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

[paul buscemi]

Alex,  is your PPO polypropylene oxide or poly phenylene oxide   ??

> On Mar 6, 2019, at 6:36 PM, Alex <alexanderwien2k at gmail.com> wrote:
> 
> 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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