[gmx-users] pdb2gmx error

Ilya Chorny ichorny at gmail.com
Sun Mar 15 05:16:42 CET 2009

I created a new ffoplsaa.rtp entry for ASN with a polysacharide attached to
the side chain nitrogen called ASBG. I want to test the new residue by
When I pdb2gmx it I get the following error.

Program pdb2gmx, VERSION 4.0.3
Source code file: pgutil.c, line: 87

Fatal error:
Atom N not found in residue 1094904186 while adding improper


If I comment out

 CA    +N     C     O     improper_O_C_X_Y

Then pdb2gmx creates the gro and top with no error messages.

I saw an much earlier post by Justin with a similar error message but no
resolution. Anyone have anythoughts?



Ilya Chorny Ph.D.
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