[gmx-users] FMNO topology

YOLANDA SMALL yas102 at psu.edu
Thu Jun 16 18:54:29 CEST 2005


There is some sort of spacing issue that I can't seem to get around.  I want to
build the topology for a non-covalently bound flavin group (FMN oxidized state)
with the command:
pdb2gmx -f FMNo.pdb -o conf.gro -p topol.top

However, I get the following error:
Fatal error: Atom FC10 in residue FMNO 1 not found in rtp entry with 36 atoms
while sorting atoms

Here is the line for that atom from the PDB file
ATOM  3     FC10A FMNO     1      42.668  36.167   7.291 

I tried several spacing options and it seems that pdb2gmx can only read 4 spaces
of atom name characters but this atom exists in a 5 character naming convention
in the  ffgmx.rtp file.  What am I doing wrong?


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