[gmx-users] Interaction_between_protein_small_molecule

shahid nayeem msnayeem at gmail.com
Sun Jan 2 12:44:45 CET 2011

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.

Shahid Nayeem
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