[gmx-users] long-stick molecule solvation
jalemkul at vt.edu
Wed Nov 4 15:31:39 CET 2015
On 11/4/15 9:22 AM, xy21hb wrote:
> Dear Justin,
> Below are the commands I used with all the files attached.
> pdb2gmx -f 4KE2.pdb -missing -ignh -o double
Never use -missing.
> gmx editconf -f double.gro -o d-box -c -d 0.5 -bt triclinic -princ
> gmx solvate -cp d-box.gro -cs spc216.gro -o d-solv.gro -p topol.top
> grompp -f em.mdp -c d-solv.gro -p topol.top -o em
> mdrun -v -s em
If you visualize d-solv.gro you will see that you have ridiculous coordinates
for HB atoms in the 0MET residue; this is the cause of your problem, and mdrun
points you to this fact directly:
WARNING: Listed nonbonded interaction between particles 1 and 8
at distance 6.219 which is larger than the table limit 2.000 nm.
Atom 1 is the N-terminal N, and atom 8 is HB1.
Note also that you have made your box fit very tightly to your protein, and any
small amount of rotation will lead to unphysical interactions and minimum image
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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