[gmx-users] Ligand in PRODRG server is protonated. Why?

[Justin Lemkul]

On 2/14/20 11:13 AM, Andrew Bostick wrote:
> Dear gromacs users,
>
> I am doing MD simulation of protein-ligand complex. For ligand, I used
> PRODRG server.
>
> My ligand is Tamoxifen (C26H29NO = 57 atoms). I have 3D structure of
> Tamoxifen from PDB ID 1YA4 (name of Tamoxifen in this pdb file is CTX). In
> PRODRG outputs, ligand is protonated on N atom and has 1 atom more than
> original structure (58 atoms). I don't want this output. My aim is studying
> unprotonated structure of Tamoxifen.
>
> How to resolve that.

Protonation is addressed in their FAQ: 
http://prodrg1.dyndns.org/prodrg_faq.html

I strongly discourage you from using PRODRG. Its topologies are of 
inadequate quality for MD simulations and were never intended to be used 
for such.

-Justin

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Justin A. Lemkul, Ph.D.
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