[gmx-users] procedure to measure end-to-end distance of a protein
Rahul Karyappa
r.karyappa at ncl.res.in
Mon Sep 19 06:55:47 CEST 2005
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chain???????
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Dear Sir,
I am mailing this second time. Please reply this mail. As you told I first =
created index file by using make_ndx command as
follows ( here I selected group 1 and entered q to save and quit).
There are: 3027 OTHER residues
There are: 1 PROTEIN residues
There are: 0 DNA residues
Analysing Protein...
Analysing Other...
0 System : 9369 atoms
1 Protein : 288 atoms
2 Protein-H : 288 atoms
3 C-alpha : 0 atoms
4 Backbone : 0 atoms
5 MainChain : 0 atoms
6 MainChain+Cb : 0 atoms
7 MainChain+H : 0 atoms
8 SideChain : 288 atoms
9 SideChain-H : 288 atoms
10 Prot-Masses : 288 atoms
11 Non-Protein : 9081 atoms
12 SOL : 9081 atoms
13 Other : 9081 atoms
nr : group ! =20
'name' nr name 'splitch' nr 'l': list
residues
'a': atom =20
& 'del'
nr 'splitres'
nr 'h': help
't': atom type | 'keep' nr 'splitat' nr
'r': residue =20
'res': group res 'chain' char 'q': save and quit
"name": group 'case':
case
sensitive =20
'v': verbose output
> 'protein'
Copied index group 1 'Protein'
14 Protein : 288 atoms
> q
Then I used g_mindist command to get the end-to-end distance of the polymer=
chain as follows:
You can compute the distances between a first group
and a number of other groups.
How many other groups do you want (>=3D 1) ?
1
Group 0 ( System) has 9369 elements
Group 1 ( Protein) has 288 elements
Group 2 ( Protein-H) has 288 elements
Group 3 ( C-alpha) has 0 elements
Group 4 ( Backbone) has 0 elements
Group 5 ( MainChain) has 0 elements
Group 6 (MainChain+Cb) has 0 elements
Group 7 ( MainChain+H) has 0 elements
Group 8 ( SideChain) has 288 elements
Group 9 ( SideChain-H) has 288 elements
Group 10 ( Prot-Masses) has 288 elements
Group 11 ( Non-Protein) has 9081 elements
Group 12 ( SOL) has 9081 elements
Group 13 ( Other) has 9081 elements
Group 14 ( Protein) has 288 elements
Select a group: 1
Selected 1: 'Protein'
Select a group: 1
Selected 1: 'Protein'
Reading frame 0 time 0.000
Back Off! I just backed up mindist.xvg to ./#mindist.xvg.1#
Last frame 1000 time 1000.000
Is this correct or I am doing wrong? PLease help me out.
Thanking you in advance.
Rahul Karyappa
NCL, Pune
_______________________________________________
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<br><font face=3D"Arial" size=3D"2"><TABLE STYLE=3D"border-color: blue; bor=
der-left: 1px solid blue; padding-left: 5px;"><tbody><TR><TD>Dear Sir,<br>
I am mailing this second time. Please reply this mail. As you told I first =
created index file by using make_ndx command as
follows ( here I selected group 1 and entered q to save and quit).<br>
<br>
<font size=3D"2">There are: 3027 OTHER residues<br>
There are: 1 PROTEIN residues<br>
There are: 0 DNA residues<br>
Analysing Protein...<br>
Analysing Other...<br>
<br>
0 System : 9369 atoms<br>
1 Protein : 288 atoms<br>
2 Protein-H : 288 atoms<br>
3 C-alpha : 0 atoms<br>
4 Backbone : 0 atoms<br>
5 MainChain : 0 atoms<br>
6 MainChain+Cb : 0 atoms<br>
7 MainChain+H : 0 atoms<br>
8 SideChain : 288 atoms<br>
9 SideChain-H : 288 atoms<br>
10 Prot-Masses : 288 atoms<br>
11 Non-Protein : 9081 atoms<br>
12 SOL : 9081 atoms<br>
13 Other : 9081 atoms<br>
<br>
nr : group ! =20
'name' nr name 'splitch' nr 'l': list
residues<br>
'a': atom =20
& 'del'
nr 'splitres'
nr 'h': help<br>
't': atom type | 'keep' nr 'splitat' nr<br>
'r': residue =20
'res': group res 'chain' char 'q': save and quit<br>
"name": group 'case':
case
sensitive =20
'v': verbose output<br>
<br>
> 'protein'<br>
<br>
Copied index group 1 'Protein'<br>
<br>
14 Protein : 288 atoms<br>
> q<br>
<br>
<font size=3D"3">Then I used g_mindist command to get the end-to-end distan=
ce of the polymer chain as follows:<br>
<font size=3D"2"><br>
You can compute the distances between a first group<br>
and a number of other groups.<br>
How many other groups do you want (>=3D 1) ?<br>
1<br>
Group 0 ( System) has 9369 elements<br>
Group 1 ( Protein) has 288 elements<br>
Group 2 ( Protein-H) has 288 elements<br>
Group 3 ( C-alpha) has 0 elements<br>
Group 4 ( Backbone) has 0 elements<br>
Group 5 ( MainChain) has 0 elements<br>
Group 6 (MainChain+Cb) has 0 elements<br>
Group 7 ( MainChain+H) has 0 elements<br>
Group 8 ( SideChain) has 288 elements<br>
Group 9 ( SideChain-H) has 288 elements<br>
Group 10 ( Prot-Masses) has 288 elements<br>
Group 11 ( Non-Protein) has 9081 elements<br>
Group 12 ( SOL) has 9081 elements<br>
Group 13 ( Other) has 9081 elements<br>
Group 14 ( Protein) has 288 elements<br>
Select a group: 1<br>
Selected 1: 'Protein'<br>
Select a group: 1<br>
Selected 1: 'Protein'<br>
Reading frame 0 time 0.000<br>
Back Off! I just backed up mindist.xvg to ./#mindist.xvg.1#<br>
Last frame 1000 time 1000.000</font><br>
<br>
Is this correct or I am doing wrong? PLease help me out.<br>
Thanking you in advance.<br>
<br>
Rahul Karyappa<br>
NCL, Pune<br>
</font><br>
<br>
<br>
<br>
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<font color=3D"#000000">
</font><br>
</TD></TR></tbody></TABLE>_______________________________________________<b=
r><br>
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