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

[paul buscemi]

Alex,

Just create the n2t file.  Gromacs will tell x2top to read it.  The documentation explains this. It’s a very simple format.

How long is >50 for you ??   ATB can handle up to at least 600 atoms - it may have moved to 1000 by now.. So if you can construct the polymer ATB should provide the itp for you.  From there it’s plug and play.   I’ve had good luck with ~ 100 molecules. Just be sure to add hydrogens and minimize it in your molecular modeler


the x2top route is a bit more cumbersome, but it works.   



> 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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