Thank you, Dr.Case, I just need to add -ref file.cre to my run files too, I
used my coordinate file and, got this error "*cudaMemcpy
GpuBuffer::Download failed an illegal memory access was encountered *
*> *". any idea? (I used the same reference file for previous (min, heat,
and equilibrium ) steps )
Best
Parviz
On Sun, Aug 27, 2017 at 4:45 PM, David A Case <david.case.rutgers.edu>
wrote:
> On Sun, Aug 27, 2017, Parviz Seifpanahi Shabane wrote:
>
> > I need to put a restraint on just part of my proteins during the
> production
> > step. My system is the slice of Nucleosome ( the mixture of DNA and
> histone
> > protein), first I created the PDB file from my topology and coordinate
> > files by "ambpdb", from this PDB files I found the residue number which I
> > wanted to be free (residue 111 to 134). I tried different methods for
> > applying restraint (below), but none of them worked. I checked "mdout"
> file
> > the restrained energy in all of the cases is zero.
>
> Did you set ntr=1 in the cntrl namelist?
>
> The restrainmask syntax is much simpler, e.g.
>
> ntr=1, restraint_wt=10.0, restraintmask=":1-110,135-201",
>
> will restrain all residues in the range 1-201 except for 111-134. You
> don't
> need any group cards here.
>
> ...hope this helps....dac
>
>
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--
Parviz Seifpanahi
Ph.D. Candidate
Department of Physics
Virgina Tech, Blacksburg, Va 24061
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Received on Sun Aug 27 2017 - 16:00:03 PDT
