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

pbuscemi at q.com pbuscemi at q.com
Wed Mar 6 23:00:06 CET 2019


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.

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

Hope this helps

Paul Buscemi, Ph.D.

-----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.
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