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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Received on Wed Sep 07 2016 - 12:30:02 PDT
