[gmx-users] Index file

[Justin Lemkul]

On 5/26/15 2:32 PM, Giannis Gl wrote:
> Dear all,
>
> I am very amateur in GROMACS, so please forgive my silly question.
> I want to group the following atoms
>
> ATOM  2285b  C1  LIG X   6      32.880  59.958 110.850  0.00
> 0.00
> ATOM  2285c  CL1 LIG X  6      31.972  61.400 110.520  0.00
> 0.00
> ATOM  2285d  N1  LIG X   6      32.318  58.744 110.532  0.00
> 0.00
> ATOM  2285e  C2  LIG X   6      33.272  57.852 110.816  0.00
> 0.00
> ATOM  2285f  N2  LIG X    6      34.376  58.450 111.368  0.00
> 0.00
> ATOM  22860  C3  LIG X   6      34.138  59.800 111.370  0.00
> 0.00
> ATOM  22861  C4  LIG X   6      35.550  57.768 111.896  0.00
> 0.00
> ATOM  22862  H1  LIG X   6      35.550  57.880 112.984  0.00
> 0.00
> ATOM  22863  H2  LIG X   6      35.460  56.692 111.730  0.00
> 0.00
> ATOM  22864  C5  LIG X   6      34.992  60.962 111.784  0.00
> 0.00
> ATOM  22865  H3  LIG X   6      35.626  61.290 110.956  0.00
> 0.00
> ATOM  22866  H4  LIG X   6      34.380  61.822 112.070  0.00
> 0.00
> ATOM  22867  O1  LIG X   6      35.840  60.652 112.888  0.00
> 0.00
> ATOM  22868  H5  LIG X   6      36.496  60.016 112.550  0.00
> 0.00
> ATOM  22869  C6  LIG X   6      33.084  56.380 110.604  0.00
> 0.00
> ATOM  2286a  H6  LIG X   6      33.950  55.966 110.086  0.00
> 0.00
> ATOM  2286b  H7  LIG X   6      33.040  55.868 111.568  0.00
> 0.00
> ATOM  2286c  C7  LIG X   6      31.828  56.028 109.792  0.00
> 0.00
> ATOM  2286d  H8  LIG X   6      30.938  56.388 110.312  0.00
> 0.00
> ATOM  2286e  H9  LIG X   6      31.860  56.538 108.828  0.00
> 0.00
> ATOM  2286f  C8  LIG X    6      31.688  54.518 109.558  0.00  0.00
>
> ...
>
> but the command,
>
> a 2285b-2286f
>
> or the command,
>
> a 2285b 2285c 2285d ... 2286f
>
> doesn't recognize atoms' numbers followed by a character
>
> "Found 0 atoms with names 2285B 2285C"
>
> Is there any other way that I could select these atoms?
> I know I could try a dynamic selection (g_select), but unfortunately, my
> pdb file contains 10 ligands and all of them have the same resname. Thus,
> there is no feature besides the atom
> that I could use to destinguish them. Even the coordinates are useless;
> there are ligands with
> almost the same x-coordinate but different y.
> Thanking you in advance!
> I hope I made clear my problem and didn't confuse you.
>

An index file expects integers, not letters.  Number the coordinate file 
appropriately and you can do whatever analysis you want.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==================================================