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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