[gmx-users] Crashes during protein-ligand simulation
jmsstarlight at gmail.com
Fri Jul 6 21:56:46 CEST 2012
I've experimented with 2 dirrerent COM groups
comm-grps = SOL_NA_CL XW Protein_CCl4_ADN ; 3 groups
comm-grps = SOL_NA_CL_XW Protein_CCl4_ADN; 2 groups
but the crashes were in both cases after 12- 15ns of simulation
this time I've changed to the
comm-grps = System
and there have not been any crashes yet (to this time I've already
calculated addition 20ns after privious crhased simulation using
checkpoint file for the last simulation ). But it's posible that it
was lucky coincidence :)
Could you tell me how I could devide largest group in the above
axample into several smaller sub-groups ? Should I do that separation
randomly or there are most correct way for that ? (e.g within third
cgnr separate all nitrogens and oxygens with corresponded hydrogens in
the separate cgrp's from carbons)
2012/7/6, Justin A. Lemkul <jalemkul at vt.edu>:
> On 7/6/12 2:05 PM, James Starlight wrote:
>> 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
>> 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
> Large charge groups could account for errors in neighbor searching, leading
> clashes that cause the simulation to collapse.
>> 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 :)
> OK, just be ready for reviewers to ask why you didn't do docking ;)
>> 3) It's strange that the simulation crashes without any reasons ( the
>> system is very stable during calculated 10-15ns trajectory)
> There's always a reason, you just haven't found it yet. The charge group
> could indeed be the problem; neighbor searching can fail at any time when
> atoms run into one another.
>> 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.
> I see no reason to add such complexity to the system. Breaking the crystal
> waters into their own COM removal group does not make sense to me.
> they are basically part of the protein.
>> 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
> And what was the outcome? I see no reason that two COM motion removal
> wouldn't be appropriate (as layers can slide with respect to one another,
> like a
> membrane) but three groups does not sound appropriate.
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
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