[gmx-users] Itp for a longer molecule out of a shorter one

[Alex]

Thanks Paul,

On Wed, Mar 6, 2019 at 5:00 PM <pbuscemi at q.com> wrote:

> Alex,
>
> Having the itp for the shorter molecule you have most of what you need. Use
> x2top to create the top file for the longer molecule. Adjust, if necessary,
> the atomname2type.n2t file  in the ff  file to create any necessary atom
> types being sure to select the proper ff.  Charges, bond lengths can be
> taken from the existing pdb and itp when needed.  Use Avogadro for a quick
> reference to model parameters.  I've made various models of Pebax , nylon
> to
> 100k's MW using this method.
>
I am using gromos54a7 and there is no "atomname2type.n2t" in the gromos54a7
directory which causes crashing the gmx x2top.

>
> Also ATB can get the itp for polymers up to 600 atoms if you use
> gromos54a7

ff.
>
Indeed I got the gromos54a7 FF for the shorter molecule (< 50 atoms) from
ATB, however for larger system (> 50 atoms) the ATB just gives a
semi-empirical parameterized FF which basically is just a TOP file template
for large molecules.
Best regards,
Alex

>
> Hope this helps
>
> Paul Buscemi, Ph.D.
> UMN BICB
>
> -----Original Message-----
> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se
> <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> On Behalf Of Alex
> Sent: Wednesday, March 06, 2019 2:54 PM
> To: gmx-users at gromacs.org
> Subject: [gmx-users] Itp for a longer molecule out of a shorter one
>
> Dear all,
> I have the itp file for a molecule (OH-[PPE]1-[PPO]2-[PPE]1-H   it is a
> short surfactant), out of that itp, I am trying to create an itp file for a
> longer molecule in the form of OH-[PPE]2-[PPO]16-[PPE]2-H where the PPE and
> PPO parts are being repeated 2 and 16 times each. For each extra PPO, 10
> atoms, 10 bonds 24 pairs, 19 angles and 4 dihedral entries would be added
> to
> the itp file. Doing that for a longer molecule is so tedious, so, I wonder
> if anybody has already a script or tools for doing that?
> I would be really appreciated.
> Regards,
> Alex
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