On 12/31/12 11:58 AM, Shima Arasteh wrote:
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!
It could be that both your last SOL and both CL ions have the same residue
number. Renumber the file with genconf and try again. The only other thing I
can think of is that you don't have an entry for CL in residuetypes.dat
indicating that it is an ion. The "Ion" group should be generated by default
whenever an ion is encountered, but you don't have one.
-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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