Problems with MD

BioBB
1

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.

2

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-

3

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

4

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-

5

PERFECT!!! Thanks so much Adam!

6

Hi Adam,

I am writing to you because I am working again with a system similar to the one you helped me to solve some problems. The problem is again with the ionic metal. I am working with an x-ray structure (PDB code: 6aci) where the metal Mn has been modified by Mg and is coordinated to two carbonyl oxygens of a UDP molecule.

Last time we were talking about the atom type problems for Mg we could solve it but when I launched the free molecular dynamics I could observe a distortion of the oxygen atoms of the terminal phosphate group of the UDP. I don’t know if there would be any solution for that.

Also, in this same case I realized that when I changed the Mn to Mg I forgot to add the two positive charges to the metal. When I have now done so, I find this error:

/home/usuario/anaconda3/envs/biobb_AMBER_MDsetup_tutorials/bin/teLeap: Error!
Could not find bond parameter for atom types: O2 - Mg2+
*** for atom OD2 at position 39.211000, -19.819000, 5.246000 ***
*** and atom MG at position 39.232000, -21.635000, 6.528000.***

/home/usuario/anaconda3/envs/biobb_AMBER_MDsetup_tutorials/bin/teLeap: Error!
Could not find bond parameter for atom types: O - Mg2+
*** for atom OD1 at position 37.824000, -22.611000, 5.309000 ***
*** and atom MG at position 39.232000, -21.635000, 6.528000.***

/home/usuario/anaconda3/envs/biobb_AMBER_MDsetup_tutorials/bin/teLeap: Error!
Could not find bond parameter for atom types: OH - Mg2+
*** for atom OG at position 40.832000, -22.350000, 4.982000 ***
*** and atom MG at position 39.232000, -21.635000, 6.528000.***

/home/usuario/anaconda3/envs/biobb_AMBER_MDsetup_tutorials/bin/teLeap: Error!
Could not find bond parameter for atom types: Mg2+ - o
*** for atom MG at position 39.232000, -21.635000, 6.528000 ***
*** and atom O1A at position 40.763000, -20.610000, 7.698000.***

/home/usuario/anaconda3/envs/biobb_AMBER_MDsetup_tutorials/bin/teLeap: Error!
Could not find bond parameter for atom types: Mg2+ - o
*** for atom MG at position 39.232000, -21.635000, 6.528000 ***
*** and atom O1B at position 39.449000, -23.421000, 7.774000.***
Building angle parameters.

/home/usuario/anaconda3/envs/biobb_AMBER_MDsetup_tutorials/bin/teLeap: Error!
Could not find angle parameter for atom types: O2 - Mg2+ - O
*** for atom OD2 at position 39.211000, -19.819000, 5.246000,***
*** atom MG at position 39.232000, -21.635000, 6.528000,***
*** and atom OD1 at position 37.824000, -22.611000, 5.309000.***

/home/usuario/anaconda3/envs/biobb_AMBER_MDsetup_tutorials/bin/teLeap: Error!
Could not find angle parameter for atom types: O2 - Mg2+ - OH
*** for atom OD2 at position 39.211000, -19.819000, 5.246000,***
*** atom MG at position 39.232000, -21.635000, 6.528000,***
*** and atom OG at position 40.832000, -22.350000, 4.982000.***

/home/usuario/anaconda3/envs/biobb_AMBER_MDsetup_tutorials/bin/teLeap: Error!
Could not find angle parameter for atom types: O2 - Mg2+ - o
*** for atom OD2 at position 39.211000, -19.819000, 5.246000,***
*** atom MG at position 39.232000, -21.635000, 6.528000,***
*** and atom O1A at position 40.763000, -20.610000, 7.698000.***

/home/usuario/anaconda3/envs/biobb_AMBER_MDsetup_tutorials/bin/teLeap: Error!
Could not find angle parameter for atom types: O2 - Mg2+ - o
*** for atom OD2 at position 39.211000, -19.819000, 5.246000,***
*** atom MG at position 39.232000, -21.635000, 6.528000,***
*** and atom O1B at position 39.449000, -23.421000, 7.774000.***

/home/usuario/anaconda3/envs/biobb_AMBER_MDsetup_tutorials/bin/teLeap: Error!
Could not find angle parameter for atom types: CO - O2 - Mg2+
*** for atom CG at position 38.803000, -18.693000, 5.581000,***
*** atom OD2 at position 39.211000, -19.819000, 5.246000,***
*** and atom MG at position 39.232000, -21.635000, 6.528000.***

/home/usuario/anaconda3/envs/biobb_AMBER_MDsetup_tutorials/bin/teLeap: Error!
Could not find angle parameter for atom types: O - Mg2+ - OH
*** for atom OD1 at position 37.824000, -22.611000, 5.309000,***
*** atom MG at position 39.232000, -21.635000, 6.528000,***
*** and atom OG at position 40.832000, -22.350000, 4.982000.***

/home/usuario/anaconda3/envs/biobb_AMBER_MDsetup_tutorials/bin/teLeap: Error!
Could not find angle parameter for atom types: O - Mg2+ - o
*** for atom OD1 at position 37.824000, -22.611000, 5.309000,***
*** atom MG at position 39.232000, -21.635000, 6.528000,***
*** and atom O1A at position 40.763000, -20.610000, 7.698000.***

/home/usuario/anaconda3/envs/biobb_AMBER_MDsetup_tutorials/bin/teLeap: Error!
Could not find angle parameter for atom types: O - Mg2+ - o
*** for atom OD1 at position 37.824000, -22.611000, 5.309000,***
*** atom MG at position 39.232000, -21.635000, 6.528000,***
*** and atom O1B at position 39.449000, -23.421000, 7.774000.***

/home/usuario/anaconda3/envs/biobb_AMBER_MDsetup_tutorials/bin/teLeap: Error!
Could not find angle parameter for atom types: C - O - Mg2+
*** for atom CG at position 36.784000, -23.074000, 4.835000,***
*** atom OD1 at position 37.824000, -22.611000, 5.309000,***
*** and atom MG at position 39.232000, -21.635000, 6.528000.***

/home/usuario/anaconda3/envs/biobb_AMBER_MDsetup_tutorials/bin/teLeap: Error!
Could not find angle parameter for atom types: HO - OH - Mg2+
*** for atom HG at position 41.017000, -23.236000, 4.652000,***
*** atom OG at position 40.832000, -22.350000, 4.982000,***
*** and atom MG at position 39.232000, -21.635000, 6.528000.***

/home/usuario/anaconda3/envs/biobb_AMBER_MDsetup_tutorials/bin/teLeap: Error!
Could not find angle parameter for atom types: OH - Mg2+ - o
*** for atom OG at position 40.832000, -22.350000, 4.982000,***
*** atom MG at position 39.232000, -21.635000, 6.528000,***
*** and atom O1A at position 40.763000, -20.610000, 7.698000.***

/home/usuario/anaconda3/envs/biobb_AMBER_MDsetup_tutorials/bin/teLeap: Error!
Could not find angle parameter for atom types: OH - Mg2+ - o
*** for atom OG at position 40.832000, -22.350000, 4.982000,***
*** atom MG at position 39.232000, -21.635000, 6.528000,***
*** and atom O1B at position 39.449000, -23.421000, 7.774000.***

/home/usuario/anaconda3/envs/biobb_AMBER_MDsetup_tutorials/bin/teLeap: Error!
Could not find angle parameter for atom types: 2C - OH - Mg2+
*** for atom CB at position 41.781000, -21.469000, 4.400000,***
*** atom OG at position 40.832000, -22.350000, 4.982000,***
*** and atom MG at position 39.232000, -21.635000, 6.528000.***

/home/usuario/anaconda3/envs/biobb_AMBER_MDsetup_tutorials/bin/teLeap: Error!
Could not find angle parameter for atom types: Mg2+ - o - p5
*** for atom MG at position 39.232000, -21.635000, 6.528000,***
*** atom O1A at position 40.763000, -20.610000, 7.698000,***
*** and atom PA at position 41.837000, -21.184000, 8.554000.***

/home/usuario/anaconda3/envs/biobb_AMBER_MDsetup_tutorials/bin/teLeap: Error!
Could not find angle parameter for atom types: Mg2+ - o - p5
*** for atom MG at position 39.232000, -21.635000, 6.528000,***
*** atom O1B at position 39.449000, -23.421000, 7.774000,***
*** and atom PB at position 40.604000, -23.817000, 8.630000.***

/home/usuario/anaconda3/envs/biobb_AMBER_MDsetup_tutorials/bin/teLeap: Error!
Could not find angle parameter for atom types: o - Mg2+ - o
*** for atom O1A at position 40.763000, -20.610000, 7.698000,***
*** atom MG at position 39.232000, -21.635000, 6.528000,***
*** and atom O1B at position 39.449000, -23.421000, 7.774000.***
Building proper torsion parameters.

/home/usuario/anaconda3/envs/biobb_AMBER_MDsetup_tutorials/bin/teLeap: Error!
*** ** No torsion terms for atom types: O2-Mg2±O-C***
*** for atom OD2 at position 39.211000, -19.819000, 5.246000,***
*** atom MG at position 39.232000, -21.635000, 6.528000,***
*** atom OD1 at position 37.824000, -22.611000, 5.309000,***
*** and atom CG at position 36.784000, -23.074000, 4.835000.***

/home/usuario/anaconda3/envs/biobb_AMBER_MDsetup_tutorials/bin/teLeap: Error!
*** ** No torsion terms for atom types: O2-Mg2±OH-2C***
*** for atom OD2 at position 39.211000, -19.819000, 5.246000,***
*** atom MG at position 39.232000, -21.635000, 6.528000,***
*** atom OG at position 40.832000, -22.350000, 4.982000,***
*** and atom CB at position 41.781000, -21.469000, 4.400000.***

/home/usuario/anaconda3/envs/biobb_AMBER_MDsetup_tutorials/bin/teLeap: Error!
*** ** No torsion terms for atom types: O2-Mg2±OH-HO***
*** for atom OD2 at position 39.211000, -19.819000, 5.246000,***
*** atom MG at position 39.232000, -21.635000, 6.528000,***
*** atom OG at position 40.832000, -22.350000, 4.982000,***
*** and atom HG at position 41.017000, -23.236000, 4.652000.***

/home/usuario/anaconda3/envs/biobb_AMBER_MDsetup_tutorials/bin/teLeap: Error!
*** ** No torsion terms for atom types: O2-Mg2±o-p5***
*** for atom OD2 at position 39.211000, -19.819000, 5.246000,***
*** atom MG at position 39.232000, -21.635000, 6.528000,***
*** atom O1A at position 40.763000, -20.610000, 7.698000,***
*** and atom PA at position 41.837000, -21.184000, 8.554000.***

/home/usuario/anaconda3/envs/biobb_AMBER_MDsetup_tutorials/bin/teLeap: Error!
*** ** No torsion terms for atom types: O2-Mg2±o-p5***
*** for atom OD2 at position 39.211000, -19.819000, 5.246000,***
*** atom MG at position 39.232000, -21.635000, 6.528000,***
*** atom O1B at position 39.449000, -23.421000, 7.774000,***
*** and atom PB at position 40.604000, -23.817000, 8.630000.***

/home/usuario/anaconda3/envs/biobb_AMBER_MDsetup_tutorials/bin/teLeap: Error!
*** ** No torsion terms for atom types: O2-CO-O2-Mg2+***
*** for atom OD1 at position 37.929000, -18.525000, 6.455000,***
*** atom CG at position 38.803000, -18.693000, 5.581000,***
*** atom OD2 at position 39.211000, -19.819000, 5.246000,***
*** and atom MG at position 39.232000, -21.635000, 6.528000.***

/home/usuario/anaconda3/envs/biobb_AMBER_MDsetup_tutorials/bin/teLeap: Error!
*** ** No torsion terms for atom types: CO-O2-Mg2±O***
*** for atom CG at position 38.803000, -18.693000, 5.581000,***
*** atom OD2 at position 39.211000, -19.819000, 5.246000,***
*** atom MG at position 39.232000, -21.635000, 6.528000,***
*** and atom OD1 at position 37.824000, -22.611000, 5.309000.***

/home/usuario/anaconda3/envs/biobb_AMBER_MDsetup_tutorials/bin/teLeap: Error!
*** ** No torsion terms for atom types: CO-O2-Mg2±OH***
*** for atom CG at position 38.803000, -18.693000, 5.581000,***
*** atom OD2 at position 39.211000, -19.819000, 5.246000,***
*** atom MG at position 39.232000, -21.635000, 6.528000,***
*** and atom OG at position 40.832000, -22.350000, 4.982000.***

/home/usuario/anaconda3/envs/biobb_AMBER_MDsetup_tutorials/bin/teLeap: Error!
*** ** No torsion terms for atom types: CO-O2-Mg2±o***
*** for atom CG at position 38.803000, -18.693000, 5.581000,***
*** atom OD2 at position 39.211000, -19.819000, 5.246000,***
*** atom MG at position 39.232000, -21.635000, 6.528000,***
*** and atom O1A at position 40.763000, -20.610000, 7.698000.***

/home/usuario/anaconda3/envs/biobb_AMBER_MDsetup_tutorials/bin/teLeap: Error!
*** ** No torsion terms for atom types: CO-O2-Mg2±o***
*** for atom CG at position 38.803000, -18.693000, 5.581000,***
*** atom OD2 at position 39.211000, -19.819000, 5.246000,***
*** atom MG at position 39.232000, -21.635000, 6.528000,***
*** and atom O1B at position 39.449000, -23.421000, 7.774000.***

/home/usuario/anaconda3/envs/biobb_AMBER_MDsetup_tutorials/bin/teLeap: Error!
*** ** No torsion terms for atom types: 2C-CO-O2-Mg2+***
*** for atom CB at position 39.510000, -17.497000, 4.923000,***
*** atom CG at position 38.803000, -18.693000, 5.581000,***
*** atom OD2 at position 39.211000, -19.819000, 5.246000,***
*** and atom MG at position 39.232000, -21.635000, 6.528000.***

/home/usuario/anaconda3/envs/biobb_AMBER_MDsetup_tutorials/bin/teLeap: Error!
*** ** No torsion terms for atom types: O-Mg2±OH-2C***
*** for atom OD1 at position 37.824000, -22.611000, 5.309000,***
*** atom MG at position 39.232000, -21.635000, 6.528000,***
*** atom OG at position 40.832000, -22.350000, 4.982000,***
*** and atom CB at position 41.781000, -21.469000, 4.400000.***

/home/usuario/anaconda3/envs/biobb_AMBER_MDsetup_tutorials/bin/teLeap: Error!
*** ** No torsion terms for atom types: O-Mg2±OH-HO***
*** for atom OD1 at position 37.824000, -22.611000, 5.309000,***
*** atom MG at position 39.232000, -21.635000, 6.528000,***
*** atom OG at position 40.832000, -22.350000, 4.982000,***
*** and atom HG at position 41.017000, -23.236000, 4.652000.***

/home/usuario/anaconda3/envs/biobb_AMBER_MDsetup_tutorials/bin/teLeap: Error!
*** ** No torsion terms for atom types: O-Mg2±o-p5***
*** for atom OD1 at position 37.824000, -22.611000, 5.309000,***
*** atom MG at position 39.232000, -21.635000, 6.528000,***
*** atom O1A at position 40.763000, -20.610000, 7.698000,***
*** and atom PA at position 41.837000, -21.184000, 8.554000.***

/home/usuario/anaconda3/envs/biobb_AMBER_MDsetup_tutorials/bin/teLeap: Error!
*** ** No torsion terms for atom types: O-Mg2±o-p5***
*** for atom OD1 at position 37.824000, -22.611000, 5.309000,***
*** atom MG at position 39.232000, -21.635000, 6.528000,***
*** atom O1B at position 39.449000, -23.421000, 7.774000,***
*** and atom PB at position 40.604000, -23.817000, 8.630000.***

/home/usuario/anaconda3/envs/biobb_AMBER_MDsetup_tutorials/bin/teLeap: Error!
*** ** No torsion terms for atom types: C-O-Mg2±OH***
*** for atom CG at position 36.784000, -23.074000, 4.835000,***
*** atom OD1 at position 37.824000, -22.611000, 5.309000,***
*** atom MG at position 39.232000, -21.635000, 6.528000,***
*** and atom OG at position 40.832000, -22.350000, 4.982000.***

/home/usuario/anaconda3/envs/biobb_AMBER_MDsetup_tutorials/bin/teLeap: Error!
*** ** No torsion terms for atom types: C-O-Mg2±o***
*** for atom CG at position 36.784000, -23.074000, 4.835000,***
*** atom OD1 at position 37.824000, -22.611000, 5.309000,***
*** atom MG at position 39.232000, -21.635000, 6.528000,***
*** and atom O1A at position 40.763000, -20.610000, 7.698000.***

/home/usuario/anaconda3/envs/biobb_AMBER_MDsetup_tutorials/bin/teLeap: Error!
*** ** No torsion terms for atom types: C-O-Mg2±o***
*** for atom CG at position 36.784000, -23.074000, 4.835000,***
*** atom OD1 at position 37.824000, -22.611000, 5.309000,***
*** atom MG at position 39.232000, -21.635000, 6.528000,***
*** and atom O1B at position 39.449000, -23.421000, 7.774000.***

/home/usuario/anaconda3/envs/biobb_AMBER_MDsetup_tutorials/bin/teLeap: Error!
*** ** No torsion terms for atom types: HO-OH-Mg2±o***
*** for atom HG at position 41.017000, -23.236000, 4.652000,***
*** atom OG at position 40.832000, -22.350000, 4.982000,***
*** atom MG at position 39.232000, -21.635000, 6.528000,***
*** and atom O1A at position 40.763000, -20.610000, 7.698000.***

/home/usuario/anaconda3/envs/biobb_AMBER_MDsetup_tutorials/bin/teLeap: Error!
*** ** No torsion terms for atom types: HO-OH-Mg2±o***
*** for atom HG at position 41.017000, -23.236000, 4.652000,***
*** atom OG at position 40.832000, -22.350000, 4.982000,***
*** atom MG at position 39.232000, -21.635000, 6.528000,***
*** and atom O1B at position 39.449000, -23.421000, 7.774000.***

/home/usuario/anaconda3/envs/biobb_AMBER_MDsetup_tutorials/bin/teLeap: Error!
*** ** No torsion terms for atom types: OH-Mg2±o-p5***
*** for atom OG at position 40.832000, -22.350000, 4.982000,***
*** atom MG at position 39.232000, -21.635000, 6.528000,***
*** atom O1A at position 40.763000, -20.610000, 7.698000,***
*** and atom PA at position 41.837000, -21.184000, 8.554000.***

/home/usuario/anaconda3/envs/biobb_AMBER_MDsetup_tutorials/bin/teLeap: Error!
*** ** No torsion terms for atom types: OH-Mg2±o-p5***
*** for atom OG at position 40.832000, -22.350000, 4.982000,***
*** atom MG at position 39.232000, -21.635000, 6.528000,***
*** atom O1B at position 39.449000, -23.421000, 7.774000,***
*** and atom PB at position 40.604000, -23.817000, 8.630000.***

/home/usuario/anaconda3/envs/biobb_AMBER_MDsetup_tutorials/bin/teLeap: Error!
*** ** No torsion terms for atom types: H1-2C-OH-Mg2+***
*** for atom HB3 at position 41.730000, -20.495000, 4.884000,***
*** atom CB at position 41.781000, -21.469000, 4.400000,***
*** atom OG at position 40.832000, -22.350000, 4.982000,***
*** and atom MG at position 39.232000, -21.635000, 6.528000.***

/home/usuario/anaconda3/envs/biobb_AMBER_MDsetup_tutorials/bin/teLeap: Error!
*** ** No torsion terms for atom types: H1-2C-OH-Mg2+***
*** for atom HB2 at position 42.764000, -21.862000, 4.642000,***
*** atom CB at position 41.781000, -21.469000, 4.400000,***
*** atom OG at position 40.832000, -22.350000, 4.982000,***
*** and atom MG at position 39.232000, -21.635000, 6.528000.***

/home/usuario/anaconda3/envs/biobb_AMBER_MDsetup_tutorials/bin/teLeap: Error!
*** ** No torsion terms for atom types: 2C-OH-Mg2±o***
*** for atom CB at position 41.781000, -21.469000, 4.400000,***
*** atom OG at position 40.832000, -22.350000, 4.982000,***
*** atom MG at position 39.232000, -21.635000, 6.528000,***
*** and atom O1A at position 40.763000, -20.610000, 7.698000.***

/home/usuario/anaconda3/envs/biobb_AMBER_MDsetup_tutorials/bin/teLeap: Error!
*** ** No torsion terms for atom types: 2C-OH-Mg2±o***
*** for atom CB at position 41.781000, -21.469000, 4.400000,***
*** atom OG at position 40.832000, -22.350000, 4.982000,***
*** atom MG at position 39.232000, -21.635000, 6.528000,***
*** and atom O1B at position 39.449000, -23.421000, 7.774000.***

/home/usuario/anaconda3/envs/biobb_AMBER_MDsetup_tutorials/bin/teLeap: Error!
*** ** No torsion terms for atom types: XC-2C-OH-Mg2+***
*** for atom CA at position 41.637000, -21.324000, 2.869000,***
*** atom CB at position 41.781000, -21.469000, 4.400000,***
*** atom OG at position 40.832000, -22.350000, 4.982000,***
*** and atom MG at position 39.232000, -21.635000, 6.528000.***

/home/usuario/anaconda3/envs/biobb_AMBER_MDsetup_tutorials/bin/teLeap: Error!
*** ** No torsion terms for atom types: Mg2±o-p5-os***
*** for atom MG at position 39.232000, -21.635000, 6.528000,***
*** atom O1A at position 40.763000, -20.610000, 7.698000,***
*** atom PA at position 41.837000, -21.184000, 8.554000,***
*** and atom O5’ at position 41.784000, -20.779000, 10.134000.***

/home/usuario/anaconda3/envs/biobb_AMBER_MDsetup_tutorials/bin/teLeap: Error!
*** ** No torsion terms for atom types: Mg2±o-p5-o***
*** for atom MG at position 39.232000, -21.635000, 6.528000,***
*** atom O1A at position 40.763000, -20.610000, 7.698000,***
*** atom PA at position 41.837000, -21.184000, 8.554000,***
*** and atom O2A at position 43.345000, -20.783000, 8.116000.***

/home/usuario/anaconda3/envs/biobb_AMBER_MDsetup_tutorials/bin/teLeap: Error!
*** ** No torsion terms for atom types: Mg2±o-p5-os***
*** for atom MG at position 39.232000, -21.635000, 6.528000,***
*** atom O1A at position 40.763000, -20.610000, 7.698000,***
*** atom PA at position 41.837000, -21.184000, 8.554000,***
*** and atom O3A at position 41.872000, -22.807000, 8.551000.***

/home/usuario/anaconda3/envs/biobb_AMBER_MDsetup_tutorials/bin/teLeap: Error!
*** ** No torsion terms for atom types: Mg2±o-p5-os***
*** for atom MG at position 39.232000, -21.635000, 6.528000,***
*** atom O1B at position 39.449000, -23.421000, 7.774000,***
*** atom PB at position 40.604000, -23.817000, 8.630000,***
*** and atom O3A at position 41.872000, -22.807000, 8.551000.***

/home/usuario/anaconda3/envs/biobb_AMBER_MDsetup_tutorials/bin/teLeap: Error!
*** ** No torsion terms for atom types: Mg2±o-p5-o***
*** for atom MG at position 39.232000, -21.635000, 6.528000,***
*** atom O1B at position 39.449000, -23.421000, 7.774000,***
*** atom PB at position 40.604000, -23.817000, 8.630000,***
*** and atom O2B at position 41.260000, -25.260000, 8.291000.***

/home/usuario/anaconda3/envs/biobb_AMBER_MDsetup_tutorials/bin/teLeap: Error!
*** ** No torsion terms for atom types: Mg2±o-p5-o***
*** for atom MG at position 39.232000, -21.635000, 6.528000,***
*** atom O1B at position 39.449000, -23.421000, 7.774000,***
*** atom PB at position 40.604000, -23.817000, 8.630000,***
*** and atom O3B at position 40.290000, -23.923000, 10.216000.***

/home/usuario/anaconda3/envs/biobb_AMBER_MDsetup_tutorials/bin/teLeap: Error!
*** ** No torsion terms for atom types: o-Mg2±o-p5***
*** for atom O1A at position 40.763000, -20.610000, 7.698000,***
*** atom MG at position 39.232000, -21.635000, 6.528000,***
*** atom O1B at position 39.449000, -23.421000, 7.774000,***
*** and atom PB at position 40.604000, -23.817000, 8.630000.***

/home/usuario/anaconda3/envs/biobb_AMBER_MDsetup_tutorials/bin/teLeap: Error!
*** ** No torsion terms for atom types: p5-o-Mg2±o***
*** for atom PA at position 41.837000, -21.184000, 8.554000,***
*** atom O1A at position 40.763000, -20.610000, 7.698000,***
*** atom MG at position 39.232000, -21.635000, 6.528000,***
*** and atom O1B at position 39.449000, -23.421000, 7.774000.***
Building improper torsion parameters.
*** total 1284 improper torsions applied***
Building H-Bond parameters.
Incorporating Non-Bonded adjustments.

I hope you can help me.

Many thanks in advance.

Best reegards,
Jonathan

7

Hi Jonathan,

without seeing the tleap input file is difficult to find out, but I guess you are defining new bonds between the Mg and the oxygen atoms? That would explain tleap complaining about not having the parameters for bond, torsion, and angle terms. Atom coordination is much more complex and requires specific parameterization. Take a look here: Metal Ion Modeling Tutorial

What you can do is to just restraint the atoms so that they maintain the distances. It is not exactly the same experiment, but depending on the observable you want to analyse, maybe it’s enough.

Please remember that this forum is focused on problems with the BioBB Python library wrapping biomolecular simulation tools. We will always try to help you anyway, but tool-specific questions should be posted to the official forums (in this case the AMBER mailing list / AMBER archive).

Hope it helps!

Regards,

-Adam-