On 7/6/12 2:05 PM, James Starlight wrote:
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
Large charge groups could account for errors in neighbor searching, leading to
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 size
could indeed be the problem; neighbor searching can fail at any time when some
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. Physically,
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 groups
wouldn't be appropriate (as layers can slide with respect to one another, like a
membrane) but three groups does not sound appropriate.
-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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