[gmx-users] About membrane protein
t.piggot at soton.ac.uk
Wed Jan 15 11:49:21 CET 2014
Are you sure that this is not just a visualisation artefact of the
Justin Lemkul wrote:
> On 1/14/14, 2:13 PM, paulxie wrote:
>> Justin Lemkul wrote
>>> You will have to position the protein differently if it is oriented
>>> asymmetrically with respect the the membrane. The same principles
>>> box vectors will certainly be different, as will the editconf command.
>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>>> a mail to
>> Thanks Justin! It Is asymmetric because the protein consists of a
>> outer-membrane domain and a transmembrane helix. I placed the protein
>> asymmetrically to let the transmembrane helix in the middle of the
>> (dppc128) and adjusted the size of box. I confirmed that by checking the
>> coordinates in the system.gro and system_inflated.gro. But after that
>> after I did
>> " grompp -f minim.mdp -c system_inflated.gro -o confout.tpr -maxwarn 1"
>> "mdrun -deffnm confout -nt 1"
>> the coordinates of protein were dramatically changed, i.e. the protein
>> totally away from the bilayer.
>> I think that should be something wrong, but cannot find it.
> Without seeing your exact commands, neither can anyone else.
Dr Thomas Piggot
University of Southampton, UK.
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