tend to be coordinated with protein side chains.

Hope this helps!

-Adam-

I am using the BioBB MD setup for AMBER and not GROMACS. I have changed the chain id as you say but I have the same error. My PDB looks something like this:

ATOM 4852 HH2 TRP A 304 41.652 -28.987 13.161 1.00 0.00 H
TER 4852 TRP A 304
HETATM 4853 MG MG B 305 39.253 -21.652 6.581 1.00 19.00 MG
END

Hi Jonathan,

ok, then we need to add the proper ions parameters for the Amber tleap program, which can be for example the ones associated to the TIP3P water model (the one used in the workflow). For that, you need to add this parameters in the forcefield property of the leap_gen_top building block:

prop = {
    "forcefield" : ["protein.ff14SB","water.tip3p"]
}

And the PDB should look like this:

ATOM   1417  OXT ALA A 178      14.104  17.472   1.698  1.00 94.14           O
TER    1417      ALA A 178
HETATM 1418  MG  MG  A 179      10.849  31.802  25.007  1.00 29.34          MG

Hope this helps!

-Adam-

PERFECT!!! Thanks so much Adam!