[gmx-users] Regarding topology creation

Dilip H N cy16f01.dilip at nitk.edu.in
Sun Apr 2 17:22:58 CEST 2017

I want to create a topology for n glycine molecules....
I have 1 glycine molecule and in charmm FF i am able to get the topology of
1glycine molecule, but now i have few more glycine molesules in .pdb
format, but if i give the command
gmx pdb2gmx -f gly.pdb -o gly.gro
it shows the following error..
Fatal error:
Atom OT1 in residue GLY 1 was not found in rtp entry GLY with 9 atoms
while sorting atoms.

But when i gave the same command for 1 glycine molecule to create the
topology, the topology file was created, but now it is not creating (for
more glycine molecules).. why is this happening.?? since the same OT1 is
also present in 1 glycine molecule, why is the above error message coming
for more molecules..??

here is the 1 molecule glycine.pdb (only residue)

ATOM      1  N   GLY

ATOM      2  H1  GLY

ATOM      3  H2  GLY

ATOM      4  H3  GLY

ATOM      5  CA  GLY

ATOM      6  HA1 GLY

ATOM      7  HA2 GLY


ATOM      9  OT1 GLY

ATOM     10  OT2 GLY

Thank you

With Best Regards,

Ph.D Student

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