[gmx-users] make_ndx bug?
gromacsquery at gmail.com
Fri Sep 19 23:15:44 CEST 2014
Hope it makes sense now :) Here is the link (small piece of some pdb
I used this command: (note residue 2 is missing so using 'r 2' will not
make_ndx -f test_noH.pdb -o ndx_noH.ndx
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
On Fri, Sep 19, 2014 at 9:37 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
> 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
>> 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
>> the atom number). I think hydrogens were missing so it just uses line
> 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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