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From: Georcki Ropon (groponp_at_gmail.com)
Date: Wed Nov 17 2021 - 20:22:44 CST

I am using topogromacs to make MDs in gromacs,

but I have two proteins A and B, so the serials of each of them start with 1, and since topogromacs does not generate position restraint file, I want to do this, using the atom serials of my PDB, but the serials of the PDB and TOP are different , so I want to renumber them.

Geo.

> On Nov 17, 2021, at 21:19, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:
>
> renumber what where and for what purpose?
>
> On Wed, Nov 17, 2021 at 9:17 PM Georcki Ropon <groponp_at_gmail.com <mailto:groponp_at_gmail.com>> wrote:
> There is pathway to renumber it, with tcl?
>
>
> Best,
>
> Geo.
>
>> On Nov 17, 2021, at 21:14, Axel Kohlmeyer <akohlmey_at_gmail.com <mailto:akohlmey_at_gmail.com>> wrote:
>>
>> You cannot change the "serial" property. It is "index + 1" and both are read-only.
>>
>> On Wed, Nov 17, 2021 at 8:37 PM Georcki Ropon <groponp_at_gmail.com <mailto:groponp_at_gmail.com>> wrote:
>> Dear user,
>>
>> I want change serial atom number , my number start with 3000 but I want all number (para chain B) start 1 2 3 4 ….
>>
>> Bellow my code but not fix it.
>>
>> mol new prot_orient_add_ter.pdb
>>
>> set prob [atomselect top "segid PROB"]
>>
>> set serials [$prob get serial]
>>
>> set count 0
>> foreach atom $serials {
>> $prob set serial $count
>> incr $count
>>
>> }
>>
>> set all [atomselect top all]
>> $all writepdb renum.pdb
>> quit
>>
>>
>> --
>> Dr. Axel Kohlmeyer akohlmey_at_gmail.com <mailto:akohlmey_at_gmail.com> https://urldefense.com/v3/__http://goo.gl/1wk0__;!!DZ3fjg!vx-NH4s7itxJtNB01qUnJIG1P1Io7r4FvGFaJjfTQB50zHTK8JdnzhOgQM6N78r3tQ$ <https://urldefense.com/v3/__http://goo.gl/1wk0__;!!DZ3fjg!vx-NH4s7itxJtNB01qUnJIG1P1Io7r4FvGFaJjfTQB50zHTK8JdnzhOgQM6N78r3tQ$ >
>> College of Science & Technology, Temple University, Philadelphia PA, USA
>> International Centre for Theoretical Physics, Trieste. Italy.
>
>
>
> --
> Dr. Axel Kohlmeyer akohlmey_at_gmail.com <mailto:akohlmey_at_gmail.com> https://urldefense.com/v3/__http://goo.gl/1wk0__;!!DZ3fjg!vx-NH4s7itxJtNB01qUnJIG1P1Io7r4FvGFaJjfTQB50zHTK8JdnzhOgQM6N78r3tQ$ <https://urldefense.com/v3/__http://goo.gl/1wk0__;!!DZ3fjg!vx-NH4s7itxJtNB01qUnJIG1P1Io7r4FvGFaJjfTQB50zHTK8JdnzhOgQM6N78r3tQ$ >
> College of Science & Technology, Temple University, Philadelphia PA, USA
> International Centre for Theoretical Physics, Trieste. Italy.