Thank you very much, that was very helpful!!!
On Tue, Nov 15, 2016 at 3:45 AM, Dr. Anselm Horn <anselm.horn.fau.de> wrote:
> 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.
>
>
> Regards,
>
> 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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> >
> >
>
>
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Received on Fri Nov 18 2016 - 10:30:04 PST
