[gmx-users] Questions about position restraint for charged proteins

Mark Abraham mark.j.abraham at gmail.com
Mon May 19 09:31:05 CEST 2014


First, you need a membrane for simulating this protein at all
realistically. Second, you need to consider what residue protonation states
are relevant for the system you are trying to model - neither the contents
of the PDB file nor the defaults of the topology building program can be
used blindly.

Mark
On May 19, 2014 3:07 AM, "Koki Yokoi" <kyokoi at uwm.edu> wrote:

> Dear Mark,
>
> Thank you for the reply. The muscarinic acetylcholine receptor consists of
> seven coils(
> http://en.wikipedia.org/wiki/File:Muscarinic_acetylcholine_receptor_M2-3UON.png).
> These coils are connected by intra/extracellular loops in vivo. However, in
> the PDB file of M2(3UON.pdb), one loop is replaced by lysozyme, which I
> don't need in my system, so I removed it. I couldn't replace it with an
> original loop because I don't know its structure. Above link shows M2
> without lysozyme. You see two coils on near side are not connected to other
> coils. These two and the remaining five coils are positively charged. I
> would like to maintain this structure of M2(without lysozyme) as it is and
> immobilize it during my simulation, but position restraint doesn't seem to
> work..
> Any help would be appreciated. Thank you very much.
>
> Koki
>
>
> On May 16, 2014 11:36 PM, "Koki Yokoi" <kyokoi at uwm.edu> wrote:
> >
> > Hello. I am currently using GROMACS4.6.5 and trying to simulate a
> fluorescent protein(GFP,1EMB.pdb) fused to a muscarinic acetylcholine
> receptor(M2,3UON.pdb). PDB file of M2(3UON.pdb) included a lysozyme
> part(res#1002-1161), so I removed it to make the simulation consistent with
> our experimental data. As a result, there is a gap in M2 structure, which
> means M2 is divided into two chains(res#20-217, res#377-456), and when in
> NVT equilibration process, these chains move apart from each other because
> both are positively charged.
>
> Why do these positively charged parts stay together in the system you are
> modeling?
>
> Mark
>
> >I would like to keep the conformation of M2 and immobilize it in
> simulation to see only the motion of the fluorescent protein, so I applied
> position restrains to M2, but two chains still move away from each other
> and eventually I get many LINCS warnings during NVT equilibration process
> and simulation collapses.
> >
> > My question is:
> > Position restrain is a proper way to keep conformations of proteins which
> have the same charge? Or is there any other way to do so?
> >
> > I am using all-bonds constraint and 2fs time step to save the simulation
> time. Other fundamental parameters are default.
> > Any help would be appreciated. Thank you very much.
> >
> > Koki
> >
> >
> > Below is the error messages during NVT equilibration process:
> > -----------------------------------------------------------------------
> > relative constraint deviation after LINCS:
> > rms 0.050664, max 3.739141 (between atoms 962 and 963)
> > bonds that rotated more than 30 degrees:
> >  atom 1 atom 2  angle  previous, current, constraint length
> >     962    963   89.9    0.1109   0.5118      0.1080
> >     964    965   90.1    0.1106   0.4336      0.1111
> >     964    966   31.9    0.1104   0.1199      0.1111
> > Wrote pdb files with previous and current coordinates
> >
> > Step 575382, time 575.382 (ps)  LINCS WARNING
> > relative constraint deviation after LINCS:
> > rms 611.466194, max 51433.625000 (between atoms 570 and 573)
> > bonds that rotated more than 30 degrees:
> >  atom 1 atom 2  angle  previous, current, constraint length
> >     555    557   46.2    0.1345   0.1917      0.1345
> >     557    558   49.3    0.0997   0.1394      0.0997
> >     557    559   82.2    0.1430   0.4301      0.1430
> >     559    560   78.3    0.1080   0.3101      0.1080
> >     559    561   84.3    0.1538   1.6306      0.1538
> >     559    574   80.8    0.1490   0.3913      0.1490
> >     561    562   85.8    0.1111   1.4345      0.1111
> >     561    563   85.0    0.1111   1.3860      0.1111
> >     561    564   88.6    0.1538   7.0559      0.1538
> >     564    565   88.3    0.1111   6.1646      0.1111
> >     564    566   88.8    0.1538   6.5956      0.1538
> >     564    570  145.8    0.1538  18.8304      0.1538
> >     566    567   87.6    0.1111   1.7574      0.1111
> >     566    568   87.6    0.1111   1.7576      0.1111
> >     566    569   88.0    0.1111   1.7916      0.1111
> >     570    571   90.0    0.1111  10.2121      0.1111
> >     570    572  125.4    0.1111  10.2996      0.1111
> >     570    573   90.0    0.1111 5714.3872      0.1111
> >     574    575   42.6    0.1230   0.1646      0.1230
> >     574    576   42.1    0.1345   0.1834      0.1345
> >     916    917   33.8    0.0997   0.1182      0.0997
> >     916    918  115.0    0.1428   2.7045      0.1430
> >     918    919   92.6    0.1079   2.7119      0.1080
> >     918    920  149.6    0.1533   2.6632      0.1538
> >     920    921   36.5    0.1111   0.1355      0.1111
> >     920    922   35.7    0.1111   0.1401      0.1111
> >     933    934  106.0    0.1226   2.8814      0.1230
> >     933    960   86.3    0.1372   9.0101      0.1345
> >     935    962  121.3    0.1295  70.4373      0.1490
> >     936    940  172.6    0.1365   9.4523      0.1400
> >     937    955  150.4    0.1411   9.9921      0.1450
> >     938    939   43.2    0.1241   4.6305      0.1220
> >     938    940   79.6    0.1482   1.2946      0.1490
> >     940    941   48.9    0.1378   3.7713      0.1360
> >     941    942   42.8    0.1098   0.1650      0.1100
> >     941    943   33.2    0.1444   0.2096      0.1450
> >     955    956   73.3    0.1086   4.4738      0.1080
> >     955    957   68.8    0.1085   3.8836      0.1080
> >     955    958   43.4    0.1509   4.5246      0.1490
> >     958    959   33.6    0.1226   0.1674      0.1230
> >     958    969   36.3    0.1343   0.1844      0.1345
> >     962    963  103.5    0.5118  19.1058      0.1080
> >     962    964  131.9    0.1441 141.6376      0.1538
> >     964    965   88.9    0.4336 2773.4438      0.1111
> >     964    966   58.9    0.1199  82.5709      0.1111
> >     964    967   55.1    0.1502 133.7226      0.1420
> >     967    968  105.8    0.0947  47.8773      0.0960
> > Wrote pdb files with previous and current coordinates
> >
> > WARNING: Listed nonbonded interaction between particles 557 and 564
> > at distance 3f which is larger than the table limit 3f nm.
> >
> > This is likely either a 1,4 interaction, or a listed interaction inside
> > a smaller molecule you are decoupling during a free energy calculation.
> > Since interactions at distances beyond the table cannot be computed,
> > they are skipped until they are inside the table limit again. You will
> > only see this message once, even if it occurs for several interactions.
> >
> > IMPORTANT: This should not happen in a stable simulation, so there is
> > probably something wrong with your system. Only change the
> table-extension
> > distance in the mdp file if you are really sure that is the reason.
> >
> --
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