[gmx-users] Index file
shima_arasteh2001 at yahoo.com
Mon Dec 31 17:58:04 CET 2012
These are the last line of my gro file:
5SOL HW299818 7.429 8.372 11.524
5CL CL99819 0.485 3.864 11.451
5CL CL99820 5.689 6.730 9.692
9.21490 8.92980 12.40750
Here, I brought you the output of make_ndx command. As you see CL ions are not recognized here.
Analysing residue names:
There are: 48 Protein residues
There are: 238 Other residues
There are: 12624 Water residues
Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
0 System : 99817 atoms
1 Protein : 720 atoms
2 Protein-H : 356 atoms
3 C-alpha : 48 atoms
4 Backbone : 144 atoms
5 MainChain : 190 atoms
6 MainChain+Cb : 234 atoms
7 MainChain+H : 240 atoms
8 SideChain : 480 atoms
9 SideChain-H : 166 atoms
10 Prot-Masses : 720 atoms
11 non-Protein : 99097 atoms
12 Other : 31892 atoms
13 POPC : 31892 atoms
14 Water : 67205 atoms
15 SOL : 67205 atoms
16 non-Water : 32612 atoms
nr : group ! 'name' nr name 'splitch' nr Enter: list groups
'a': atom & 'del' nr 'splitres' nr 'l': list residues
't': atom type | 'keep' nr 'splitat' nr 'h': help
'r': residue 'res' nr 'chain' char
"name": group 'case': case sensitive 'q': save and quit
'ri': residue index
Somehow confusing for me!
----- Original Message -----
From: Justin Lemkul <jalemkul at vt.edu>
To: Shima Arasteh <shima_arasteh2001 at yahoo.com>; Discussion list for GROMACS users <gmx-users at gromacs.org>
Sent: Monday, December 31, 2012 8:19 PM
Subject: Re: [gmx-users] Index file
On 12/31/12 11:45 AM, Shima Arasteh wrote:
> It is 4.5.5.
> I need to say that I had a pdb file which was produced by VMD, May it be the reason of problem?
Without seeing the aforementioned information (substituting make_ndx screen output for editconf command, which is not relevant), it's impossible to say anything. There is no logical reason why ions present in the coordinate file (independent of format) do not show up in the selection list and I cannot reproduce the problem with any file I have available. Ions are showing up just fine in everything I can see.
Justin A. Lemkul, Ph.D.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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