Good afternoon,

I contact you as I would really appreciate your help. I have a MD trajectory which I have processed into Clusters with the Analysis ... Cluster tool. I have saved the resulting file with the members and the representative frame, but now I would like to save those representative frames in separate PDB files. This process is extremely tedious if manually done, so I have tried to perform a script:

with open("/HDD/lroldan/Master/Metals_bA/Template/2LFM/MD/GaMD/clusters_frame.txt", "r") as f:
    lines=f.readlines()
    cluster_number = 1
    for i in range(len(lines)):
        frame = i
        if mdInfo["frame number"] == frame:
            name = "/HDD/lroldan/Master/Metals_bA/Template/2LFM/MD/GaMD/Clusters/_" + str(cluster_number)
            runCommand('write format pdb 0 $name)

which would be run in the "Per-frame Commands", in order to 1) encounter the frames of the cluster and 2) save each frame in a PDB file, correctly numbered.

However, this script is not working, and I would greatly thank any help you could provide me with.

Lorena.

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Lorena Roldán Martín PhD Student in Bioinformatics Departament de Química Unitat de Química Física Campus de la UAB · 08193 Bellaterra (Cerdanyola del Vallès) · Barcelona · Spain +34 690799431 www.uab.cat