[gmx-users] Questions about position restraint for charged proteins
massimo sandal
devicerandom at gmail.com
Mon May 19 11:07:13 CEST 2014
Actually, simulating it with no loop at all is much less realistic than
modeling your own loop. Just use MODELLER to fill the gap in the loop
regions and use the result.
Also, did you check for stabilizing mutations in the crystallized protein
and did you correct them?
Cheers,
Massimo
On 19 May 2014 03:07, "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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