[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..
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 8 C GLY
ATOM 9 OT1 GLY
ATOM 10 OT2 GLY
With Best Regards,
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