[gmx-users] Residue DAN always renamed to DNA

[Dallas Warren]

Line 152 of residuetypes.dat (located in the share/gromacs/top directory)
has:
DAN     DNA

If I remove that line, then it no longer changes it to DNA and now lists it
as a stand alone residue that you can select.

Cheers.

Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.warren at monash.edu
---------------------------------
When the only tool you own is a hammer, every problem begins to resemble a
nail.


On Tue, 18 Dec 2018 at 12:23, Dallas Warren <dallas.warren at monash.edu>
wrote:

> Looking into that now, thanks.
>
> Yes, it is listed as being DNA, but the residue DAN is no longer listed as
> a possible selection.  So it means that with external scripts you can't
> select based on the residue name "DAN".
>
> Catch ya,
>
> Dr. Dallas Warren
> Drug Delivery, Disposition and Dynamics
> Monash Institute of Pharmaceutical Sciences, Monash University
> 381 Royal Parade, Parkville VIC 3052
> dallas.warren at monash.edu
> ---------------------------------
> When the only tool you own is a hammer, every problem begins to resemble a
> nail.
>
>
> On Tue, 18 Dec 2018 at 12:20, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>> On Mon, Dec 17, 2018 at 8:17 PM Dallas Warren <dallas.warren at monash.edu>
>> wrote:
>>
>> > Are the GROMACS scripts meant to rename residues when processing?  I
>> have
>> > one that is called DAN, and it is always changed to DNA, whether need to
>> > select a group and haven't passed an .ndx file but using a .tpr file, or
>> > for an example of processing by make_ndx, see ...
>> >
>> > https://twitter.com/dr_dbw/status/1074835027068735488
>> >
>> >
>> I can't make much out in that image, but nothing is getting changed. The
>> residue "DAN" is listed in residuetypes.dat as being DNA. Perhaps some
>> force field has a residue named DAN that's some kind of custom base or
>> something. If you don't want that behavior, edit residuetypes.dat.
>>
>> -Justin
>>
>> --
>>
>> ==========================================
>>
>> 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
>>
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>> http://www.thelemkullab.com
>>
>>
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>