I have a phosphorylated protein ligand docked to my protein receptor, i would like to simulate the structure , but after adding forcefield using charmM , an error is occuring saying- "T2P not found in residue topology database". Kindly help !
you can use the below-mentioned command:
gmx pdb2gmx -f 3HTB_clean.pdb -o 3HTB_processed.gro -missing
while doing forcefield command in GROMACS but only when you know that missing atom is not necessary.
In GROMACS you can type gmx help pdb2gmx as a command and get a list of parameters you may need to know while working on gromacs.
The error message "T2P not found in residue topology database" suggests that GROMACS cannot recognize the phosphorylated residue in your system, which may be due to the lack of the corresponding topology files in the CHARMM force field. One way to overcome this is to generate the topology files for the phosphorylated residue manually. You can use a software such as CHARMM-GUI to generate the topology files for the phosphorylated ligand, which can be added to the existing CHARMM force field files. Alternatively, you can use a different force field that includes the parameters for phosphorylated residues, such as the AMBER force field. In this case, you need to convert your CHARMM files to AMBER files using a conversion tool such as ACPYPE. Regarding the presence of zinc, you can add the necessary parameters to the force field files for the zinc ion. You can find the parameters for the zinc ion in the literature or in online databases such as the Metal Ion Parameter Database (MIPDB). After adding the necessary parameters to the force field files, you can use GROMACS to perform energy minimization, equilibration, and production MD simulations for the protein-phosphorylated protein complex in the presence of zinc.
Susanta Roy thank you for your warm response. I have used CHARMM-GUI for the topology generation but they are omitting the phosphorylated residue after adding force field to it. Can you suggest the exact procedure in order to restrict the removal of phorphorylated residue?
https://www.swissparam.ch/
paramiter
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charge
https://upjv.q4md-forcefieldtools.org/RED/
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