[gmx-users] pdb2gmx charmm issue with version 2018.3

Akshay akshays.sridhar at gmail.com
Sat Oct 13 02:11:20 CEST 2018

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.


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