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

Peggy Yao peggy.yao at gmail.com
Wed Feb 4 00:42:39 CET 2009

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

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

Then I tried all other force fields. Only the following didn't give that

 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?

Thanks a lot!

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