[gmx-users] Unnatural amino acid problems

Ashutosh Jogalekar ajogale at emory.edu
Thu Apr 20 00:35:35 CEST 2006

I am parametrizing an unnatural amino acid, phenylglycine (PHG), in  
the OPLS FF in GROMACS. I have put in the necessary parameters in  
the .hdb, .rtp, and the aminoacids.dat file.
1. When I do grompp for the EM, I get an error saying that I have not  
put in the appropriate parameters for the bonds, angles and  
dihedrals. Surprisingly, when I do put in the parameters (from the  
ffoplsaabon.itp file), the angles, bonds, and dihedrals get even more  
distorted, a counterintuitive observation. In fact the simulation is  
much better off when I ignore the warnings and the program puts in  
zeros after the required parameters in the .top file. Why is this  

Another question related to this:
2. When I do parametrize a single peptide with a single PHG residue  
and then simulate it (with zeros for the parameters in the .top  
file), the PHG turns out fine and does not get distorted. But when I  
simulate many PHG containing peptides, say 10 of them stacked on top  
of and besides each other, I observe that some of the PHGs get  
distorted while others don't. By distorted, I especially mean the  
Halpha-Calpha-aromaticC angle, which gets distorted to almost 90 from  
its normal value of about 109. Whatever the cause for this distortion  
is, why is it affecting only some PHG residues and not others?
Thank you
Ashutosh Jogalekar
Emory University.

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