[gmx-users] pdb2gmx - generating topology for helicase-DNA complex (3PJR)

[Max Winokan]

Dear GMX-Users,

 

Firstly, in light of the current situation with CoVID-19 I would like to wish everyone the best of luck with staying healthy and safe during these uncertain times. Now on to my Gromacs issue:

 

I am relatively new to Gromacs and molecular dynamics. For my research I am studying enzymes, and so far have successfully simulated solvated Lysozyme and Helicase enzymes (using CHARMM36). Of course the more interesting properties of enzymes involve interactions with ligands. One case study I have been attempting to simulate is DNA helicase separating a DNA fragment. 

 

The PDB I am having trouble simulating is 3PJR (https://www.rcsb.org/structure/3PJR). I am using Gromacs 2018 on my faculty’s HPC cluster. I have made attempts with the CHARMM-36 force field, namely the March 2019 release (http://mackerell.umaryland.edu/charmm_ff.shtml#gromacs). I chose this FF because it includes amino acid, DNA nucleotide, and ATP residues, but am not otherwise partial to CHARMM – so I am open to suggestions for alternatives. I have also attempted generating the topology with charmm36-jul2017 to no avail.

 

The specific error that I run into is:

 

“

Program:     gmx pdb2gmx, version 2018

Source file: src/gromacs/gmxpreprocess/pdb2top.cpp (line 1132)

 

Fatal error:

atom N not found in buiding block 1DG while combining tdb and rtp

“

 

(log file result of $ gmx_mpi pdb2gmx -f 3pjr.pdb -o 3pjr_processed.gro -ff charmm36-mar2019 -water spce)

 

It seems that similar error messages were produced when creating DNA topologies with CHARMM in the 4.0.99 version of Gromacs and were subsequently fixed (https://redmine.gromacs.org/issues/465). I have tried generating the topology for their DNA structure but with my methodology and get the same error, suggesting that the fix is not included in the FFs I have tried or there is an error in my method. Please could someone let me know how I can fix the problem if it is an error in my methodology, or how I can report this issue if it is due to a bug?

 

Thank you for your time and best regards,

 

Max Winokan

 

PhD Candidate in Theoretical Physics

Leverhulme Quantum Biology Doctoral Training Centre University of Surrey