[gmx-users] make_ndx bug?

[Justin Lemkul]

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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