[gmx-users] Atomtype sy not found error

chaijz at intern.bii.a-star.edu.sg chaijz at intern.bii.a-star.edu.sg
Tue Feb 13 10:40:13 CET 2018

Hi all,

   I was trying to pass a file through GROMACS using following command:

> $gmx grompp -f minim_gmx5.mdp -c Solv.gro -p topol.top -o ions.tpr

  Then the follwing error popped up:

> Atomtype sy not found

  This is due to the presence of sulphur atom in my drug molecule  
Zafirlukast. I used AMBER beforehand to generate topologies for my  
molecule and this is the output under "atom" section:

> ;name   bond_type     mass     charge   ptype   sigma          
> epsilon       Amb
> sy       sy          0.00000  0.00000   A     3.56359e-01    
> 1.04600e+00 ; 2.00  0.2500

   Another additional information, I am using a customized version of  
force field in my work. So can I fix this problem by simply pasting  
this result into appropriate sections of my force field files? If that  
is the case, where should I paste or add them? If this information is  
insufficient to resolve this issue, does it means that I need to  
generate other parameters using some expert techniques that were far  
beyond for an undergraduate? Hope someone can answer my question,  
thank you in advance!

Yours Sincerely,

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