[gmx-users] Regarding structure

[Vytautas Rakeviius]

If you interested in just one glycine one possible solution is to prepare it with acpype instead. It respects your hydrogens and you can set charge as command line option.
 

    On Friday, March 24, 2017 6:14 AM, Jonathan Saboury <jsabou1 at gmail.com> wrote:
 

 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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