Hi,
I'm am working with irreversible enzyme inhibitors. I'm using GROMACS for my MD simulation. I need to know how to create a topology for the covalent inhibitors whether the topology for inhibitor alone is enough or I need to create a topology for the entire protein along with the inhibitors?
In my opinion you have to create topology file for both of them using different parameter file for ligand and protein and after making the both topology files u have mentioned the both file name in .top file.
For covalent inhibitors, generate topology using ATB and then compile the file as explained by Sidra Rafi.
Thank you, Sidra Rafi, and Anu Manhas. Can you suggest any Softwares other than ATB for creating topologies for CHARMM and OPLSAA force field? Is there any tutorial for it?
SwissParam, it providess topologies and parameters for small organic molecules compatible with the CHARMM all atoms force field, for use with CHARMM and GROMACS
http://www.swissparam.ch/
Since a covalent inhibitor is attached to a side chain (Cys, I guess?),you would need to create a non-standard aminoacid. This can be done either by combining SwissParam (http://www.swissparam.ch) with SwissSideChain (http://www.swisssidechain.ch), or by using CGenFF (http://mackerell.umaryland.edu/~kenno/cgenff/faq.php).
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