[gmx-users] Missing atom error when using some force fields

Justin A. Lemkul jalemkul at vt.edu
Wed Feb 4 00:51:32 CET 2009

Peggy Yao wrote:
> Dear all,
> I am new to MD simulation. I am trying to do an all-atom MD simulation 
> with explicit water of a protein which has a few missing side-chain 
> atoms of a GLN residue.
> 1. Which force field would you recommend? The protein is an x-ray 
> crystal structure, about 200 residues. Hydrogen atoms and hydrogen 
> bonding are important.
> 2. According to the Gromacs manual, OPLS is recommended for all-atom MD 
> simulation. However, when I tried to use OPLS-AA as the force field, 
> pdb2gmx returned me an error:
> Fatal error:
> Atom CG not found in residue GLN82 while adding hydrogens

Right, because as you said before, you have missing atoms!  This is not a 
problem that can be magically fixed by Gromacs tools or specific force fields.

> Then I tried all other force fields. Only the following didn't give that 
> error:
>  0: GROMOS96 43a1 force field
>  1: GROMOS96 43a2 force field (improved alkane dihedrals)
>  2: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205)
>  3: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656)
>  4: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656)
>  6: [DEPRECATED] Gromacs force field (see manual)
> Is any of them good enough? If not, is there any way (such as a good 
> free software) to fill in the missing atoms?

That depends on your definition of "good enough."  The big DEPRECATED warning on 
ffgmx suggests (very strongly) that it should not be used.  The decision among 
Gromos96 variants is yours, based on reading the primary literature for the 
parameter sets (conveniently cited in the pdb2gmx output!)

As for free software, AmberTools is now available so that you can use xLeap to 
modify structures.  Other possibilities might include DeepView (Swiss-PDBViewer) 
or Modeller.


> Thanks a lot!
> Peggy
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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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