[gmx-users] Trjconv

farial tavakoli farial.tavakoli at ymail.com
Mon Oct 23 10:24:06 CEST 2017

 blockquote, div.yahoo_quoted { margin-left: 0 !important; border-left:1px #715FFA solid !important; padding-left:1ex !important; background-color:white !important; }   Dear gromacs users
I minimized my complex ( protein-peptide) by:
Gmx grompp -f em.mdp -c solv_ions.gro -p topol.top -o em.tprGmx mdrun -v -deffnm em
Now I need to view the em.gro file to check if my ligand is placed in the pocket? So I created this command and I wanted to know if it is correct?
Gmx trjconv -s em.tpr -f em.gro -o em.pdb -pbc nojump
Thanks in advanceFarial

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