[gmx-users] Problem with pdb2gmx

[Justin Lemkul]

On 4/10/20 12:15 PM, Elham Taghikhani wrote:
> 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.
The full screen output of pdb2gmx would be informative here. If the long 
bond occurs between the residues flanking your modified residue, you 
forgot step 5 in 
http://manual.gromacs.org/documentation/current/how-to/topology.html#adding-a-new-residue

If that doesn't solve it, please post the full screen output from pdb2gmx.

-Justin

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Justin A. Lemkul, Ph.D.
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