[gmx-users] rmsd between different monomers

[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) has   249 elements
Group     2 (C-alpha_chain3) has   249 elements
Group     3 (C-alpha_chain4) has   249 elements
Select a group: 0
Selected 0: 'C-alpha_chain1'
Select group for RMSD calculation
Group     0 (C-alpha_chain1) has   249 elements
Group     1 (C-alpha_chain2) has   249 elements
Group     2 (C-alpha_chain3) has   249 elements
Group     3 (C-alpha_chain4) has   249 elements
Select a group:1
Selected 1: 'C-alpha_chain2'

---------------------------------

Is it not superimposing these two chins and calculating RMSD between them???

--
anupam


> 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 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....
>>>
>>
>> It doesn't matter. The structure for calculation (-f) and the reference
>> structure (-s) are identical, so the RMSD has to be zero, regardless of
>> the fitting group and calculation groups chosen.
>
> Exactly. Only if you can fit group A from one file to group B from a
> file (which may or may not be the same file) can Anupam do this
> calculation. g_rms seems not to allow this.
>
> Instead, Anupam should use trjconv or editconf to select groups
> beforehand, as I think I suggested a few days back. Thus (say) editconf
> produces file_with_group_A.pdb and editconf produces
> file_with_group_B.pdb, which allows g_rms -f file_with_group_A -s
> file_with_group_B. This will work if the two groups have the same atoms
> in matching orders, which should be the case for a tetramer setup.
>
> Mark
>
>>>>> 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.
>>>>
>>>>
>>>
>>>
>>
> --
> 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.