From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Wed Jun 11 2014 - 20:55:34 CDT
On Jun 12, 2014 3:39 AM, "Gurpreet Kaur Dhindsa" <el2275_at_wayne.edu> wrote:
> 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.
The confusion is on your side.
People have given you good advice, but you don't understand.
After the modification you want, the resulting file would no longer be a
valid pdb file and correct software cannot read (or write) it.
> ----- Original Message -----
> From: "Joaquim Rui de Castro Rodrigues" <joaquim.rodrigues_at_ipleiria.pt>
> To: "Ivan Gregoretti" <ivangreg_at_gmail.com>, "Gurpreet Kaur Dhindsa" <
> 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..
> Hi Gurpreet,
> 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,
> Rui Rodrigues
> De: owner-namd-l_at_ks.uiuc.edu [owner-namd-l_at_ks.uiuc.edu] Em Nome De Ivan
> 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..
> Hello Gurpreet,
> 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.
> Thank you,
> Ivan Gregoretti, PhD
> On Wed, Jun 11, 2014 at 10:39 AM, Gurpreet Kaur Dhindsa
> <el2275_at_wayne.edu> wrote:
> > 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
> > ATOM 2 CA ARM1N 1 -62.463 -17.910 1.081 0.00 0.00
> > ATOM 3 CA ARM1N 1 -62.463 -17.910 4.648 0.00 0.00
> > ATOM 4 CA ARM1N 1 -62.463 -14.343 -9.620 0.00 0.00
> > ATOM 5 CA ARM1N 1 -62.463 -16.127 -7.837 0.00 0.00
> > 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
> > Thanks,
> > Gurpreet.
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