Atomype SD not found

User discussions
1

GROMACS version: 2021.3

Hi everyone,

I am trying to solvate a protein in DMSO. However, end up with the following error on grompp command:

ERROR 1 [file dmso.itp, line 7]:
Atomtype SD not found

I have added the #include “dmso.itp” in the topol.top file as well.

Any help would be appreciated on resolving this error?

Thank you.

Best regards,
MQ

topol.top

…
#include “dmso.itp”
…

dmso.itp

[ moleculetype ]
; name nrexcl
DMSO 2

[ atoms ]
; nr type resnr residu atom cgnr charge mass
1 SD 1 DMSO SD 1 0.139 32.065
2 CD 1 DMSO CD1 1 0.16 32.065
3 OD 1 DMSO OD 1 -0.459 16.000
4 CD 1 DMSO CD2 1 0.16 32.065

[ bonds ]
; ai aj funct b0 kb
1 2 1 0.195 376560
1 3 1 0.153 502080
1 4 1 0.195 376560

[ angles ]
; ai aj ak funct theta kt
3 1 2 1 106.75 460.240
3 1 4 1 106.75 460.240
2 1 4 1 97.40 460.240

[ dihedrals ]
; ai aj ak al funct xi kxi
1 2 4 3 2 35.264 334.720

2

Not sure how useful this late reply will still be, but this means the atom name SD was not defined beforehand. There should be an [ atomtypes ] section in some .itp file defining the atom before it can be used (an example being the 2nd GROMACS tutorial where lipid.itp contained the necessary definitions)