[gmx-users] question about ligand

Justin A. Lemkul jalemkul at vt.edu
Thu Jan 29 20:52:42 CET 2009

Xiang Mao wrote:
> Dear All:
>      How are you.
>  Sorry to bother you. I am trying do use gromacs  to do MD on a 
> protein-ligand complex. I am following Dr. Kerrigan's tutorial on 
> simulation of protein-ligand complex. Here I have a question about the 
> topology of ligand generated by prodrg. And when I run pdb2gmx on my 
> protein(with gmx force field), I noticed hydrogens were added to benzene 
> rings. But when I look at the itp file and pdb file with polar H 
> generated by prodrg, I noticed there are no hydrogens added to benzene 
> ring of my ligand. I am just wondering  if this will affect the 
> simulation, and what I should do. Thank you so much for your help.

The first step is to not use ffgmx.  It has been deprecated for a long time (see 
the notes in the pdb2gmx output).  At the very least, use the PRODRG beta server 
to generate your initial Gromos96-compatible topology.  It includes hydrogens on 
aromatic rings.  Note that in the PRODRG output, "polar hydrogens" and "aromatic 
hydrogens" are distinct entities, and there are options to download either 
structure file.

Be aware that the charges and charge groups generated by PRODRG are often 
unsatisfactory, and require adjustment and validation.


> Best Regards,
> mao
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Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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