On 4/28/12 2:06 PM, Peter C. Lai wrote:
#2
Generally a good idea to keep the names consistent, however - why are you using
POP in the coordinate file instead of POPC?
If it is a .pdb file, the standard residue name occupies 3 characters. Many
files (including those from Tieleman) are distributed with such names.
To the OP's original question - the commands you issue depend on what you're
trying to achieve. What group do you need to create?
-Justin
--
Sent from my Android phone with K-9 Mail. Please excuse my brevity.
Shima Arasteh <shima_arasteh2...@yahoo.com> wrote:
Dear gmx users,
I want to simulate POPC in water. In equilibration step, I have to make an
index file. But when I enter this command, I do not know to choose which
group to make a suitable .ndx file which matches the molecule types and
molecules sections in .top file .
The .top file contains these:
[ moleculetype ]
; Name nrexcl
POPC 3
.
.
.
.
[ system ]
; name
POPC in water
[ molecules ]
; name number
POPC 128
SOL 3800
It is the command I enter:
# make_ndx -f em.gro -o index.ndx
0 System : 18056 atoms
1 Other : 6656 atoms
2 POP : 6656 atoms
3 Water : 11400 atoms
4 SOL : 11400 atoms
5 non-Water : 6656 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
Now, what is the correct answer? Anybody can suggest me?
Thanks in advance,
Shima
ge
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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