[gmx-users] Interaction_between_protein_small_molecule

Justin A. Lemkul jalemkul at vt.edu
Sun Jan 2 15:19:15 CET 2011

shahid nayeem wrote:
> Dear Gromacs Users
> I wanted to study the interaction between a small molecule and protein. 
> I prepared the system by inserting small molecule -nmol and protein by 
> genbox and then I solvated it with water. when I tried to do PR dynamics 
> it started giving many LINC WARNINGS. I reduced the time 
> of equilibration and then PR run was completed without any warning. When 
> I used production run it started giving LINC warning.Even after setting 
> GMX_MAXCONSTRWARN to -1 I am getting LINC warning and programme 
> termination with fatal error. Instead of simple docking I want to do MD 
> with GROMACS to see interaction between the two molecule. Please suggest 
> me, how can I do this.
> Thanking you.

Your system is physically unstable, either due to the simulation parameters 
(.mdp), topology (likely of the ligand), or the initial geometry.  Please 
consult the following:


If you want more useful advice, you'll have to post more useful diagnostic 
information (.mdp settings, topology, etc).


> Shahid Nayeem


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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