[gmx-users] Regarding topology creation

Peter Stern peter.stern at weizmann.ac.il
Sun Apr 2 17:51:52 CEST 2017


OT1 and OT2 are only for the C-terminal amino acids and for one glycine it is both N-terminal and C-terminal.
For everything else you need to use change it to O.
You will have the same problem with H1, etc.  Except for N-terminal aa it needs to be HN.


-----Original Message-----
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se [mailto:gromacs.org_gmx-users-bounces at maillist.sys.kth.se] On Behalf Of Dilip H N
Sent: Sunday, April 02, 2017 6:23 PM
To: gromacs.org_gmx-users at maillist.sys.kth.se
Subject: [gmx-users] Regarding topology creation

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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