RE: [AMBER] protein protrudes from unit cell

From: Ross Walker <>
Date: Wed, 18 Mar 2009 15:39:23 +0000

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

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

All the best

|\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 - 01:09:24 PDT
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