[gmx-users] Bug/typo in ffG53a5/ffG53a6.rtp

Justin A. Lemkul jalemkul at vt.edu
Fri Jun 12 19:47:31 CEST 2009

Hi all,

I have noticed that there is a problem with the NH2 directive in ffG53a5.rtp and 
ffG53a5.rtp.  The following lines are incorrect:

  [ impropers ]
     -C -O N -CA gi_1
      N  H H  -C gi_1

They refer to the H atoms by type, not name.  They should instead read:

  [ impropers ]
     -C -O N -CA gi_1
      N  H1 H2  -C gi_1

If the user runs pdb2gmx on a structure containing NH2 they will get a fatal error:

"Atom H not found in residue 17 while adding improper"

I find that this typo has been present at least since version 3.3, and remains 
in version 4.0.5.



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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