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

[Justin Lemkul]

On 3/17/20 1:00 PM, Max Winokan wrote:
> Dear GMX-Users,
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> 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:
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> 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.
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> 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.
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> The specific error that I run into is:
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> “
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> Program:     gmx pdb2gmx, version 2018
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> Source file: src/gromacs/gmxpreprocess/pdb2top.cpp (line 1132)
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> Fatal error:
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> atom N not found in buiding block 1DG while combining tdb and rtp
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> (log file result of $ gmx_mpi pdb2gmx -f 3pjr.pdb -o 3pjr_processed.gro -ff charmm36-mar2019 -water spce)

You need to manually choose termini types. Due to some technical reasons 
for the way we convert CHARMM files to GROMACS format, we can't produce 
separate .rtp file for amino acids, RNA, DNA, etc. so unfortunately that 
means that .tdb files have to contain both protein and nucleic acid 
termini types. The default choices (based on order in the files) is protein.

-Justin

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> 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?
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> Thank you for your time and best regards,
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> Max Winokan
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> PhD Candidate in Theoretical Physics
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> Leverhulme Quantum Biology Doctoral Training Centre University of Surrey
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-- 
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Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

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