[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:
/home/user/SW/gromacs/gromacs-5.0.4/src/gromacs/gmxpreprocess/toppush.c,
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
#!/bin/bash
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"
#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
; i funct fcx fcy fcz
1 1 1000 1000 1000
#endif
; 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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