[gmx-users] make_ndx question

[Christopher Neale]

what about "editconf -f orig.pdb -o new.gro" followed by figuring out the new residue numbers and running make_ndx on new.gro ?

I don't think you'll need the  "-resnr 1" editconf flag, but if you run into other problems then you might try that.

Chris.



________________________________________
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Giannis Gl <igaldadas at gmail.com>
Sent: 27 May 2015 10:32
To: gromacs.org_gmx-users at maillist.sys.kth.se
Subject: [gmx-users] make_ndx question

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.
--
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