[gmx-users] pdb2gmx and periodic molecule

Justin Lemkul jalemkul at vt.edu
Sun Apr 26 05:41:52 CEST 2015

On 4/25/15 11:34 PM, Alex wrote:
> Justin,
> I am not entirely sure I understand your sequence of steps. Why do you
> want to first run it normally, but then also without adding the
> hydrogens? The hydrogens (a total of two) are only added at the
> termini by default, and in the final product there's no
> need for them anyway.

I was speaking in generalizations; most starting structures need H added.  If 
that's not relevant, then just skip it.

> Here's what I'm able to understand: run as usual, delete all bonded data
> relevant to termini, add bonded descriptions for the residues at the
> boundary, modify pdb to remove termini (actually, I can generate the
> periodic ones automatically). Am I missing something that
> should make my life easier?

In theory, if you assign a phosphate as one of your termini (rather than the 
normal C5'-OH and C3'-OH) then you have to modify very little.

> Also, is there a way to automate this by modifying the forcefield?
> See, right now (on the periodic structure without termini) pdb2gmx
> sees the first residue and looks it up as one with a terminus, which
> is really the gist of the error it throws, so I doubt it even gets to
> the point of looking at the boundary. Is it that the utility behavior
> cannot be changed at the ff level, and thus our only
> option is manual modification of the topology?

It's got nothing to do with the force field and everything to do with software 
and convention.  It's the same case with cyclic peptides or circular DNA.  It 
can be made to work, but that's not really how the software was designed because 
it's not a common procedure.  DNA is assumed to be a linear polymer of finite 
length.  If you don't do that, it's up to you to hack it together.

The force field parameters for a phosphodiester are the same in a linear, finite 
DNA as they will be in your infinite chain.  The problem is in telling pdb2gmx 
"don't link i,i+1 here, instead link i,i+(some number of intervening nucleotides)."



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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