[gmx-users] how can we merge SOL into protein.itp?

[Mark Abraham]

Hi,

In that case, gmx pdb2gmx -merge and/or -chainsep probably can be made to
work. Maybe you will need to hack your .pdb file to add chain identifiers,
not sure.

Mark

On Mon, Jun 15, 2015 at 2:52 PM Albert <mailmd2011 at gmail.com> wrote:

> I am trying to use GMXPBSAS to calculate the ligand binding energy, but
> this program will delete all solvent molecules automatically. In this
> case, I have to merge the protein and crystal water into a single .itp
> file so that GMXPBSA treat the crystal water as a part of protein....
>
> However, I am not sure how can we to do this....
>
> thx a lot
>
>
>
>
> On 06/15/2015 12:24 PM, Mark Abraham wrote:
> > What are you trying to achieve? Whether you need to do something like you
> > tried below depends on the objective.
> >
> > Mark
>
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