[gmx-users] make_ndx bug?

Justin Lemkul jalemkul at vt.edu
Fri Sep 19 22:37:21 CEST 2014

On 9/19/14 8:43 AM, gromacs query wrote:
> Hi All
> I have some pdb file and I removed hydrogens. When I try to make ndx file
> using some residue option then rather printing atom numbers in that residue
> it prints line number where that residue starts and ends.
> make_ndx -f no_H.pdb -o test.ndx
> selecting as:
> r 300-330
> Then in ndx file I get the line number where residue number 300 starts (not
> the atom number). I think hydrogens were missing so it just uses line
> number.

This doesn't make any sense.  make_ndx doesn't process line numbers.  Can you 
give an excerpt (or even better, upload the whole file somewhere) of the index 
file to show what you mean?  The coordinate file would be helpful, too.



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


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