Re: [AMBER] Density equilibration

From: Thomas Exner <>
Date: Sat, 6 Jan 2018 13:23:48 +0100

Dear all:
I think I solved my problem. I modified the topology file used during
the density equilibration so that both proteins are now considered as
one molecule.The the center of mass of the complex is moved during the
rescaling of the box dimensions and the relative orientation stays the

Thomas Exner wrote:
> Dear AMBER users:
> I have a strange problem. I want to set up a simulation of a complex
> between a big and a small molecule following standard procedures of
> first a minimization, heating period and then relaxation of the density.
> For the latter two steps, I use constraints on the backbone atoms.
> Everything looks good and I get stable simulations but when I look at
> the coordinates of the NPT simulation, I see that the two proteins are
> moved relative to each other. If I align the proteins separately, each
> show very small rmsds to the input but, due to the shift relative to
> each other, the rmsd of the complex is much larger. Can somebody please
> help me to avoid this effect? The input for the NPT simulation is below.
> I don't know if this is relevant but I use the old sander from AMBER12.
> Thank you very much.
> Thomas
> molecular dynamics run
> &cntrl
> imin=0, irest=1, ntx=5,
> ntc=2, ntf=2,
> cut=9.0,
> nstlim=250000, dt=0.002,
> ntwe=500, ntwx=500, ntpr=500,
> ntt=1, tempi=100.0, temp0=300.0,
> tautp=1.0,
> ntb=2, ntp=1, pres0=1.0,
> ntr=1, restraint_wt=5.0
> restraintmask=':1-926.Ca,C,O,N',
> /

Dr. Thomas E. Exner
Theoretische Pharmazeutische Chemie & Biophysik
Lehrstuhl Pharmazeutische Chemie
Pharmazeutisches Institut
Eberhard Karls Universität Tübingen
Auf der Morgenstelle 8 (Haus B)
72076 Tübingen
Tel.:    +49-(0)7071-2976969
Mobil:   +49-(0)171-3807485
Fax:     +49-(0)7071-295637
E-Mail:  Thomas.Exner[at] 
Fachbereich Chemie  und Zukunftskolleg
Universität Konstanz
78457 Konstanz
Tel.:   +49-(0)7531-882015
Fax:    +49-(0)7531-883587
E-Mail: Thomas.Exner[at]
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Received on Sat Jan 06 2018 - 04:00:03 PST
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