[gmx-users] Problem with pdb2gmx

Elham Taghikhani elham802011 at yahoo.com
Fri Apr 10 18:15:41 CEST 2020


Hi

I want to simulate a protein which is bound covalently to a ligand. When I get the gro file of the complex the bond between the amino acid and the ligand is broken although I had modified the .rtp file before and it seems ok in a PDB format.
In the topology, I got this warning message :
Warning:long-bond...
I don't know what should I do to retain the covalent bond.
I will appreciate it if you help me with this problem.


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