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, JZ -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.