[gmx-users] different notation for S atoms in different files

[prakash sista]

Hi all,
I am doing the simulation of a certain peptide in dmso solvent. 
After
solvating the protein in dmso solvent, I tried to do energy 
minimization.
But with grompp I got an error message. The command I used was

grompp -f emsol.mdp -o solvated.tpr -c solvation.gro -p 
betahair.top

I got an error saying

Fatal error: number of coordinates in coordinate file 
(solvation.gro,
2674) does not match topology (betahair.top, 170)

Then I opened the topology file created by pdb2gmx and removed 
the
following lines manually
; Include water topology
#ifdef FLEX_SPC
#include "flexspc.itp"
#else
#include "spc.itp"
#endif

I replaced the above lines with #include "dmso.itp"

But still grompp gives out an error message
Fatal error: Atomtype 'SD' not found!

I checked out the file ffG43a1nb.itp. In this the S atom of DMSO 
is
defined as SDMSO and in the .gro file it is defined as SD.

Do I have to manually add the lines with atom types SD in the itp 
file or
is there any other way to counter it? Can anyone suggest an 
alternate
method for this?
Regards
Prakash Sista

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