On 9/05/2010 10:01 PM, Anupam Nath Jha wrote:
Ok.
But when I run this command
g_rms -s setp_0.pdb -f setp_0.pdb -n ca_ind.ndx -o out
it ask me groups... and that i thought is for fitting///
for example -
Select group for least squares fit
Group 0 (C-alpha_chain1)
you said you have used online server for superimposition ...
which one you used...
try TOPMATCH server
On Sun, May 9, 2010 at 5:31 PM, Anupam Nath Jha wrote:
>
> Ok.
>
> But when I run this command
> g_rms -s setp_0.pdb -f setp_0.pdb -n ca_ind.ndx -o out
>
> it ask me groups... and that i tho
Ok.
But when I run this command
g_rms -s setp_0.pdb -f setp_0.pdb -n ca_ind.ndx -o out
it ask me groups... and that i thought is for fitting///
for example -
Select group for least squares fit
Group 0 (C-alpha_chain1) has 249 elements
Group 1 (C-alpha_chain2)
On 9/05/2010 9:29 PM, Justin A. Lemkul wrote:
Anupam Nath Jha wrote:
Anupam Nath Jha wrote:
Dear all
I made an index file with 4 different groups for 4 different chains
(since my
protein is a tetramer) and then run
g_rms -s setp_0.pdb -f setp_0.pdb -n ca_ind.ndx -o out
to get the rmsd bet
Anupam Nath Jha wrote:
Anupam Nath Jha wrote:
Dear all
I made an index file with 4 different groups for 4 different chains (since my
protein is a tetramer) and then run
g_rms -s setp_0.pdb -f setp_0.pdb -n ca_ind.ndx -o out
to get the rmsd between two different monomers from the same struc
>
>
> Anupam Nath Jha wrote:
>> Dear all
>>
>> I made an index file with 4 different groups for 4 different chains (since my
>> protein is a tetramer) and then run
>>
>> g_rms -s setp_0.pdb -f setp_0.pdb -n ca_ind.ndx -o out
>>
>> to get the rmsd between two different monomers from the same struct
Itamar Kass wrote:
Hi Anupam ,
To me it seems that you have used the the wrong groups for the RMSD, you
actually compare the protein to himself. Have a second look on at the
group contact, you groups should be numbered 12 or higher.
Not in this case. The headers of the .xvg file in the ori
Anupam Nath Jha wrote:
Dear all
I made an index file with 4 different groups for 4 different chains (since my
protein is a tetramer) and then run
g_rms -s setp_0.pdb -f setp_0.pdb -n ca_ind.ndx -o out
to get the rmsd between two different monomers from the same structure,
it asked me two dif
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- Original Message -
From: Anupam Nath Jha
Date: Sunday, May 9, 2010 3:48 pm
Subject: [gmx-users] rmsd between different monomers
To:
Dear all
I made an index file with 4 different groups for 4 different chains (since my
protein is a tetramer) and then run
g_rms -s setp_0.pdb -f setp_0.pdb -n ca_ind.ndx -o out
to get the rmsd between two different monomers from the same structure,
it asked me two different groups and I gave 0
On 7/05/2010 7:11 PM, Anupam Nath Jha wrote:
Dear all
How can we calculate the rmsd between different monomers from of a protein. for
example I have a tetramer and I have to calculate the rmsd between chain A to B,
A to C and A to D with time.
I was trying using g_rms but couldn't do that.
g
There is one web-server in our lab.
http://10.188.1.15/3dss/
Use third option.
On Fri, May 7, 2010 at 2:41 PM, Anupam Nath Jha wrote:
>
> Dear all
>
> How can we calculate the rmsd between different monomers from of a protein.
> for
> example I have a tetramer and I have to calculate the rmsd bet
Dear all
How can we calculate the rmsd between different monomers from of a protein. for
example I have a tetramer and I have to calculate the rmsd between chain A to B,
A to C and A to D with time.
I was trying using g_rms but couldn't do that.
thanks with regards
anupam
--
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