[gmx-users] rmsd between different monomers

[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 structure,
>> it asked me two different groups and I gave 0 and 1.
>>
>> The output file is like this
>>
>> # g_rms -s setp_0.pdb -f setp_0.pdb -n ca_ind.ndx -o New
>> #
>> # g_rms is part of G R O M A C S:
>> #
>> # Grunge ROck MAChoS
>> #
>> @    title "RMSD"
>> @    xaxis  label "Time (ps)"
>> @    yaxis  label "RMSD (nm)"
>> @TYPE xy
>> @ subtitle "C-alpha_chain2 after lsq fit to C-alpha_chain1"
>>    0.0000000    0.0000001
>>
>
> In the command you've given (with the same file for -s and -f), you're computing
> the RMSD at time zero, after fitting to the structure at time zero, so the RMSD
> must be zero.


but I am giving different groups (as chains). I am trying to get RMSD between
two monomers in same structure so what's wrong in that....

-
anupam

>>
>> so the rmsd = 0.0000001
>>
>> whereas when I use online server it gives me 1.4.
>>
>> so what am I doing wrong?
>>
>
> Then whatever you're giving the online server is different.  The Gromacs
> calculation seems to be correct.
>
> -Justin
>



>> regrads
>> anupam
>>
>>
>>
>
> --
> ========================================
>
> 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
>
> ========================================
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>
> --
> This message has been scanned for viruses and
> dangerous content by MailScanner, and is
> believed to be clean.
>
>


-- 
Science is facts; just as houses are made of stone, so is science is made of
facts; but a pile of stones is not a house, and  a collection of facts is not
necessarily science.

Anupam Nath Jha
Ph. D. Student
Saraswathi Vishveshwara Lab
Molecular Biophysics Unit
IISc,Bangalore-560012
Karnataka
Ph. no.-22932611



-- 
This message has been scanned for viruses and
dangerous content by MailScanner, and is
believed to be clean.