[gmx-users] g_rms problem

[Christopher Neale]

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