On 7/23/18 8:42 AM, farial tavakoli wrote:
Dear GMX users
I am trying to make an index.ndx file of my complex which includes a receptor
and a peptide using this command:
gmx make_ndx -f em.gro -o index.ndx
Reading structure file
Going to read 0 old index file(s)
Analysing residue names:
There are: 330 Protein residues
There are: 15278 Water residues
There are: 7 Ion residues
Analysing Protein...
Analysing residues not classified as Protein/DNA/RNA/Water and splitting into
groups...
0 System : 51172 atoms
1 Protein : 5331 atoms
2 Protein-H : 2659 atoms
3 C-alpha : 330 atoms
4 Backbone : 990 atoms
5 MainChain : 1322 atoms
6 MainChain+Cb : 1633 atoms
7 MainChain+H : 1639 atoms
8 SideChain : 3692 atoms
9 SideChain-H : 1337 atoms
10 Prot-Masses : 5331 atoms
11 non-Protein : 45841 atoms
12 Water : 45834 atoms
13 SOL : 45834 atoms
14 non-Water : 5338 atoms
15 Ion : 7 atoms
16 NA : 7 atoms
17 Water_and_ions : 45841 atoms
nr : group '!': not 'name' nr name 'splitch' nr Enter: list groups
'a': atom '&': and 'del' nr 'splitres' nr 'l': list residues
't': atom type '|': or 'keep' nr 'splitat' nr 'h': help
'r': residue 'res' nr 'chain' char
"name": group 'case': case sensitive 'q': save and quit
'ri': residue index
splitch 1
Found 10 chains
1: 189 atoms (1 to 189)
2: 108 atoms (190 to 297)
3: 283 atoms (298 to 580)
4: 130 atoms (581 to 710)
5: 173 atoms (711 to 883)
6: 10 atoms (884 to 893)
7: 4087 atoms (894 to 4980)
8: 99 atoms (4981 to 5079)
9: 125 atoms (5080 to 5204)
10: 127 atoms (5205 to 5331)
I dont know it found 10 chains instead of finding 2 chains ( chain A and chain
B).How can I make the desired index file composed of:18 protein chain A19
protein chain B
You need to use an input file format that includes chain information,
like .pdb or .tpr - there is no chain information in a .gro file.
-Justin
--
==================================================
Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry
303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061
jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com
==================================================
--
Gromacs Users mailing list
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a
mail to gmx-users-requ...@gromacs.org.
