VMD-L Mailing List

From: Martin, Erik W (Erik.Martin_at_stjude.org)
Date: Mon Nov 12 2012 - 22:04:11 CST

You can definitely automate loading pdb files, making some kind of measurement, and writing the output to a file with a tcl script. I can probably help you out with some specifics, but would need more details. are your pdbs really named 1.pdb 2.pdb ect or do they have unique names? What information do you want about the H-bonds? Just how many are predicted in the structure or would you like the donors and acceptors as well? Do you want to query the entire structure, or are you looking for a particular h-bond?
________________________________________
From: owner-vmd-l_at_ks.uiuc.edu [owner-vmd-l_at_ks.uiuc.edu] On Behalf Of George Lai [zaizhilai_at_gmail.com]
Sent: Monday, November 12, 2012 7:48 PM
To: vmd-l_at_ks.uiuc.edu
Subject: vmd-l: calculate HBOND. .

Hi,

I have a question about calculating the hydrogen bonds of pdbs. I have 200 pdbs, say 1.pbd, 2.pdb, 3.pdb, ......, 200.pdb. How can I use VMD to calculate the hydrogen bonds of each pdb quickly? and also save each output file, which includes the information of hbond, as 1.dat, 2.dat, 3.dat,......., 200.dat. Thanks

Good day,
zz

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