Hi everybody,
I did a minimization of my structure. But the output seems a bit strange
for me, since my input was the protein with its membrane in a box like
this:
# = box P = Protein M=Membrane
#
# #
# MM#
# #
# #
# #
#
On 7/11/12 6:13 AM, reising...@rostlab.informatik.tu-muenchen.de wrote:
Hi everybody,
I did a minimization of my structure. But the output seems a bit strange
for me, since my input was the protein with its membrane in a box like
this:
# = box P = Protein M=Membrane
#
#
Hi Justin,
ah okey. Thank you.
And I have another question. Why is the protein in the corner of the box
and not in the middle?
I thought I centered it with the command:
editconf -f wholeProtein.gro -o 3m71_box.gro -center 4.59340 4.59470
5.17330 -c -bt dodecahedron -d 1.0 2logErr 1logOut
Or
On 7/11/12 7:12 AM, reising...@rostlab.informatik.tu-muenchen.de wrote:
Hi Justin,
ah okey. Thank you.
And I have another question. Why is the protein in the corner of the box
and not in the middle?
I thought I centered it with the command:
editconf -f wholeProtein.gro -o 3m71_box.gro -center
Yes I tried the command you wrote but it is still in the corner of the box.
Is there anything else I can do?
The coordinates I used to center the protein are the ones which are in the
last line of the .gro file.
Thank you
On 7/11/12 7:12 AM, reising...@rostlab.informatik.tu-muenchen.de wrote:
On 7/11/12 7:34 AM, reising...@rostlab.informatik.tu-muenchen.de wrote:
Yes I tried the command you wrote but it is still in the corner of the box.
Is there anything else I can do?
The coordinates I used to center the protein are the ones which are in the
last line of the .gro file.
The
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