[gmx-users] (no subject)

Dilip H N cy16f01.dilip at nitk.edu.in
Fri Mar 24 04:26:17 CET 2017

The glycine .pdb that i have is a non zwitter ionic form, and from this if
i want to create a topology file from the following command as -
gmx pdb2gmx -f gly.pdb -o gly.gro
and selected charmm FF i am getting the following msg...

Processing chain 1 'A' (10 atoms, 1 residues)
Identified residue GLY1 as a starting terminus.
Identified residue GLY1 as a ending terminus.
8 out of 8 lines of specbond.dat converted successfully
Start terminus GLY-1: GLY-NH3+
End terminus GLY-1: COO-

It is showing tht glycine as zwitterionic form, But i dnt want it to be in
zwitterionic form... How can i solve this issue..??
With Best Regards,

Research Scholar,
Department of Chemistry, NITK.

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