From: Gurpreet Kaur Dhindsa (el2275_at_wayne.edu)
Date: Wed Jun 11 2014 - 20:34:29 CDT
I made this pdb by using one software. I didn't get it from protein data bank. I think there
is one confusion, I want to change the "1" in column which is coming after ARM1N and before "x" values.
----- Original Message -----
From: "Joaquim Rui de Castro Rodrigues" <joaquim.rodrigues_at_ipleiria.pt>
To: "Ivan Gregoretti" <ivangreg_at_gmail.com>, "Gurpreet Kaur Dhindsa" <el2275_at_wayne.edu>
Cc: "Namd Mailing List" <namd-l_at_ks.uiuc.edu>, owner-namd-l_at_ks.uiuc.edu
Sent: Wednesday, June 11, 2014 2:03:18 PM
Subject: RE: namd-l: change in pdb..
You could change it in VMD as follows:
set sel [atomselect top "all"]
$sel set resid [$sel get serial]
and write the coordinates with:
$sel writepdb ......
However, as Ivan pointed out, a residue number equal to 93000 is not compatible with the PDB format. You'll have to use another format...
Hope this helps,
De: owner-namd-l_at_ks.uiuc.edu [owner-namd-l_at_ks.uiuc.edu] Em Nome De Ivan Gregoretti [ivangreg_at_gmail.com]
Enviado: quarta-feira, 11 de Junho de 2014 16:29
Para: Gurpreet Kaur Dhindsa
Cc: Namd Mailing List; owner-namd-l_at_ks.uiuc.edu
Assunto: Re: namd-l: change in pdb..
That kind of string manipulation is calling for vim, awk, sed, R,
Python, Perl and many others. To do that with a single PDB file, I
would go for vim. For many files, I would use Python.
Now the important part: Have you checked the documentation of the PDB
format to make sure that residue names such as ARM93000 are accepted?
Here is the link:
In particular, if you go to
you will find that ARM93000 is too long a residue name.
Also, the way the PDB format is defined, each character is a column.
So, the 4th column is actually the letter "M" in the word "ATOM".
The change from 1,1,1... to 1,2,3,...,93000 can be done but the
resulting PDB would be unusable.
If somebody in the list knows better, please step in and correct me.
Ivan Gregoretti, PhD
On Wed, Jun 11, 2014 at 10:39 AM, Gurpreet Kaur Dhindsa
> Dear All,
> I have a pdb which looks like this
> ATOM 1 CA ARM1N 1 -62.463 -17.910 -2.486 0.00 0.00 NT1 C
> ATOM 2 CA ARM1N 1 -62.463 -17.910 1.081 0.00 0.00 NT1 C
> ATOM 3 CA ARM1N 1 -62.463 -17.910 4.648 0.00 0.00 NT1 C
> ATOM 4 CA ARM1N 1 -62.463 -14.343 -9.620 0.00 0.00 NT1 C
> ATOM 5 CA ARM1N 1 -62.463 -16.127 -7.837 0.00 0.00 NT1 C
> I want to change the number "1" in 4th column of my pdb to 1,2,3,4,.....93000. I have 93000 number of atoms.
> Can someone please tell me how I can change it in VMD if it is possible?
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