Hello, everyone!
Using PyMOL, I mutated arginine to citrulline by substituting O to one of the NH2 of the guanidino group. However, no forcefield can recognize the new oxygen. Does anyone know how can I generate a topology file without getting any error? Will appreciate any suggestion.
Thank you so much in advance.
You can try obtaining the parameter from SwissParm or ATB server.
Check out this resource. Maybe you will find your amino acid.
https://www.swisssidechain.ch/index.php
You'll find the topologies and parameters for the GROMACS and CHARMM forcefields on swisssidechains, residue CIR https://www.swisssidechain.ch/MD.php
Thank you Dr Thirumal Kumar D Dmitri Kireev Annemarie Honegger !
Will definitely try your suggestions.
Dmitri Kireev Annemarie Honegger
Hello.I am beginners to GROMACS and trying to simulate a Protein with a new residue.I found my residue in Swiss-SideChain. I try to put the .rtp file and .hdb file into AMBER03 directory . But I have some questions :
1.The .rtp file is missing dihedral information which is necessary for simulate.
2.The atom type does not match in the atomtype.rtp, can I modify the atom type refer to aminoacid.rtp file?
3.The total charge of all atom is not zero. I don't know what impact it will have on the system.
I would be very grateful if you can answer this question for me
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