[gmx-users] Error with a ligand molecule by ATB

이명기 myunggi at pukyong.ac.kr
Tue Nov 15 04:26:03 CET 2016

Dear users,

When I use a ligand molecule (1GHB) generated by ATB, I have got the
following error message.

Program gmx, VERSION 5.0.4
Source code file:
line: 1019

Fatal error:
Atomtype SE not found
For more information and tips for troubleshooting, please check the GROMACS

The following is my command lines

source /usr/local/gromacs/5.0.4/bin/GMXRC
gmx grompp -f ../protocol/em.mdp -c solv.gro -p comp.top -o solv.tpr

The following is comp.top

; Include forcefield parameters
#include "/home/protocols/top-share/gromos54a7_atb.ff/forcefield.itp"

; Include chain topologies
#include "topol_Protein_chain_A.itp"
#include "topol_Protein_chain_B.itp"

; Include ligand topologies
#include "1GHB_GAD.itp"

; Include water topology
#include "/home/protocols/top-share/gromos54a7_atb.ff/spc.itp"

; Position restraint for each water oxygen
[ position_restraints ]
;  i funct       fcx        fcy        fcz
   1    1       1000       1000       1000

; Include topology for ions
#include "/home/protocols/top-share/gromos54a7_atb.ff/ions.itp"

[ system ]
; Name
Protein in water

[ molecules ]
; Compound        #mols
Protein_chain_A     1
Protein_chain_B     1
1GHB                2
SOL               629
SOL             37928

Any suggestion?

Thank you for your valuable discussion in advance.

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