Hello everyone, I have to do molecular dynamics of a metalloprotein. I have read in literature that we can use the CHARMM force field in Gromacs for metal protein. Beside CHARMM I also
use OPLS-AA/L.
I have kept the protein along with Zn and run the pdb2gmx command but i got the following error:- "ZN" not found in residue topology database.
https://ambermd.org/tutorials/advanced/tutorial20/ZAFF.htm
See if this can help you, though it is for amber.
This might help you:
Check the 'toppar_water_ions.inp' file; this should have the information you need. Then, you can either call this function or copy the information into your topology and parameters file.
Which version of CHARMM forcefield are you using? maybe parameter for Zn is not present in ions.itp file of that FF. You can download a newer version of CHARMM FF (for example; charmm36-jul2017.ff, which has parameter for Zn) and keep it in your working directory, then when you will use pdb2gmx, that FF will be highlighted in first option (most probably) and you can select 1 to use that FF.
https://ambermd.org/tutorials/advanced/tutorial20/ZAFF.htm
See if this can help you, though it is for amber.
Kazi Amirul Hossain thanks for your suggestion. I am using both charmm36-jul2017 & charmm36-jul2019( separately) but again same issue has generated.
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