[gmx-users] Some atoms are not properly rotated with gmx_editconf

[ABEL Stephane]

Hello 

I would like my gramicidin A channel along the z axis. So I use the following commands in a bash script

## Select a group for determining the system size: System : 0 
## Select group for the determining the orientation ! GramicidinA : 15
## Select a group that you want to align: TRP12_CA_DLEU_32_CA : 16
## Select a group for output: System : 0

## Align the Channel along the z axis 

echo 0 15 16 0 > vector.txt


  gmx_mpi editconf -f 1JNO_GramicidineA_pep_em_step0.pdb -o 1JNO_GramicidineA_pep_em_step0_reoriented_along_Zaxis.pdb -princ -rotate -0 90 0 -align 0 90 0 -n System.ndx -box 5.0 5.0 5.0 -center 2.5 2.5 2.5 -resnr 1 < vector.txt

## Center the channel

mpirun -np 1 gmx_mpi trjconv -f 1JNO_GramicidineA_pep_em_step0_reoriented_Normal_Zaxis.pdb -s 1JNO_GramicidineA_pep_em_step0.tpr -pbc mol -ur compact -center -o 1JNO_GramicidineA_pep_em_step0_reoriented_Normal_Zaxis_center.pdb -n System.ndx

The problem is that the channel is well aligned along the z axis but "not" the TRP12_CA_DLEU_32_CA atoms used for the vector. 

How to resolve this ?

You could download the pdb file (below) and see what I mean with pymol

https://www.dropbox.com/s/l5crrpxsy3fak6e/1JNO_GramicidineA_pep_em_step0_reoriented_Normal_Zaxis_center.pdb?dl=0

Best regards 

Stéphane