Do to some strange filters put in place by my universities IT I am trying to send the code across once more, this time I put spaces in the areas where the filter mangled the code
Sorry for any confusion.
code for closest waters
pytraj code:
import pytraj as pt
x = pt. iterload (' traj .crd .nc','prmptop. parm7'
pt.closest(x,mask="1-294",n_solvents=300,frame_indices=1)
cpptraj code:
parm prmtop.parm7
trajin traj. crd. nc 1 1 # grab only one frame
closestwaters 300 ":1-294" closestout closewater.dat name closestwater outprefix closestwater
________________________________
From: Korey M Reid <koreyr.unr.edu>
Sent: Tuesday, November 13, 2018 2:17:06 PM
To: amber.ambermd.org
Subject: [AMBER] RMSD mask selection and closestwater clarification
Hello All,
I am trying to calculate the rmsd of individual water molecules nearest the protein surface to extract residue numbers for each water with an RMSD below a threshold, say 2.5Angs. My system has 294 protein residues and many more waters. From what I have attempted, using "rmsd .... perres ..." in cpptraj or pytraj.rmsd_perres, excludes waters. The selection I made was "(:1-294<:5.0)&:WAT.O". From this I was returned the RMSD of the protein residues, which makes sense considering the name of the function, but not quite what i want. What I am hoping to do is get the RMSD for each WAT.O in the selection mask, returning a matrix and a perres average RMSD for use in figures and apply a threshold for later calculations, respectively. I have also attempted to use closestwaters using the mask ":1-294", which returns many waters but when I look at the returned array in pytraj or the file written out by cpptraj the molecule numbers leave me slightly confused. The molecule number is output but in most if not all cases I
need to have residue # or so I think. Is there a way to select molecules by there molecule number so the file output/array output can be used directly? Or have I misunderstood how the functions work? Also, to test the closest water within cpptraj I produced an output parm7 file and instead of only selecting waters for output I see protein residues, salts and waters, much more than I want/need. Any help to get me on a better path would be greatly appreciated!
Thank you,
Korey R.
code for closest waters
pytraj code:
import pytraj as pt
x = pt.iterload('traj.crd.nc<
https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Ftraj.crd.nc&data=01%7C01%7Ckoreyr%40unr.edu%7C014e039ae2ec4d9c19c808d649b5da15%7C523b4bfc0ebd4c03b2b96f6a17fd31d8%7C1&sdata=5a6QAF4juSq1aUMqmISPWVG2eKzbOUJQzzwVul1iEaA%3D&reserved=0>','prmptop.parm7'
pt.closest(x,mask="1-294",n_solvents=300,frame_indices=1)
cpptraj code:
parm prmtop.parm7
trajin traj.crd.nc<
https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Ftraj.crd.nc&data=01%7C01%7Ckoreyr%40unr.edu%7C014e039ae2ec4d9c19c808d649b5da15%7C523b4bfc0ebd4c03b2b96f6a17fd31d8%7C1&sdata=5a6QAF4juSq1aUMqmISPWVG2eKzbOUJQzzwVul1iEaA%3D&reserved=0> 1 1 # grab only one frame
closestwaters 300 ":1-294" closestout closewater.dat name closestwater outprefix closestwater
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Received on Tue Nov 13 2018 - 15:00:02 PST
