Re: [AMBER] Restrained MD

From: David A Case <>
Date: Tue, 31 Mar 2015 08:32:04 -0400

On Tue, Mar 31, 2015, James Starlight wrote:
> is it possible to provide some amber mask for defining of the
> restrained atoms for iat term within DISANG file
> or alternative I should to dump some pdb from the trajectory using vmd
> and check it within it

Best to use LEaP or ambpdb to create the PDB file that has the Amber atom
numbering. What you get from VMD depends on what files you loaded, etc.

> 2) Regarding setup:
> is it correctly just to provide within my file something like this
> &cntrl
> imin=0, ! Molecular dynamics
> # here all inputs for common simulation are provided
> nmropt=1,
> &end
> &wt
> type='DISAVI' istep1=1, istep2=10, value1=0, value2=0.0,
> &end
> &wt type='END',
> &end
> DISANG=disang.rst
> and with the something like this to the disang.rst :
> &rst nstep1=1, nstep2=25000000, iat=35,40,190,185,
> iresid=0, ifvari=0,
> r1=70.0, r2=85.0, r3=115.0, r4=125.0, rk2=30.0, rk3=30.0,
> &end
> so the &wt should be exactly in the first (md input file)? I specify
> it because I'm using amber-12 for the simulation (not amber-14!) and
> what I've found in manual
> : Note that, unlike earlier versions of Amber, the &rst namelists must
> be in the DISANG file, and not in the mdin file.)

You must make a separate file, and refer to it by the DISANG keyword, as
mentioned above.


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Received on Tue Mar 31 2015 - 06:00:03 PDT
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