I want to simulate a formate dehydrogenase which contains a selenocysteine. However, I got error when I use pdb2gmx command to generate .gro and topology file. It seems like GROMACS could not recognize the nonstandard selenocysteine residue. I have tried to replace several files ( aminoacids.rtp, aminoacids.hdb, gb.itp, ffbonded.itp, ffnonbonded.itp, atomtypes.atp ) in GROMACS package using corresponding files in swisssidechain but it dose not work. Could anyone can give me some suggestion about how to simulate selenium containing enzymes using GROMACS?
Hi, Feilong, why not try ATB website https://atb.uq.edu.au to generate the .gro and topology file. It modify the force filed automaticly
Firstly, the Se element is not organic element, and most comman used force field can not generate the correct itp file of molecules include Se. So you can:1) use OBGMX to generat UFF force filed of your selenocystine 2) your can fit the force filed of selenocystine by ambertool combine with gaussian （according to General AMBER Force Field Parameters for Diphenyl Diselenides and Diphenyl Ditellurides, DOI: 10.1021/acs.jpca.6b02250） 3） find it from the reference
and then replace related file
Fei-Long Li
no,I try to replace these file form Swiss-SideChain the same as you, but it still reported error.
- Badges
- Science topic
- Similar topics
- Clinical Pharmacology
- Dosing