[gmx-users] identifying terminal residue error

[Justin Lemkul]

On 12/20/15 4:13 PM, gromacs query wrote:
> Hi All
>
> I have a modified base in normal DNA chain. Thus I added that residue in
> rtp file and updated residuetypes.dat as well (CHARMM36). When I use pdb2mx
> with -ter interactive mode then it wrongly identifies the ending terminal
> at the residue just before the modified base. e.g.
>
>
> :
> :
> TER
> DC (169th residue)
> DT
> DG (so on......)
> DC (189th residue)
> AX (moldified 190th residue)
> .
> .
> DA
> DG
> TER
> :
> :
>
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> Warning message:
>
> Identified residue DC169 as a starting terminus.
> Warning: Residue AX190 in chain has different type (Other) from starting
> residue DC169 (DNA)..
>
> More than 5 unidentified residues at end of chain - disabling further
> warnings.
> Identified residue DC189 as a ending terminus.
> 8 out of 8 lines of specbond.dat converted successfully
> Select start terminus type for DC-169
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
>
> So its wrongly identifying DC as ending terminal. Not sure what else needs
> to be modified as residuetypes.dat has been updated too in my local
> directory. I dont have any new type of connection between modified base and
> normal base.
>

Simply put, this is the function of residuetypes.dat and if you have altered it, 
either your modification is incorrect or the file is not in the working directory.

-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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