Hi Guys, I have wasted a complete day to solve this but failed. I am using "top_all22_prot_metals.inp" topology file to prepare PSF for a protein having 2 ZN ions. I have experience in NAMD, therefore I followed the same protocol separate Hetatms and protein reconds. I used psfgen to patch them again.
Here it gives me an error..unknown residue type ZN. I carefully checked the Residue type mentioned in the FF that is ZN2, i changed ZN residue type to ZN2 in pdb text file and leave atom type to ZN but still its not working. Can any one suggest me some better way to handle it.
@Subin Sahu.. My PDB file has the atom type ZN and residue type ZN2. It is identical with the FF i mentioned above, where atom type is ZN and residue type is ZN2. I am unable to generate PSF file, so don't know how to check the PSF file. I tried different things, but failed. In the metal directory of the force field the author managed a PSF for Ag, where the atom type is AG and the residue type is AGM like the FF. So I already cared for this issue.
NAMD identifies atom type from PSF file. PDB file doen't have column for atom type here is the excerpt from NAMD website about PDB file:
"ATOM 17 NE2 GLN 2 25.562 32.733 1.806 1.00 19.49 1UBQ 87
The fields seen here in order from left to right are the record type, atom ID, atom name, residue name, residue ID, x, y, and z coordinates, occupancy, temperature factor (called beta), segment name, and line number."
If you cannot generate PSF file using psfgen you can use the script below. This script is to generate SiN3 but you can cahange it to match your requirements.
http://www.ks.uiuc.edu/Training/Tutorials/nanobio/bionano-tutorial-html/node5.html
Good luck.
Thanks Subin, but here I am a bit confused. All I am doing is to generate the PSF file. If I am unable to generate the PSF file then how can I find the PSF file to look for the matching residue name with FF.
Let me conclude my question. It might help to some in future. I corrected the residue type in PDB file according to the FF name. The pdb format is like this,
"ATOM 17 NE2 GLN 2 25.562 32.733 1.806 1.00 19.49 1UBQ 87.
The bold GLN is actually a residue type in the PDB file.
Second, upon this correction I didn't notice, but psfgen was not handling the pdb file in a correct way therefore every time i got Zinc in a different position. To avoid this, I used a combine pdb file containing both HETATM records and ATOM. Apart, I kept residue names in three letter code for ZN too, like ZN2.
Thanks all of you
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