Dear all,
I'm using cpptraj to cluster ligands obtained from multiple docking runs.
I have 10 .pdbqt files (generated from 10 individual docking runs) and each
one contains 20 models.
For each .pdbqt file, after converting it to .pdb, I extracted the 20
models and then I concatenated all the models in a single file containing
200 (10*20) models.
The format of my .pdb is the following:
MODEL 1
HETATM ...
ENDMDL
CONECT ...
...
MODEL 200
HETATM ...
ENDMDL
CONECT ...
END
My cpptraj.in is :
parm 200models.pdb [top]
trajin 200models.pdb parm [top]
cluster :${LIG}&!.H= hieragglo epsilon 3 complete dme[:${LIG}&!.H=] nofit
out cluster-num-vs-time.dat summary cluster-summary.out info
cluster-info.out repout cl repfmt pdb clusterout cl-traj clusterfmt pdb
The problem is that only few of my output files ( .pdb of representative
clusters members) exhibits wrong connectivity when visualized.
This doesn't happen when I use only 20 models (i.e. output from a single
docking run) as input.
Could someone help me to figure out where the problem is?
The 'trajin' command needs a particular .pdb format ?
Thanks in advance.
Samuele
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Received on Mon Jul 19 2021 - 02:30:03 PDT
