[gmx-users] make_ndx bug?

[gromacs query]

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




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
>> 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
>
> --
> ==================================================
>
> 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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