Re: [AMBER] Parameter file for polyethyleglycol PEG

From: Jason Swails <>
Date: Tue, 8 Jul 2014 11:16:04 -0700

On Tue, Jul 8, 2014 at 11:03 AM, Iqbal, Muhammad Sajid <>

> Dear Amber users,
> I have tried leaprc.gcff force field for PEG to generate topology and
> coordinate files but it gives me error that first three atoms are not
> defined. could any one please help me how to fix it ?

​Have you worked through some of the relevant tutorials yet? Particularly
B4 and A1 that walk through setting up a custom residue. Make sure you can
finish (and more importantly, understand the steps of) those tutorials
first. See

You haven't told us enough about your process for us to be of much help,
but it appears that you just took a PDB and tried to feed it into tleap,
which won't work for anything that has non-standard residues (i.e.,
anything besides basic amino acid and nucleic acid residues).

The basic workflow is to use a program like antechamber to derive charges
and determine atom types and bonding (this creates a library file). Then
parmchk is used to fill in missing parameters from gaff. Only then can you
use tleap. One important note is that tleap requires a library in which
each atom can be uniquely identified by its name. In your PDB file, every
carbon has the same name. Same with every oxygen and every hydrogen. So
tleap will never recognize more than 3 atoms. This needs to be fixed.


Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Tue Jul 08 2014 - 11:30:03 PDT
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