Hi Justin, thank you a lot for your answer. I will try it. Best, Eva > > > On 9/20/12 6:52 AM, reising...@rostlab.informatik.tu-muenchen.de wrote: >> Hi, >> now I tried it without any restriction and still the LINCS warnings >> occur. >> Since it is always the hydrogen atom where the huge force lies on I had >> the idea just to remove the hydrogen atom to find out whether another >> atom >> will occur to have such a high force on or everything went fine. And >> indeed, without the hydrogen atom there is no problem during the MD run. >> Even when I fix all the other atoms. >> >> I can not see why this occurs. I already looked at the residue with >> pymol >> and I could see that there is no other residue or atom clashing with it. >> > > I suspect what is happening is that the topology is not stable. If > removal of > the H atom leads to stable trajectories, then it is experiencing some > interaction that leads to the crash. Likely what is happening is that it > is > experiencing a very strong 1-4 interaction with the other phosphate > oxygens and > is being pulled very hard away from the oxygen to which it is bonded, > leading to > deformed geometry and the LINCS warnings. There are two possible > solutions: > > 1. Modify the 1-4 interactions through an appropriate pair term. > 2. Add exclusions to the topology between the H atom and each of the O > atoms to > which it is not bonded. > > I would recommend testing with a very simple system of TYP in water to > validate > that the topology is stable and rule out other factors. > > -Justin > >> The residue looks like this: >> >> ATOM 955 N TYP 65 27.310 23.150 27.670 1.00 0.00 >> N >> ATOM 956 CA TYP 65 26.870 23.320 26.300 1.00 0.00 >> C >> ATOM 957 C TYP 65 27.920 23.760 25.300 1.00 0.00 >> C >> ATOM 958 O TYP 65 28.060 23.210 24.210 1.00 0.00 >> O >> ATOM 959 CB TYP 65 25.740 24.340 26.170 1.00 0.00 >> C >> ATOM 960 CG TYP 65 24.530 23.740 26.830 1.00 0.00 >> C >> ATOM 961 CD1 TYP 65 24.410 23.760 28.220 1.00 0.00 >> C >> ATOM 962 CD2 TYP 65 23.510 23.180 26.050 1.00 0.00 >> C >> ATOM 963 CE1 TYP 65 23.290 23.210 28.840 1.00 0.00 >> C >> ATOM 964 CE2 TYP 65 22.380 22.630 26.660 1.00 0.00 >> C >> ATOM 965 CZ TYP 65 22.260 22.630 28.070 1.00 0.00 >> C >> ATOM 966 OH TYP 65 21.160 22.100 28.670 1.00 0.00 >> O >> ATOM 967 P TYP 65 20.298 21.422 27.722 1.00 0.00 >> P >> ATOM 968 OP1 TYP 65 21.003 21.245 26.467 1.00 0.00 >> O >> ATOM 969 OP2 TYP 65 19.920 20.126 28.251 1.00 0.00 >> O >> ATOM 970 OP3 TYP 65 19.106 22.218 27.498 1.00 0.00 >> O >> ATOM 971 H TYP 65 27.210 23.914 28.325 1.00 0.00 >> H >> ATOM 972 HA TYP 65 26.485 22.366 25.933 1.00 0.00 >> H >> ATOM 973 HB1 TYP 65 25.524 24.543 25.119 1.00 0.00 >> H >> ATOM 974 HB2 TYP 65 26.010 25.270 26.669 1.00 0.00 >> H >> ATOM 975 HD1 TYP 65 25.154 24.234 28.821 1.00 0.00 >> H >> ATOM 976 HD2 TYP 65 23.603 23.156 24.973 1.00 0.00 >> H >> ATOM 977 HE1 TYP 65 23.200 23.222 29.916 1.00 0.00 >> H >> ATOM 978 HE2 TYP 65 21.603 22.189 26.053 1.00 0.00 >> H >> ATOM 979 H1P TYP 65 20.357 20.996 25.802 1.00 0.00 >> H >> >> >> The topology entry in the aminoacid.rtp file looks like this: >> >> [ TYP ] >> [ atoms ] >> N N -0.516300 1 >> CA CT 0.275503 2 >> HA H1 0.008223 3 >> CB CT -0.354052 4 >> HB1 HC 0.110326 5 >> HB2 HC 0.110326 6 >> CG CA 0.119728 7 >> CD1 CA -0.198938 8 >> HD1 HA 0.137143 9 >> CE1 CA -0.284884 10 >> HE1 HA 0.177179 11 >> CZ C 0.452616 12 >> OH OS -0.534452 13 >> H H 0.293600 14 >> CE2 CA -0.284884 15 >> HE2 HA 0.177179 16 >> CD2 CA -0.198938 17 >> HD2 HA 0.137143 18 >> C C 0.536600 19 >> O O -0.581900 20 >> P P 1.393213 21 >> OP1 OH -0.752821 22 >> OP2 O2 -0.822464 23 >> OP3 O2 -0.822464 24 >> H1P HO 0.423316 25 >> >> >> [ bonds ] >> N H >> N CA >> CA HA >> CA CB >> CA C >> CB HB1 >> CB HB2 >> CB CG >> CG CD1 >> CG CD2 >> CD1 HD1 >> CD1 CE1 >> CE1 HE1 >> CE1 CZ >> CZ OS >> CZ CE2 >> OS P >> CE2 HE2 >> CE2 CD2 >> CD2 HD2 >> C O >> -C N >> P OP1 >> P OP2 >> P OP3 >> H1P OP1 >> >> >> [ impropers ] >> -C CA N H >> CA +N C O >> CG CE2 CD2 HD2 >> CZ CD2 CE2 HE2 >> CD1 CZ CE1 HE1 >> CG CE1 CD1 HD1 >> CD1 CD2 CG CB >> CE1 CE2 CZ OH >> >> >> The LINCS problems lie between the oxygen atom of the phosphate where a >> hydrogen atom is bound to (OP1) and the hydrogen atom bound to the >> oxygen >> atom of the phosphate (H1P). >> >> Do you see where the problem lies? >> Thank you, >> Eva >> >>> >>> >>> On 9/18/12 8:58 AM, reising...@rostlab.informatik.tu-muenchen.de wrote: >>>> Okey, >>>> now I tried it without any fixed residues. But still the energy >>>> after >>>> the >>>> minimization is not very low and I still get the LINCS warnings. >>>> >>>> The mdp file I use for the minimization looks like this: >>>> >>>> define = -DPOSRES >>> >>> Restraints during minimization generally restrict motion in the same >>> way >>> that >>> freezing does. Again, this is a potential barrier to sufficient >>> minimization. >>> >>>> integrator = steep >>>> emtol = 10 >>>> nsteps = 1500 >>>> nstenergy = 1 >>>> energygrps = System >>>> coulombtype = PME >>>> rcoulomb = 0.9 >>>> rvdw = 0.9 >>>> rlist = 0.9 >>>> fourierspacing = 0.12 >>>> pme_order = 4 >>>> ewald_rtol = 1e-5 >>>> pbc = xyz >>>> >>>> >>>> the mdp file for the md run looks like this: >>>> >>>> define = -DPOSRES >>>> integrator = md >>>> dt = 0.001 >>>> nsteps = 5000 >>>> nstxout = 100 >>>> nstvout = 0 >>>> nstfout = 0 >>>> nstlog = 1000 >>>> nstxtcout = 500 >>>> nstenergy = 5 >>>> energygrps = Protein Non-Protein >>>> nstcalcenergy = 5 >>>> nstlist = 10 >>>> ns-type = Grid >>>> pbc = xyz >>>> rlist = 0.9 >>>> coulombtype = PME >>>> rcoulomb = 0.9 >>>> rvdw = 0.9 >>>> fourierspacing = 0.12 >>>> pme_order = 4 >>>> ewald_rtol = 1e-5 >>>> gen_vel = yes >>>> gen_temp = 200.0 >>>> gen_seed = 9999 >>>> constraints = all-bonds >>>> tcoupl = V-rescale >>>> tc-grps = Protein Non-Protein >>>> tau_t = 0.1 0.1 >>>> ref_t = 298 298 >>>> pcoupl = no >>>> >>>> >>>> >>>> The output of the minimization run is: >>>> >>>> Steepest Descents converged to machine precision in 15 steps, >>>> but did not reach the requested Fmax < 10. >>>> Potential Energy = -7.9280412e+05 >>>> Maximum force = 1.0772942e+04 on atom 979 >>>> Norm of force = 9.6685356e+01 >>>> >>> >>> Note that this outcome is even worse than before. The maximum force is >>> now over >>> 10,000. >>> >>>> >>>> >>>> >>>> The output of the MD run is: >>>> >>>> Step 1031, time 1.031 (ps) LINCS WARNING >>>> relative constraint deviation after LINCS: >>>> rms 0.001431, max 0.010707 (between atoms 976 and 979) >>>> bonds that rotated more than 30 degrees: >>>> atom 1 atom 2 angle previous, current, constraint length >>>> 976 979 81.6 0.1272 0.0970 0.0960 >>>> >>>> >>> >>> As you should expect. If you can't get a reasonable minimization, the >>> MD >>> will >>> always crash. >>> >>>> >>>> The atom 979 is the hydrogen atom on the phosphate. There has to be >>>> one >>>> hydrogen atoms because it is protonated once. The other atom 976 is >>>> the >>>> oxygen atom where the hydrogen atom is bound to. >>>> The bounding parameters for this kind of binding were already there. I >>>> didn't add them. >>>> >>>> I already did it for another phosphorylation on another position in >>>> this >>>> structure. And here I also got many LINCS errors. And again the >>>> problem >>>> is >>>> the connection between the hydrogen atom and the oxygen atom. >>>> >>>> But I do not understand why. >>> >>> Remove all restraints/freezing/whatever in the .mdp file and try the EM >>> again. >>> If it still does not converge to a reasonable value, then there are two >>> potential problems: >>> >>> 1. The topology is flawed and thus the structure cannot be run stably >>> 2. The structure cannot accommodate phosphate in this location and due >>> to >>> unresolvable clashes, the runs fail >>> >>> -Justin >>> >>> -- >>> ======================================== >>> >>> Justin A. Lemkul, Ph.D. >>> Research Scientist >>> Department of Biochemistry >>> Virginia Tech >>> Blacksburg, VA >>> jalemkul[at]vt.edu | (540) 231-9080 >>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin >>> >>> ======================================== >>> -- >>> gmx-users mailing list gmx-users@gromacs.org >>> http://lists.gromacs.org/mailman/listinfo/gmx-users >>> * Please search the archive at >>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! >>> * Please don't post (un)subscribe requests to the list. Use the >>> www interface or send it to gmx-users-requ...@gromacs.org. >>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>> >> >> > > -- > ======================================== > > Justin A. Lemkul, Ph.D. > Research Scientist > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >
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