[gmx-users] pdb2gmx charmm issue with version 2018.3

Justin Lemkul jalemkul at vt.edu
Sat Oct 13 02:18:33 CEST 2018

On 10/12/18 8:10 PM, Akshay wrote:
> Hello All,
> I have been using Gromacs version 2016 and upgraded this week to 2018.3. In
> the new version, I am having an issue with pdb2gmx. My file is a series of
> protein chains and finally a dna-double helix like the following
> chain A - Protein
> chain B - Protein
> chain C - Protein
> chain D - DNA
> chain E - DNA
> Running pdb2gmx using gromacs 2018.3 and choosing the charm27 ff, I get the
> error message "atom N not found in building block 1DG while combining tdb
> and rtp". Chains A-C are built correctly.  So, I guess it is looking for an
> amino N-terminal in the DNA chain D as I see the message "Start terminus
> DG-1169: NH3+"
> The issue seems specific to the Charmm27 FF as the Amber FFs are working
> fine. The issue was also not present with Charmm within the 2016.1 version
> I was running until last week.

You need to interactively select termini for complex systems.



Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129


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