Hi,
Restraints do not account for imaging, so make sure your input
coordinates and reference coordinates are properly imaged in both
(i.e. the DNA strands have not been "split" by an imaging artifact).
-Dan
On Sun, Aug 27, 2017 at 6:57 PM, Parviz Seifpanahi Shabane
<sparviz.vt.edu> wrote:
> 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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--
-------------------------
Daniel R. Roe
Laboratory of Computational Biology
National Institutes of Health, NHLBI
5635 Fishers Ln, Rm T900
Rockville MD, 20852
https://www.lobos.nih.gov/lcb
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Received on Mon Aug 28 2017 - 06:00:10 PDT
