Prof. David,
Thank you for your input.
Based on your suggestion I visualized the protein complex AB, especially
the dangling C Terminus of A and it turns out that the tail come in really
close contact with the protein B (in complex with protein A). There are
around 4 -5 residues from the tail that is coming into contact with
neighboring complex. I don't know how much of that is going to be the
problem.
This is 80ns simulation. Previously I have run the same simulation for 60
ns with everything same but with lower restraints (50 for 60ns and 100 fro
80ns) during minimization and I included iwrap for 80 ns. I visualized
results from this 60 ns simulation and it is fine. Proteins don't move that
much and the dangling end never comes in close contact with neighbors. For
both simulation I used TIP3PBOX 12.0. I am just surprised how much the
protein moved during the 80ns simulation. Could you please suggest me some
appropriate steps from now onward? I spent about a month to get results
from this simulation and I got stuck here.
I would really appreciate your suggestions int his regard.
minimize water-only
&cntrl
imin=1,
maxcyc=10000,
ncyc=5000,
ntmin=1,
nmropt=0,
ntpr=100,
ntb=1,
cut=10.0,
ibelly=0,
ntr=1, restraintmask=':1-238 & !.H=', restraint_wt=100.0,
/
minimize everything
&cntrl
imin=1,
maxcyc=10000,
ncyc=5000,
ntmin=1,
nmropt=0,
ntpr=100,
ntb=1,
cut=10.0,
ibelly=0,
ntr=0,
/
Heat
&cntrl
imin=0,irest=0,ntx=1,
nstlim=500000,dt=0.002,
ntc=2,ntf=2,
cut=10.0, ntb=1,
ioutfm=1, ntxo=2, ntpr=5000, ntwx=5000, ntwr=5000,
ntt=3, gamma_ln=1.0, ig=-1
tempi=0.0, temp0=300.0,
ntr=1, restraintmask=':1-238', restraint_wt=10.0,
nmropt=1,
/
&wt TYPE='TEMP0', istep1=0, istep2=500000,
value1=0.0, value2=300.0, /
&wt TYPE='END' /
Prod
&cntrl
imin=0,
irest=1,
ntx=5,
nstlim=40000000,
dt=0.002,
ntf=2,
ntc=2,
ntxo=2,
ioutfm=1,
temp0=300.0,
tempi=300.0,
ntpr=10000,
ntwx=10000,
ntwr=10000,
cut=10.0,
iwrap=1,
ntb=2,
pres0=1.0,
ntp=1,
taup=2.0,
ntr=0,
ntt=3,
gamma_ln=1.0,
ig=-1,
/
~
On Sat, May 21, 2016 at 8:21 AM, David A Case <david.case.rutgers.edu>
wrote:
> On Fri, May 20, 2016, Arati Paudyal wrote:
> >
> > My protein complex looked ok and they stayed intact for the entire
> > simulation. The protein-protein interaction part always remained inside
> the
> > water boundary . The part that is moving in-out of the boundary is a
> small
> > C-terminal tail that is just dangling. I compared my data from 60 ns and
> 80
> > ns (with iwrap) and they are very close. SO I don't think that mattered a
> > lot.
>
> Are you sure this is a problem? Remember that no part of the protein is
> going outside the solvent: the C-terminal tail is just sticking into the
> adjacent unit cell. You might want to use VMD to visualize neighboring
> cells,
> to see if you are getting any protein-protein interactions between images
> that
> you don't want. One explanation for what you describe is that your solvent
> box is rather small, so that it is hard to a single unit cell in which all
> of the protein appears to "fit" inside the solvent.
>
> ....dac
>
>
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Received on Sat May 21 2016 - 07:00:05 PDT
