[gmx-users] Regarding structure

[Jonathan Saboury]

Please be considerate to others and only post a topic once. Not only does
multiple posts annoy others but it greatly diminishes your chances of
receiving help.

I unfortunately do not have the expertize to help you, but I'm sure someone
will soon.

- Jonathan

On Thu, Mar 23, 2017 at 9:08 PM, Dilip H N <cy16f01.dilip at nitk.edu.in>
wrote:

> Hello,
> 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,
>
> DILIP.H.N
> Research Scholar,
> Department of Chemistry, NITK.
>
>
>
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