[gmx-users] ligand related problem

RINU KHATTRI nickname.mittu at gmail.com
Tue Dec 2 12:00:54 CET 2014

hello gromacs users
i am working on complex with popc membrane
i am facing the problem -- ligand is not attached in the protein
i am following the previous mail protocol
and pasted the ligand in final system_shrink.gro file after this i saw
the .gro file in vmd ligand is very distant to protein it is not
attached with the protein
kindly help

 pdb2gmx -f KALP-15_princ.pdb -o KALP-15_processed.gro -ignh -ter -water spc

grompp -f minim.mdp -c dppc128.gro -p topol_dppc.top -o em.tpr

trjconv -s em.tpr -f dppc128.gro -o dppc128_whole.gro -pbc mol -ur compact

editconf -f KALP-15_processed.gro -o KALP_newbox.gro -c -box 6.41840
6.44350 6.59650

cat KALP_newbox.gro dppc128_whole.gro > system.gro

perl inflategro.pl system.gro 4 DPPC 14 system_inflated.gro 5 area.dat

grompp -f minim.mdp -c system_solv_ions.gro -p topol.top -o em.tpr

 mdrun -v -deffnm em

perl inflategro.pl confout.gro 0.95 DPPC 0 system_shrink1.gro 5 area_shrink1.dat
28 iteration

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