From: Martin, Erik W (Erik.Martin_at_stjude.org)
Date: Tue Nov 13 2012 - 14:21:26 CST

Alright, this helps. Since your structures are numbered sequentially, that makes things easier. You can load your structures into VMD with the command "mol new pdb_name.pdb". Since your structures are numbered sequentially, you can load and delete them with a simple tcl loop. Inside that loop you can include a command to measure hbonds and write the output to a file:

set hbondcutoff 3 ;# the cutoff distance between heavy atoms for a hbond
set hbondangle 30 ;# the cutoff angle (from 180) between donor, proton and acceptor

for {set i 1} {$i <= 200} {incr $i} {
set id [mol new $i_solvated.pdb]
set A [atomselect $id "protein"]
set lst [measure hbonds $hbondcutoff $hbondangle $A]
set file [open $i.dat w]
puts $file $lst
close $file
mol delete $id
}

…. Running this from the directory including your pdb's should do the job (although I didn't test it)

One caveat, the output file will contain three fields including a list of donors, acceptors and protons. The numbers will be the VMD indices. These don't have a ton of meaning unless you have the structure loaded in VMD. If you want, you can also include in the loop some commands to build lists of resid, or resid and name or whatever.

Hope this helps,
Erik

From: George Lai <zaizhilai_at_gmail.com<mailto:zaizhilai_at_gmail.com>>
Date: Tue, 13 Nov 2012 12:54:23 -0600
To: Erik Martin <erik.martin_at_stjude.org<mailto:erik.martin_at_stjude.org>>
Cc: "vmd-l_at_ks.uiuc.edu<mailto:vmd-l_at_ks.uiuc.edu>" <vmd-l_at_ks.uiuc.edu<mailto:vmd-l_at_ks.uiuc.edu>>
Subject: Re: vmd-l: calculate HBOND

hi, thanks for your kind help.
The names of the pdbs are 1_solvated.pdb, 2_solvated.pdb, ......, 200_solvated.pdb. (which include water)
I would like to know the number of the h-bond and also the donors and acceptors.
I don't look for a particular h-bond, I just want to know the information of the entire structure.

Thanks,
zzlai

On Mon, Nov 12, 2012 at 11:04 PM, Martin, Erik W <Erik.Martin_at_stjude.org<mailto:Erik.Martin_at_stjude.org>> wrote:
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<mailto:owner-vmd-l_at_ks.uiuc.edu> [owner-vmd-l_at_ks.uiuc.edu<mailto:owner-vmd-l_at_ks.uiuc.edu>] On Behalf Of George Lai [zaizhilai_at_gmail.com<mailto:zaizhilai_at_gmail.com>]
Sent: Monday, November 12, 2012 7:48 PM
To: vmd-l_at_ks.uiuc.edu<mailto: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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