[gmx-users] Dihedral calculations in topology

[Justin Lemkul]

On 12/21/16 9:21 AM, Kamps, M. wrote:
> Mark,
>
> Thanks again for the swift reply! Stupid of me to miss that message! I
> noticed some other code that was generated as output of pdb2gmx, which
> I do not fully understand. Can you maybe explain some of it?
>
> Processing chain 1 (4 atoms, 2 residues)
> Warning: Starting residue EthB1 in chain not identified as Protein/RNA/DNA.
> Warning: Starting residue EthE1 in chain not identified as Protein/RNA/DNA.
> Problem with chain definition, or missing terminal residues.
> This chain does not appear to contain a recognized chain molecule.
> If this is incorrect, you can edit residuetypes.dat to modify the behavior.
>
> I understand the two warnings. To my directory I added a file
> residuetypes.dat, where I specificy that (among others) EthB and EthE
> (which are the ending and beginning residues of polyethylene) are
> Polymer. What does the rest of this message mean? I don't understand
> how I could fix this message? Or even what it wants to do, since i've
> defined my own terminal residues. Is it not possible to define my own
> 'group'?
>
> residuetypes.dat:
> EthB    Polymer
> EthE    Polymer
>

There are certain types of molecules that pdb2gmx understands.  If you're not 
doing something that is Protein/DNA/RNA, then just call it "Other" and it will 
work fine.  The "warning" probably shouldn't be called that.  It's merely 
information that is used to point out instances when the user may not be doing 
something consistent, e.g. a modified amino acid hasn't been added as protein, 
so there's a discontinuity in the chain.  If all you have is polymer, that's fine.

-Justin

-- 
==================================================

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
http://mackerell.umaryland.edu/~jalemkul

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