Re: [AMBER] Restraints not working, What Am I doing Wrong?

From: Dr. Anselm Horn <>
Date: Tue, 15 Nov 2016 09:45:07 +0100

Dear The Cromicus Productions,

the flag ntr=1 is necessary to tell sander that there are restraints,
which should be taken into account. Without the flag, the simulation
goes unrestrained, as you observed,

However, the error message
'Error opening unit 10: File "refc" is missing or unreadable'
tells you the problem. Amber needs a set of coordinates to use as
reference for the restraints, if you specify ntr=1. Most often, you use
the input coordinates for that, but you have to specify the respective
file explicitely upon sander invocation. If you do not give any file
name on the command line via the "-ref <name>" input, sander tries to
read the coordinates from the default file "refc" - and in your case it
does not exist, thus the error message arises.

Have a look into the manual for the command line argument flags of
sander (section 18.2 on page 306 in current Amber16.pdf):

sander [-help] [-O] [-A] -i mdin -o mdout -p prmtop -c inpcrd -r restrt
-ref refc -mtmd mtmd -x mdcrd -y inptraj -v mdvel -frc mdfrc -e mden
-inf mdinfo -radii radii -cpin cpin -cpout cpout -cprestrt cprestrt
-evbin evbin -suffix suffix

An additional note: The weight of your restraints is very large, which
may cause problems during the simulation. Maybe you want to test a
smaller value first (<= 10).

If you are absolutely new to Amber, I recommend working through some of
the basic tutorials from the Amber web site. They are clearly written,
very instructive and cover exactly these types of problems you run into
on first contact with Amber.


Anselm Horn

Am 15.11.2016 08:28, schrieb The Cromicus Productions:
> Hi everyone,
> I'm absolutely new to Amber and I'm starting to learn how to handle DNA. I
> have the following question. This is the code of my simulation:
> 10-mer DNA MD Generalise Born, 12A cut off
> &cntrl
> imin = 0, ntb = 0,
> igb = 1, ntpr = 100, ntwx = 100,
> ntt = 3, gamma_ln = 1.0,
> tempi = 300.0, temp0 = 300.0,
> nstlim = 100000, dt = 0.001,
> cut = 12, restraint_wt=500.0,
> restraintmask=':1,10,11,20',
> /
> I'm trying to restrain the bases number 1, 10, 11 and 20, but I see in vmd
> that they are still moving. What am I doing wrong? I tried to add the
> line ntr=1 but that gives me an error "Error opening unit 10: File "refc"
> is missing or unreadabl".
> Since now thanks a lot!
> _______________________________________________
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Received on Tue Nov 15 2016 - 01:00:02 PST
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