Justin,
I've done all steps in accordance to your tutorial. I've already done
the same systems with another ligands but had no problem.
This time I've made topology of the ligand via ATB server. I've only
noticed that some cgnr are too big in that topology . This is the
example
ADN 3
[ atoms ]
; nr type resnr resid atom cgnr charge mass total_charge
1 NT 1 ADN N6 1 -0.844 14.0067
2 H 1 ADN H11 1 0.422 1.0080
3 H 1 ADN H12 1 0.422 1.0080 ; 0.000
4 C 1 ADN C8 2 0.097 12.0110
5 HC 1 ADN H01 2 0.177 1.0080
6 NR 1 ADN N3 2 -0.642 14.0067
7 C 1 ADN C4 2 0.175 12.0110
8 C 1 ADN C5 2 0.092 12.0110
9 NR 1 ADN N7 2 -0.556 14.0067
10 C 1 ADN C6 2 0.657 12.0110 ; 0.000
11 C 1 ADN C5' 3 -0.677 12.0110
12 C 1 ADN C4' 3 0.834 12.0110
13 OE 1 ADN O4' 3 -0.248 15.9994
14 C 1 ADN C1' 3 -0.558 12.0110
15 C 1 ADN C2' 3 0.603 12.0110
16 C 1 ADN C3' 3 -0.212 12.0110
17 NR 1 ADN N9 3 0.415 14.0067
18 OA 1 ADN O2' 3 -0.606 15.9994
19 H 1 ADN H08 3 0.482 1.0080
20 OA 1 ADN O3' 3 -0.606 15.9994
21 H 1 ADN H06 3 0.482 1.0080
22 OA 1 ADN O5' 3 -0.246 15.9994
23 H 1 ADN H03 3 0.337 1.0080 ; -0.000
24 C 1 ADN C2 4 0.502 12.0110
25 HC 1 ADN H10 4 0.106 1.0080
26 NR 1 ADN N1 4 -0.608 14.0067 ; 0.000
; total charge of the molecule: -0.000
2) To the binding pocket I've inserted this ligand manually by means
of superimposition with the reference x-ray structure wich include the
same protein in the same conformation with the same ligand. I've done
some systems already and that aproach was good :)
3) It's strange that the simulation crashes without any reasons ( the
system is very stable during calculated 10-15ns trajectory)
Also I suppose that such problems could be with the COM groups
this is the example from my mdp
comm-grps = SOL_NA_CL XW Protein_CCl4_ADN
here XW is the water wich were coppied from X-ray structure .
Also in that system Ccl4 is the membrane mimicking layer so I've
merged it with protein and ligand in the same group.
On the current stage I've tried to make changes in the mdp on
comm-grps = System
to check if the problem was with that COM motion
James
2012/7/6, Justin A. Lemkul <jalem...@vt.edu>:
>
>
> On 7/6/12 1:12 AM, James Starlight wrote:
>> Dear Gromacs users!
>>
>> I have some problems with the simulation of protein-ligand complex
>> embedded in the ccl4-water environment. In addition there are some
>> crystallography waters (xw) embedded in the protein interiour of the
>> protein. I've done equilibration and minimisation of my system and run
>> it in NVT ensemble.
>>
>> Finally I've already simulated this system in the apo form as well as
>> without XW and there were no any problems.
>>
>> In the current case my system always crashed after 10-15 ns of
>> simulation with the errors like
>>
>> Step 6651310, time 13302.6 (ps) LINCS WARNING
>> relative constraint deviation after LINCS:
>> rms 0.060675, max 1.520945 (between atoms 3132 and 3130)
>> bonds that rotated more than 30 degrees:
>> atom 1 atom 2 angle previous, current, constraint length
>> 3148 3147 90.0 0.1281 0.1483 0.1000
>> 3150 3149 90.0 0.1084 0.1444 0.1000
>> 3131 3130 90.0 0.1321 0.1325 0.1000
>> 3132 3130 90.0 0.1067 0.2521 0.1000
>>
>> -------------------------------------------------------
>> Program mdrun_mpi.openmpi, VERSION 4.5.5
>> Source code file: /tmp/build/gromacs-4.5.5/src/mdlib/constr.c, line: 189
>>
>>
>> here both atoms 3132 and 3130 are from LIGAND.
>>
>> During data analysing I didnt observed any serious artifacts in that
>> system. In addition RMSD both of protein and ligand were very stable.
>> Finally there are no fluctuations in energy or temperature. So I could
>> understand why this crasshes could occur. If I try to continue this
>> simulation from the crasshed checkpoint my simulation always goon but
>> within next 5-10ns I've always obtain second crash etc.
>>
>> This is the last step from log file
>>
>> DD step 6649999 vol min/aver 0.758 load imb.: force 1.0% pme
>> mesh/force 0.708
>>
>> Step Time Lambda
>> 6650000 13300.00000 0.00000
>>
>> Energies (kJ/mol)
>> Angle G96Angle Proper Dih. Improper Dih.
>> LJ-14
>> 5.78299e+01 1.24988e+04 2.10966e+03 1.81619e+03
>> 8.94229e+01
>> Coulomb-14 LJ (SR) LJ (LR) Disper. corr. Coulomb
>> (SR)
>> 4.65481e+04 8.27301e+04 -6.89535e+03 -2.15286e+03
>> -7.16722e+05
>> Coul. recip. Potential Kinetic En. Total Energy Conserved
>> En.
>> -1.72813e+05 -7.52733e+05 1.46708e+05 -6.06025e+05
>> -1.37045e+06
>> Temperature Pres. DC (bar) Pressure (bar) Constr. rmsd
>> 3.10968e+02 -9.74796e+01 2.52993e+02 1.55693e-05
>>
>>
>> Could you explain me what could be wrong with that system and what
>> addition data should I provide to help sheld light on that problem ?
>>
>
> If the addition of a ligand causes the simulation to crash (and the
> simulation
> runs normally in the apo form with and without crystal waters), then that
> sounds
> like a problem with the ligand topology or its initial placement.
>
> What is the ligand? How did you generate and validate its topology? How
> did
> you place it?
>
> -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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