[gmx-users] Parametrisation of the cyclic nucleotides in Gromos force fields
Justin Lemkul
jalemkul at vt.edu
Fri Dec 7 16:44:47 CET 2012
On 12/7/12 10:41 AM, James Starlight wrote:
> Today I've tried to simulate complexes of my protein with the cyclic
> GMP parametrized by ATB's. (below the recent parametrisation for
> charges of that molecule done by am1 algorithm)
>
> [ moleculetype ]
> ; Name nrexcl
> _N4P 3
> [ atoms ]
> ; nr type resnr resid atom cgnr charge mass total_charge
> 1 NT 1 _N4P N2 1 -0.848 14.0067
> 2 H 1 _N4P H22 1 0.424 1.0080
> 3 H 1 _N4P H21 1 0.424 1.0080 ; 0.000
> 4 NR 1 _N4P N1 2 -0.684 14.0067
> 5 H 1 _N4P H1 2 0.437 1.0080
> 6 C 1 _N4P C2 2 0.779 12.0110
> 7 NR 1 _N4P N3 2 -0.678 14.0067
> 8 C 1 _N4P C4 2 0.440 12.0110
> 9 NR 1 _N4P N9 2 -0.294 14.0067 ; 0.000
> 10 C 1 _N4P C8 3 0.272 12.0110
> 11 HC 1 _N4P H01 3 0.141 1.0080
> 12 O 1 _N4P O6 3 -0.555 15.9994
> 13 C 1 _N4P C6 3 0.608 12.0110
> 14 C 1 _N4P C5 3 0.101 12.0110
> 15 NR 1 _N4P N7 3 -0.567 14.0067 ; 0.000
> 16 OE 1 _N4P O4* 4 -0.451 15.9994
> 17 CH1 1 _N4P C1* 4 0.451 13.0190 ; 0.000
> 18 OA 1 _N4P O5* 5 -0.394 15.9994
> 19 P 1 _N4P PAQ 5 0.974 30.9738
> 20 OM 1 _N4P OAR 5 -0.616 15.9994
> 21 OA 1 _N4P O3* 5 -0.390 15.9994
> 22 OA 1 _N4P OAS 5 -0.584 15.9994
> 23 H 1 _N4P H03 5 0.491 1.0080
> 24 CH2 1 _N4P C5* 5 0.281 14.0270
> 25 CH1 1 _N4P C4* 5 0.238 13.0190 ; 0.000
> 26 CH1 1 _N4P C3* 6 0.000 13.0190 ; 0.000
> 27 CH1 1 _N4P C2* 7 0.181 13.0190
> 28 OA 1 _N4P O2* 7 -0.645 15.9994
> 29 H 1 _N4P H8M 7 0.464 1.0080 ; 0.000
>
> In all cases my system have always been crushed after equilibration
> run ( during that phase with the posres applied on both protein as
> well as ligand the system was stabile) with the errors like
>
> Step 19, time 0.038 (ps) LINCS WARNING
> relative constraint deviation after LINCS:
> rms 1.203662, max 11.750027 (between atoms 4289 and 4287)
> bonds that rotated more than 30 degrees:
> atom 1 atom 2 angle previous, current, constraint length
> 4288 4287 89.5 0.2277 1.1291 0.1000
> 4292 4287 90.5 0.1304 0.9898 0.1350
> 4289 4287 90.4 0.1056 1.2750 0.1000
> 4318 4303 30.8 0.1531 0.1816 0.1530
> 4304 4303 45.2 0.1097 0.1531 0.1090
> 4309 4310 90.0 0.2629 0.3419 0.1000
> 4299 4290 84.2 0.1404 0.1641 0.1400
> 4292 4290 89.4 0.1362 0.5025 0.1380
> 4291 4290 89.2 0.1563 0.2142 0.1000
> 4293 4292 89.1 0.1252 0.5682 0.1320
> 4294 4293 78.1 0.1387 0.3906 0.1350
> 4300 4294 92.2 0.1385 0.4639 0.1390
> 4295 4294 91.1 0.1365 0.5711 0.1380
> 4303 4295 43.4 0.1482 0.1954 0.1470
> 4296 4295 36.6 0.1408 0.1593 0.1400
> 4301 4296 89.9 0.1323 0.5162 0.1320
> 4297 4296 32.5 0.1089 0.1343 0.1090
> 4299 4298 87.0 0.1230 0.2758 0.1230
> 4300 4299 89.8 0.1431 0.5922 0.1430
> 4301 4300 79.0 0.1381 0.1928 0.1380
>
>
> Fatal error:
> 1 particles communicated to PME node 26 are more than 2/3 times the
> cut-off out of the domain decomposition cell of their charge group in
> dimension y.
> This usually means that your system is not well equilibrated.
> For more information and tips for troubleshooting, please check the GROMACS
>
> After that my system have been crashed and than produced many
> step*.pdb files in the work dirr.
>
> It's intresting that with the prodrg topology of that mollecule ( with
> worst charge distribution) I've never such problems. Might that error
> be due to the wrong geometry parametrisation (e.g incorect dihedrals)
> of the cGMP made by ATB ?
>
Simulate all components of your system separately and follow
http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System.
Dihedrals should not be a major issue, since all of them can be adequately
described by those already present in the parent force field. Check against DGUA.
-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
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