VMD-L Mailing List

From: George Lai (zaizhilai_at_gmail.com)
Date: Tue Nov 13 2012 - 12:54:23 CST

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>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 [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
>
> Email Disclaimer: www.stjude.org/emaildisclaimer
> Consultation Disclaimer: www.stjude.org/consultationdisclaimer
>
>