[gmx-users] Questions about position restraint for charged proteins
Koki Yokoi
kyokoi at uwm.edu
Mon May 19 18:26:19 CEST 2014
Dear Mark,
I understand. I will try to do it.
Thank you very much. I appreciate your help.
Regards,
Koki
>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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