[gmx-users] About membrane protein

Justin Lemkul jalemkul at vt.edu
Tue Jan 14 23:50:42 CET 2014

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 apply,
>> but
>> box vectors will certainly be different, as will the editconf command.
>> -Justin
>> -
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send
>> a mail to
>> gmx-users-request@
>> .
> 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 bilayer
> (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 step,
> after I did
> " grompp -f minim.mdp -c system_inflated.gro -o confout.tpr -maxwarn 1"
> and
> "mdrun -deffnm confout -nt 1"
> the coordinates of protein were dramatically changed, i.e. the protein was
> 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.



Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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