Re: [AMBER] Protein moving out of the water box

From: Arati Paudyal <>
Date: Sat, 21 May 2016 09:32:51 -0400

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

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
  ntr=1, restraintmask=':1-238 & !.H=', restraint_wt=100.0,

minimize everything
  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,
 &wt TYPE='TEMP0', istep1=0, istep2=500000,
  value1=0.0, value2=300.0, /
 &wt TYPE='END' /



On Sat, May 21, 2016 at 8:21 AM, David A Case <>

> 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
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