[gmx-users] g_rms problem

[Christopher Neale]

I thought you said that you have 1000 structures. It seems like you only have 6? Nevertheless, I am glad that trjcat worked for you.

I don't know what is going on with your RMSD values, but I suggest that you start a separate post with a new subject line for that. I suspect that you need to do some fitting.

Chris.

-- original message --

thanks a lot for kind reply.
The outout for

for i in $(ls *pdb); do grep ^ATOM $i|wc -l; done |sort -n |head

is:
1838
1838
1838
1838
1838
1838

The output for

for i in $(ls *pdb); do grep ^ATOM $i|wc -l; done |sort -n |tail

is also:
1838
1838
1838
1838
1838
1838


It seems that trjcat works fine, although the time is 0 for all frames. 
Here is the command I use:

trjcat -cat -keeplast -f *.pdb -o out.xtc

g_rms -f out.xtc -s 001.pdb -o rmsd.xvg

However, I find a problem with the results. Since most part of each PDB 
file overlapped very well only a small loop is different. I first 
calculate the rmsd of backbone and got:

@ subtitle "Backbone after lsq fit to Backbone"
    0.0000000    0.0000003
    0.0000000    0.3306260
    0.0000000    0.2545602
    0.0000000    0.3293277
    0.0000000    0.2299789
    0.0000000    0.3216407

Then I calculate the loop region and got:

@ subtitle "Backbone_&_r_120-131 after lsq fit to Backbone"
    0.0000000    0.0000003
    0.0000000    0.1526730
    0.0000000    0.1202507
    0.0000000    0.1449232
    0.0000000    0.1318949
    0.0000000    0.1675032

As we can see, the rmsd of loop region is smaller than the backbone 
which I think it should be reversed.......

thank you very much.

On 10/28/2012 05:03 PM, Christopher Neale wrote:
> First, please let me complain that you did not run those 2 commands and post the full output with the line on which you entered the command (for each one). Each command is expected to give you 10 lines of output, but you posted a single group of 12 lines. That seems like unlikely output and just confuses things.
>
> Second, I am not sure that you can simply cat the results of rosetta together (or any pdb files). I suggest that you try using trjcat -cat -keeplast to put them together or convert them all to .gro files with a loop over editconf and then join them with cat (or trjcat).
>
> Chris.
>
>
>> How many atoms are in each .pdb file?
>>
>> for i in $(ls *pdb); do grep ^ATOM $i|wc -l; done |sort -n |head
>> for i in $(ls *pdb); do grep ^ATOM $i|wc -l; done |sort -n |tail
>>
>> Chris.
> Hi Chris:
>
>    they are 1838 atoms in each PDB file and all of them are full atoms. I
> run the command you provide and I got:
>
> 1838
> 1838
> 1838
> 1838
> 1838
> 1838
> 1838
> 1838
> 1838
> 1838
> 1838
> 1838
>
> When I try to reuse g_rms, the problem is still the same.
>
> thank you very much
>