Dear researcher,
I want to simulate a selenium containing enzyme. But when i processed the selenium containing enzyme using pdb2gmx command so it is showing an error.
"Atom SE46 in residue CYS 597 was not found in rtp entry CYS with 11 atoms while sorting atoms"
please give me any suggestion how i can add the selenium during MDS.
You should first check the literature to see if this selenocysteine is actually functional. Sometimes the heavy atom derivative of a side chain (e.g. selenomethionine, selenocysteine) is used to simply get better diffraction of crystals, and the actual enzyme has the normal sulfur-containing amino acids. If that's the case, just replace Se by S and proceed as normal.
If it really is a selenocysteine, you will have to parametrize it. To do this, you must follow the prescribed parametrization procedure of the parent force field. This can be quite laborious to do.
Go to your force field topology parameter files in Gromacs Set up.
Check how the atom Selenium is defined there in atom types.
change name of Selenium in your input PDB file according to that file
Dear Chamikara
The selenocysteine is not defined in the gromacs rtp file. Is there any other option to generate the topology.
You may have to look for the values of the bond lengths and dihedral angles established through experiments between the metal and the atoms of the amino acids involved and then generate the rtp file manually.
You should first check the literature to see if this selenocysteine is actually functional. Sometimes the heavy atom derivative of a side chain (e.g. selenomethionine, selenocysteine) is used to simply get better diffraction of crystals, and the actual enzyme has the normal sulfur-containing amino acids. If that's the case, just replace Se by S and proceed as normal.
If it really is a selenocysteine, you will have to parametrize it. To do this, you must follow the prescribed parametrization procedure of the parent force field. This can be quite laborious to do.
Thanks for your answer @Justin Lemkul
It is really a functionally important residue in our enzyme. If i will generate the Se topology from ATB server. Can i add the generated topology to the rtp file or directly in the generated .top file and in .gro file.
Dear Rohit
Once you generate the Se topology. Just add the coordinate information in the .gro file and add the information of .itp file as like "#include "selenocytine.itp"" in the topol.top file.
It will work if everything else is right.
regards
Tanuj
The #include mechanism will not work for a single residue in a polymer chain. The proper approach is to parametrize the residue, introduce it into the .rtp, .hdb, etc and run pdb2gmx.
Thanks @ Tanuj sharma
Dear justin sir, I will find a paper where i can parameterize the Se parameter. But if you have some paper so please suggest me.
Dear @ Sir Justin
I found the residue topology in ATB server. Can i include this topology in rtp file and then generate the gromacs topology.
Dear Rohit
Any Force field, used in Gromacs basically uses physical properties of an atom to calculate interaction energy.
So whenever you generate any parameter that is values for physical properties of an atom you have to add values in
1. residuetypes.dat
2. ffnanonbonded.itp
3. ffnonbonded.itp
4. atomtypes.atp
For adding parameters for any amino acid, add values of parameters in
1. aminoacids.hdb
2. aminoacids.rtp
3. aminoacids.c.tdb
4. aminoacids.n.tdb
regards
Tanuj
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