[gmx-users] identifying terminal residue error

[gromacs query]

Ah! Thanks Justin, I just need extra coffee. Required file was not in
working directory.



On Sun, Dec 20, 2015 at 9:17 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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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