[gmx-users] pdb2gmx charmm issue with version 2018.3

[Justin Lemkul]

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

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

303 Engel Hall
340 West Campus Dr.
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jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

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