Re: [AMBER] Combined cartesian and NMR restraints

From: Parker de Waal <>
Date: Fri, 26 Sep 2014 03:26:14 +0000

Hi David,

Thank you for the input. I've adjusted the input per your suggestion as follows:

NVT prod
  irest=1, ntx =5,
  nstlim=5000000, dt=0.002,
  ntpr=500, ntwr=500, ntwx=500,
  ntt=3, gamma_ln=5, ntb=1, ntp=0,
  ntc=2, ntf=2, ig=-1,
  ioutfm = 1,
  iwrap=1, nmropt=1,
  ntr=1, restraint_wt=20., restraintmask=':1-708',
 &wt type='END' /

The only problem now is that when I run pmemd.CUDA the follow error occurs:
Error: an illegal memory access was encountered launching kernel kClearForces
cudaFree GpuBuffer::Deallocate failed an illegal memory access was encountered

I'm currently using the most recent version of AMBER14 (updated and recompiled today) with NVIDIA Driver Version: 340.32 and Cuda compilation tools, release 6.5, V6.5.12 (I'm running arch so rolling back is difficult, but I'm trying now to 5.5)


From: David A Case []
Sent: Thursday, September 25, 2014 10:56 PM
To: AMBER Mailing List
Subject: Re: [AMBER] Combined cartesian and NMR restraints

On Fri, Sep 26, 2014, Parker de Waal wrote:
> After reading through some of the old mailing list threads regarding
> the various workarounds for ntr =1 and nmropt=1, I still need some
> clarification.
> I have an NVT as show below:
> Now I wish to add cartesian restraints, following the snippet here:
> into my rst.dist file as
> seen below:

The group cards for cartesian restraints go into the mdin file, not into the
restraints file.

> # N373 D69 VS
> &rst
> ixpk= 0, nxpk= 0, iat= 5235, 6651, r1= 0.00, r2= 0.00, r3= 6, r4= 7,
> rk2=0.0, rk3=25.0, ir6=1, ialtd=0,
> &end
> ... (lines removed)
> # A150 F244 VS
> &rst
> ixpk= 0, nxpk= 0, iat= 2310, 9472, r1= 0.00, r2= 0.00, r3= 6, r4= 7,
> &end
> Hold GPCR fixed
> 20.0
> RES 1 708
> However whenever I run this the follow error occurs:
> default_name
> DISANG=rst.dist

Note that the program thinks the DISANG card is the title for the cartesian
restraints; so somehow it is not reading the NMR-like restraints correctly.
The first thing you need to do is set ntr=0, and make sure that you are
getting the NMR restraints correctly processed. Follow the example in the
$AMBERHOME/test/nmr directory.

By far the simplest thing to do for cartsian restraints is to set them
in the cntrl namelist:

   ntr=1, restraint_wt=20., restraintmask=':1-708',

Then there is no need for any GROUP input.

Beyond this:

You could try using the correct "/" rather than the obsolete (and never
standard "&end" to end namelists. But that is probably not the source of the
problem. You may need to let us know which program you are running
(sander or pmemd?) and which version. Posting the entire mdout file is
probably also required...there is something subtle that is preventing your
file from being parsed correctly.


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Received on Thu Sep 25 2014 - 20:30:02 PDT
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