[gmx-users] ligand related problem

Justin Lemkul jalemkul at vt.edu
Tue Dec 2 14:04:05 CET 2014

On 12/2/14 6:00 AM, RINU KHATTRI wrote:
> 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

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> 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

These commands are just copied and pasted directly from my tutorial; these are 
not what you should be using for any arbitrary system.  The logic is the same, 
but the actual commands must be tailored to your system.

Old versions of InflateGRO, IIRC, deleted ligands, so you had to place the 
protein-ligand complex in the proper box (to get the correct translated 
coordinates), remove the ligand, build, and paste the ligand back in.  Perhaps 
that is not the case any more and you can keep the entire protein-ligand complex 
intact throughout the whole process.



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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