I submited the lig_fix.mol2 file to genarate topology into a str file and got this messege error:
"readmol2 warning: non-unique atoms were renamed. Now processing molecule LIG ... attype warning: unknown sulfur type not supported; skipped molecule."
Hi,
check if your molecule have SO2 or SO groups... then change the sulfur atom type to plain "S" and try again.
The sulfur atom type is already "S".
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
Regards
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