A good minded advice Shima: think more for your self; science is not easy, or
if it's not possible, ask ur adviser, or look for a new job.
________________________________________
From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf
Of Shima Arasteh [shima_arasteh2...@yahoo.com]
Sent: Monday, December 31, 2012 5:58 PM
To: Justin Lemkul; Discussion list for GROMACS users
Subject: Re: [gmx-users] Index file
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 Protein...
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!
Sincerely,
Shima
----- Original Message -----
From: Justin Lemkul <jalem...@vt.edu>
To: Shima Arasteh <shima_arasteh2...@yahoo.com>; Discussion list for GROMACS
users <gmx-users@gromacs.org>
Cc:
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
-- ========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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