[gmx-users] make_ndx bug?

[gromacs query]

>> then the make_ndx output matches the atom numbers in the coordinate file.

Thats true but its bit surprising make_ndx was made to read 'residue number
column' (as I said r 2 does not work) but not 'atom number column'. Though
not a big issue but one should be careful in such case.

best regards

On Fri, Sep 19, 2014 at 10:20 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 9/19/14 5:15 PM, gromacs query wrote:
>
>> Hi Justin
>>
>> Hope it makes sense now :) Here is the link (small piece of some pdb
>> without hydrogens)
>>
>> http://s000.tinyupload.com/?file_id=09348261523279878452
>> <http://s000.tinyupload.com/index.php?file_id=09348261523279878452>
>>
>> I used this command: (note residue 2 is missing so using 'r 2' will not
>> work )
>>
>> make_ndx -f test_noH.pdb -o ndx_noH.ndx
>>
>>
>> selected as:
>>
>>
>> r 3
>>
>>
>> It gives correct number of atoms info but gives atom numbers as line
>> numbers (9 to 16) and 'real' atom numbers are: 34,36,38,41 ... so on
>>
>>
>> It seems it reads residue column correctly from pdb, e.g. if you use  r 2
>> then it complains that residue is missing but I think atom numbers are not
>> read from 'atom number column' itself but as line numbers
>>
>>
> make_ndx is assuming the coordinate file is numbered starting at 1, which
> is true for most coordinate files.  If you renumber the file, then the
> make_ndx output matches the atom numbers in the coordinate file.
>
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 601
> 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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