[gmx-users] protein-protein complex gets "separated" in EM step

[Gregor Hagelueken]

Dear Justin,
Thank you! That fixed the problem!
Cheers,
Gregor

Von meinem iPhone gesendet

> Am 25.10.2016 um 16:19 schrieb Justin Lemkul <jalemkul at vt.edu>:
> 
> 
> 
>> On 10/25/16 10:16 AM, Gregor Hagelüken wrote:
>> Dear all,
>> 
>> I am attempting to do a MD simulation off a protein-protein complex. I have successfully performed MD runs on the individual proteins.
>> Now, I have taken the complex structure (X-ray structure) and ran it through pdb2gmx to get a topology. This also worked. The program does not complain and the complex structure in the resulting .gro file looks just like the input .pdb file in PyMOL.
>> 
>> Next, I performed an energy minimization using these commands:
>> 
>> grompp -v -f minim.mdp -c protein.gro -p protein.top -o protein-EM-vacuum.tpr
>> mdrun -v -deffnm protein-EM-vacuum -c protein-EM-vacuum.gro
>> 
>> This runs fine, but I noticed that in the resulting protein-EM-vacuum.gro file, the two components of my complex (chains A and B) are separated by ~50 Å. Even if I only run the minimisation for 5 steps.
>> Any idea why this happens?
>> 
>> Thank you very much for your help!
>> Cheers,
>> Gregor
>> 
>> 
>> 
>> P.S.: I took the minim.mdp file from this website: http://cgmartini.nl/%7Emdcourse/md.html <http://cgmartini.nl/~mdcourse/md.html>
>> 
> 
> That .mdp file uses PBC in all dimensions, which is not normal for a vacuum minimization or simulation.  Your box is probably too small relative to the protein complex, and then the structures start to jump across PBC because you're using "pbc = xyz."  For a true in vacuo minimization or simulation, use "pbc = no" and the box size becomes irrelevant.
> 
> -Justin
> 
> -- 
> ==================================================
> 
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
> 
> Department of Pharmaceutical Sciences
> School of Pharmacy
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> University of Maryland, Baltimore
> 20 Penn St.
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> 
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
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