Hello!
The protein of my interest has a covalently bound inhibitor, which is a sulfone compound. I am currently trying to prepare all the files necessary for the MD simulation and use CGenFF server to generate topology of the modified residue (with the inhibitor bound). However, CGenFF is unable to recognize the sulfur type and generates the following error: "attype warning: unknown sulfur type not supported;skipped molecule".
Is there any way to fix this problem or do I have to choose another way of creating the topology file? Can you give me any recommendations on which servers I can use instead then?
Any advice would be appreciated.
Hi,
I have encountered a similar issue, please recheck your inhibitors structure and the valency of the sulfur atom, In my case, the inhibitor was no longer bound to two oxygen atoms and yet had a valency more than two, and was hence throwing an error, Once I rechecked the structure and fixed it, cgenff worked
I had the same issues..... but interestingly cgenff server only support topologies for the following sulphur types..
### Supported S atoms in CGenFF
MASS -1 SG2D1 32.06000 ! thiocarbonyl S
MASS -1 SG2R50 32.06000 ! THIP, thiophene
MASS -1 SG311 32.06000 ! sulphur, SH, -S-
MASS -1 SG301 32.06000 ! sulfur C-S-S-C type
MASS -1 SG302 32.06000 ! thiolate sulfur (-1)
MASS -1 SG3O1 32.06000 ! sulfate -1 sulfur
MASS -1 SG3O2 32.06000 ! neutral sulfone/sulfonamide sulfur
MASS -1 SG3O3 32.06000 ! neutral sulfoxide sulfur
As mentioned by Harikrishnan Ajith check the state of S atom in your compound and rectify accordingly.. It worked for me after rectifying the structure..
Regards
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