Hi,
First, because you only specified one mask, the 'nativecontacts'
command is looking for all contacts *within* that selection - to get
contacts between two distinct regions you need two masks (consult the
docs for more details).
Second, this won't really get you what you want since the 'mask'
command is the only action that distance-based masks will update for
frame-by-frame. I think you might be able to get what you want by just
using the distance cutoff in 'nativecontacts' and the mask for residue
133 atom H1 and all other hydrogens, e.g.
nativecontacts :133.H1 .H= distance 5.0 ...
I haven't tested this though.
Hope this helps,
-Dan
On Wed, Sep 7, 2016 at 3:09 PM, Kris Feher <kris.feher.yahoo.com> wrote:
> Dear All,
> I want to list of all hydrogen atoms within a given distance (5A) from a particlular atom (residue 133, atom name H1). I want to list them together with their corresponding distances at each time point of the trajectory. I was trying to use nativecontacts:
> parm ../m1-mpp+.prmtop
> reference ./m1-mpp+_aver.pdb
> trajin ../m1-mpp+_rms.netcdf
> nativecontacts "(:133.H1<:5.0)&.H" \
> writecontacts contacts.out \
> resout residues.out \
> distance 5.0 \
> out nativecontacts.out \
> reference \
> contactpdb contact.pdb \
> name contact.dataset
>
> I get this contacts.out below, which does not make sense to me, because I expect that one end of the contact should be residue 133 and atom H1, instead I get this:
>
> # Contacts: contact.dataset
> # Native contacts determined from mask '(:133.H1<:5.0)&.H'
> # Contact Nframes Frac. Avg Stdev
> 1 :47.H_:48.H 100000 1 2.7 0.222
> 2 :3.H_:4.H 99999 1 2.73 0.905
> 3 :2.H_:3.H 99993 1 4.51 0.385
> 4 :2.H_:4.H 12956 0.13 4.75 0.214
> 5 :3.H_:130.H 4645 0.0464 4.7 0.303
> 6 :2.H_:130.H 108 0.00108 4.75 0.168
>
> What do I do wrong?
> Thank you,Kris
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--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Wed Sep 07 2016 - 12:30:02 PDT
