On 4/24/13 4:49 AM, Giuseppe wrote:
Dear Justin,
there were for sure some errors in the command, but even having solved them,
the protein still move during the optimization. What I noticed is that the
coordinates of the residues seems to decrease to zero and than "restart"
from a point out from the box. I mean, taking the first atom of the first
residue, after one EM the coordinates were:
1MET N 1 6.100 15.879 0.231
after the second EM were
1MET N 1 5.469 15.262 0.228
after the third EM were
1MET N 1 4.870 14.676 0.225
and so on till the thirteenth EM in which the coordinates were
1MET N 1 0.321 10.201 0.207
after this EM, protein moves off the membrane and the coordinates of the
first atom of the first residue become:
1MET N 1 12.791 9.867 0.206
there is obviously something wrong with the x axis, but what?
The box vectors in this case were 6.23910 6.17970 6.91950 and the
complete editconf command was "editconf -f protein.gro -o protein_newbox.gro
-box 6.23910 6.17970 6.91950 -center 3.20920 2.72175 6.2 -rotate 145 -45
55".
The only way that this is possible is if your protein is much larger than your
box. Note that the y-coordinate of the N atom of Met1 begins at nearly 16 nm,
which is more than twice the box vector in the y-dimension. I suspect that your
protein is ill-suited to being positioned within a box of these dimensions.
Note too that centering on z=6.2 almost assuredly places your protein outside
the box if the z-dimension is 6.9195 nm.
If there are further problems, separate the rotation and placement steps. I
don't recall off-hand which operation is done first, but this can be a source of
complication. Rotate your configuration first, then position it in a second step.
I also tried to use a larger box, which vectors were 12 12 12, and in this
case the complete editconf command was "editconf -f protein.gro -o
proetin.newbox.gro -box 12 12 12 -center 6 6 8.75 -rotate 145 -45 55" and to
decrease the scaling factor from 4 to 2, but it was useless. I'm sorry to
bother you so much, but I'm stucked with my project. Thank you so much.
A box size of 12 is still incompatible with the coordinates shown above.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
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@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists