[gmx-users] Regarding phenyl rings absolutely flat.

Mark Abraham Mark.Abraham at anu.edu.au
Thu Jul 14 10:47:44 CEST 2011

On 14/07/2011 5:50 PM, HARESH AJANI wrote:
> Hello Dear, I am using gromacs 4.5.3 version. I am doing simulation of 
> Protein-Ligand complex. My all system is right but I have confusion 
> related to Planarity aromatic ring. My ligand have 3 aromatics ring. I 
> have generated .itp file from Prodrg and i have setup very well. My 
> ligand planer/flat(3 phenyl ring) during EM/NVT/NPT but after given 
> mdrun I have given for 10 ns. I have dump pdb file at 1ns but my 
> ligand lost planer structure.

Probably your topology lacks the improper dihedrals (see manual) used to 
preserve planarity in such cases. You should read the PRODRG 
documentation about how it handles such cases.

> I have lot of question related to Ligand and Protein ? 1. Have any 
> problem with protein-ligand H-bond interaction ? 

Don't know what you mean.

> 2. As per chemistry aromatics structure should have remain planer ? 


> 3. Any problem with simulation ? 


> 4. sily question- If aromatics structure bent then any problem with 
> Protein-ligand interaction/ Binding site ? 

It doesn't model reality, so yes, there's a problem.


> Hope I will get best answer. Thanks In advance 

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