Re: [AMBER] protein protrudes from unit cell

From: Carlos Simmerling <>
Date: Wed, 18 Mar 2009 15:49:43 +0000

Ross is right of course, but if the ligand is out of the pocket this
would only be a problem if you already have iwrap=1, if you left iwrap
at default then it would not get imaged away from its pocket. do as
Ross suggests, but for multiple molecules you need to image in steps.
so, if you have a dimer and 2 ligands, I would suggest something like
this protocol:

center on one monomer
center on the dimer (both monomers)
center on 3 molecules
center on all 4

this will put it all back together in case the 4 molecules got wrapped
to different places in the main cell
note that the lines above are just schematic, you need to sue the
correct ptraj syntax of course, which Ross provided and is explained
in more detail in the ptraj manual..

2009/3/18 Ross Walker <>:
> Hi Jeffrey
>> I performed NPT¡¡simulation (NTT=1) for a dimmer solvated in a
>> truncated octahedral box, with a minimum distance of 10 angstrom from the
>> atoms of protein to the edge of the solvent box. After about 5ns NPT
>> simulation, the protein protruded from the unit cell. It seems that the
>> protein didn't rotate around its center (geometry or center of mass),
>> which caused the problem. Can the problem be avoided by translating and
>> orienting center of the initial dimmer model to overlap with the origin of
>> the coordinate set and then solvating it in the OCT box? Or this problem
>> is due to the parameters used (DT, NSCM etc.)?
> This is likely not an error but simply a visualization problem. Sander by
> default does not wrap anything in terms of the coordinates it writes to
> disk. Thus it looks like water tunnels out into vacuum etc. This is simply a
> coordinate system choice, internally the program wraps everything correctly.
> You can force it to wrap everything by setting iwrap = 1 this will keep all
> molecules in the central box when writing mdcrd files. However, it wraps by
> molecule and so if a large molecule starts to drift out of the central box
> it will not be wrapped until it has entirely left the central box. The
> calculation, however, is fine it is just a choice on how to represent the
> coordinates.
> You can fix most of this in ptraj after the simulation. I would suggest
> loading all of the trajectories and doing an RMS fit to your molecule of
> interest and then set the center to be the residues corresponding to your
> molecule of interest and then do an image origin center familiar. This
> should result in what you 'expect' to see in terms of your molecule
> remaining at the origin in the center of the box.
>> Another surprising phenomena is that the ligand in one protein of the
>> dimmer run away from the binding pocket while the other one kept in the
>> original position of the other protein in the dimmer.
> Some dimer proteins truly only bind one ligand at a time so what you see may
> be real. It also of course could be that the initial structure was high in
> energy and this kicked one of the ligands out of the binding pocket and due
> to entropy it doesn't come back. Alternatively it could be a simple imaging
> problem like above that processing through ptraj will 'fix'.
>> NPT production
>> &cntrl
>> imin=0,
>> ntx=5, irest=1,
>> ntpr=100, ntwx=1000,ntwr=5000,
>> dt=0.002,nstlim=1000000, nscm=5000,
>> cut=9.,dielc=1.0,
>> ntc=2, ntf=2,
>> ntb=2,
>> ntp=1,pres0=1.0,taup=3.0,
>> ntt=1, tautp=3.0,temp0=300.0,
>> ioutfm=1
>> /
> set iwrap=1 this will fix a lot. You don't need to re-run though you can do
> this post simulation using ptraj.
>> Jeffrey
> Since your email address does not indicate your full name and institution
> could you please sign you emails with first and lastname as well as your
> affiliation.
> All the best
> Ross
> /\
> \/
> |\oss Walker
> | Assistant Research Professor |
> | San Diego Supercomputer Center |
> | Tel: +1 858 822 0854 | EMail:- |
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Received on Fri Mar 20 2009 - 01:09:32 PDT
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