I am tryin to simulate the glucose oxidase from Penicillium amagasakiense package in Gromacs. I added this molecule to the gromacs but when I want to calculate the force field, I get the error "residue not found" . According to some papers seems that I need to moves sugar parts and add H atoms to the molecule using YASARA. I have no idea how to do it. I cannot find any tutorial regarding removing some parts in YASARA and seems that YASARA is not free!!
Is there any other options to work with Penicillium amagasakiense without molecule manipulation?
Im trying to simulate the glucose oxidase just like what has been done in this paper
Article Molecular Effects of Encapsulation of Glucose Oxidase Dimer ...
Hi Safoora,
The pdb is a text file, so removal of the sugars (and crystal waters) is quite simple:
(Assuming you are working command line)
sed '/HETATM/d' file.pdb >no_sugars.pdb
If crystal waters are catylatic, you may need to keep some in. Refer to the publication you linked.
For the hydrogens:
When you build the pdb file using gmx pdb2gmx, use the -ignh flag. This will ignore all hydrogens on the protein, and re-add them as best determined by Gromacs
Cheers,
John
Hi Safoora Khosravi ,
You could first try John H Dupuis's suggestion and remove all the heteroatom (HETATM) lines from your PDB/GRO file and re-run pdb2gmx with -ignh flag.
If that does not help, have a quick read at this:
http://www.gromacs.org/Documentation/Errors#Residue_'XXX'_not_found_in_residue_topology_database
There may be a mismatch in the residue name mentioned in your PDB file compared to the residue name in the forcefield you are using. If this is the case, changing the residue name in the PDB file according to the one mentioned in the forcefield will help. If there is no such residue in the forcefield at all, then you may have to remove it from your PDB file and continue simulating.
Hope that helps.
Let know if you have any questions.
you can use ex: grep -V HETATM protein.pdb > protein_nosugar.pdb
or you can open pymol, and en cmd console type "remove het" or "delete het" and finally save pdb file, and add flag ignh this ignore hydrogens for incorrect match with your pdb, but if you not have hydrogens or prototation state assigned to you current pdb, this flag not is necessary to add.
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