[gmx-users] pdb generator

[Momin Ahmad]

Hi Ali,

thanks for you help. How can you distinguish between a C atom from 
residue XXX and another C atom from residue YYY when there are about 
2000 atoms in the file. Did you write a script for that? If there doesnt 
exist a tool with a GUI to solve this then i will have to write my own 
builder.

Cheers

Momin

Am 13.11.18 um 16:31 schrieb Ali Ahmed:
> well if you use Linux then you can use GVim to do highlight and do simple
> changes on one type only then use find and replace option. That what I do
> when I have more than one type. It needs one hour practice then you will be
> ok. Or you can write a script for such things.
> Best
>
> On Tue, Nov 13, 2018 at 9:15 AM Momin Ahmad <momin.ahmad at kit.edu> wrote:
>
>> Hi Ali,
>>
>> my problem is that there is not only one molecule but two different
>> molecules which build up a crystaline structure. For example i have 10
>> XXX and 100 YYY in the .pdb file.
>>
>> Cheers
>>
>> Momin
>>
>> Am 13.11.18 um 16:12 schrieb Ali Ahmed:
>>> Hi,
>>> I use Avogadro and it is easy to change LIG to anything you want. I just
>>> use find and replace option which takes less than a minute.
>>> Best
>>> Ali
>>>
>>> On Tue, Nov 13, 2018 at 8:04 AM Momin Ahmad <momin.ahmad at kit.edu> wrote:
>>>
>>>> Hi,
>>>>
>>>> is there a tool where i can use for example a .cif file (or .xyz) file
>>>> to generate a .pdb file with correct classification? For example
>>>> Avogadro classifies all atoms as LIG and i cannot change it. Is there
>>>> also another tool which can be used to generate large scale crystal
>>>> structures with building blocks as input?
>>>>
>>>>
>>>> Cheers
>>>>
>>>> Momin
>>>>
>>>> --
>>>> Momin Ahmad
>>>>
>>>> Karlsruhe Institute of Technology (KIT)
>>>> Steinbuch Centre for Computing (SCC)
>>>> Hermann-von-Helmholtz-Platz 1
>>>> 76344 Eggenstein-Leopoldshafen
>>>> Phone: +49 721 608-24286
>>>> E-Mail: Momin.Ahmad at kit.edu
>>>>
>>>> --
>>>> Gromacs Users mailing list
>>>>
>>>> * Please search the archive at
>>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>>>> posting!
>>>>
>>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>>
>>>> * For (un)subscribe requests visit
>>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>>>> send a mail to gmx-users-request at gromacs.org.
>>>>
>> --
>> Momin Ahmad
>>
>> Karlsruhe Institute of Technology (KIT)
>> Steinbuch Centre for Computing (SCC)
>> Hermann-von-Helmholtz-Platz 1
>> 76344 Eggenstein-Leopoldshafen
>> Phone: +49 721 608-24286
>> E-Mail: Momin.Ahmad at kit.edu
>>
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>> posting!
>>
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>> * For (un)subscribe requests visit
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> send a mail to gmx-users-request at gromacs.org.
>>
-- 
Momin Ahmad

Karlsruhe Institute of Technology (KIT)
Steinbuch Centre for Computing (SCC)
Hermann-von-Helmholtz-Platz 1
76344 Eggenstein-Leopoldshafen
Phone: +49 721 608-24286
E-Mail: Momin.Ahmad at kit.edu