Hi Dan,
this is better, I got this:
# Contacts: contact.dataset
# Native contacts determined from mask ':133.H1' and mask '.H*'
# Contact Nframes Frac. Avg Stdev
1 :133.H1_:133.H1 100000 1 0 0
2 :133.H1_:133.H2 100000 1 2.44 0.106
3 :133.H1_:132.HC2 100000 1 2.53 0.304
4 :133.H1_:133.H5 100000 1 2.61 0.184
5 :133.H1_:132.HC1 100000 1 2.85 0.366
6 :133.H1_:133.H3O 100000 1 3.44 0.288
7 :133.H1_:133.H2O 100000 1 3.73 0.215
8 :133.H1_:133.H3 100000 1 3.81 0.103
9 :133.H1_:133.H4 100000 1 4 0.106
10 :133.H1_:132.HC 99963 1 4.27 0.404
11 :133.H1_:133.H61 90763 0.908 4.7 0.174
12 :133.H1_:133.H62 86145 0.861 4.58 0.293
13 :133.H1_:133.H6O 53544 0.535 4.38 0.351
14 :133.H1_:133.H4O 51977 0.52 4.6 0.266
15 :133.H1_:132.HM2 47485 0.475 4.4 0.553
16 :133.H1_:132.HM1 47246 0.472 4.4 0.555
17 :133.H1_:132.HM3 46960 0.47 4.4 0.55
......So, with nativecontacts the pairs are determined on the reference and then those pairs are evaluated for each frame, isn't it? How could the pairs be evaluated for each frame?
I tried the mask too:
parm ../m1-mpp+.prmtop
trajin ../m1-mpp+_rms.netcdf
mask "(:133.H1<:5.0)&@H" maskout Man133H1.dat
The output is strange:#Frame AtomNum Atom ResNum Res MolNum
104 1453 H 93 TYR 1
169 1425 H 91 ASN 1
240 1608 H 103 LYS 1
248 1608 H 103 LYS 1
248 1729 H 111 ASN 1
343 1729 H 111 ASN 1
344 1729 H 111 ASN 1
358 1453 H 93 TYR 1
393 1453 H 93 TYR 1
397 1453 H 93 TYR 1
....... 99967 2013 H 131 ALA 4
99969 2013 H 131 ALA 4
99972 2013 H 131 ALA 4
99996 2013 H 131 ALA 4
Do you have any better idea how to modify this?
Thanks a lot,Kris
From: Daniel Roe <daniel.r.roe.gmail.com>
To: AMBER Mailing List <amber.ambermd.org>
Sent: Wednesday, September 7, 2016 9:26 PM
Subject: Re: [AMBER] distance based mask
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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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
--
-------------------------
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 - 13:00:02 PDT
