Re: [gmx-users] rmsd between different monomers

2010-05-09 Thread Mark Abraham
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)

Re: [gmx-users] rmsd between different monomers

2010-05-09 Thread Bharath.K. Chakravarthi
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

Re: [gmx-users] rmsd between different monomers

2010-05-09 Thread Anupam Nath Jha
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)

Re: [gmx-users] rmsd between different monomers

2010-05-09 Thread Mark Abraham
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

Re: [gmx-users] rmsd between different monomers

2010-05-09 Thread Justin A. Lemkul
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

Re: [gmx-users] rmsd between different monomers

2010-05-09 Thread Anupam Nath Jha
> > > 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

Re: [gmx-users] rmsd between different monomers

2010-05-09 Thread Justin A. Lemkul
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

Re: [gmx-users] rmsd between different monomers

2010-05-09 Thread Justin A. Lemkul
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

Re: [gmx-users] rmsd between different monomers

2010-05-09 Thread Itamar Kass
toria 3800 | Australia | | Tel: +61 3 9902 9376 | Fax: +61 3 9902 9500 | E-mail: itamar.k...@med.monash.edu.au - Original Message - From: Anupam Nath Jha Date: Sunday, May 9, 2010 3:48 pm Subject: [gmx-users] rmsd between different monomers To:

[gmx-users] rmsd between different monomers

2010-05-08 Thread Anupam Nath Jha
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

Re: [gmx-users] rmsd between different monomers

2010-05-07 Thread Mark Abraham
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

Re: [gmx-users] rmsd between different monomers

2010-05-07 Thread Shankar Prasad Kanaujia
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

[gmx-users] rmsd between different monomers

2010-05-07 Thread Anupam Nath Jha
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 -- Science is facts

Re: [gmx-users] RMSD between

2008-08-09 Thread David van der Spoel
On Sat, 9 Aug 2008, jayant james wrote: hi ! I am interested in plotting the RMSD between two amino acids to see if they come close or move away during simulations. Any suggestions would be helpful. g_mindist Thanks Jayant James -- Jayasundar Jayant James www.chick.com/reading/tracts/0096/0

[gmx-users] RMSD between

2008-08-09 Thread jayant james
hi ! I am interested in plotting the RMSD between two amino acids to see if they come close or move away during simulations. Any suggestions would be helpful. Thanks Jayant James -- Jayasundar Jayant James www.chick.com/reading/tracts/0096/0096_01.asp) ___