VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Wed Nov 17 2021 - 20:52:39 CST

this doesn't make much sense to me.
the position restraint section in the input for gromacs has an extremely
simple structure, so it could easily be generated with a simple script.
of course that can be done in Tcl, but also with Python, Bourne shell, or
other suitable script languages. You don't really need the original PDB
files for that.

On Wed, Nov 17, 2021 at 9:22 PM Georcki Ropon <groponp_at_gmail.com> wrote:

> 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> wrote:
>
>> There is pathway to renumber it, with tcl?
>>
>>
>> Best,
>>
>> Geo.
>>
>> On Nov 17, 2021, at 21:14, Axel Kohlmeyer <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> 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]
>>> $all writepdb renum.pdb
>>> quit
>>>
>>
>>
>> --
>> Dr. Axel Kohlmeyer akohlmey_at_gmail.com https://urldefense.com/v3/__http://goo.gl/1wk0__;!!DZ3fjg!qe3MLVVophuKzlPrOLlJCICDdM_qAS9JfkIuvVmVlqwlpKWY4lLlEz9mhvJagFs1MA$
>> College of Science & Technology, Temple University, Philadelphia PA, USA
>> International Centre for Theoretical Physics, Trieste. Italy.
>>
>>
>>
>
> --
> Dr. Axel Kohlmeyer akohlmey_at_gmail.com https://urldefense.com/v3/__http://goo.gl/1wk0__;!!DZ3fjg!qe3MLVVophuKzlPrOLlJCICDdM_qAS9JfkIuvVmVlqwlpKWY4lLlEz9mhvJagFs1MA$
> College of Science & Technology, Temple University, Philadelphia PA, USA
> International Centre for Theoretical Physics, Trieste. Italy.
>
>
> 

-- 
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com  https://urldefense.com/v3/__http://goo.gl/1wk0__;!!DZ3fjg!qe3MLVVophuKzlPrOLlJCICDdM_qAS9JfkIuvVmVlqwlpKWY4lLlEz9mhvJagFs1MA$ 
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.