[gmx-users] rmsd between different monomers

[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 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
>>>
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>>
>>
>