Hello Momin
The best tool I have found for dealing with cif files, including exporting
to pdb, is Mercury. You can download it for free from:
https://www.ccdc.cam.ac.uk/Community/csd-community/freemercury/
Hope this helps
Victor
El mar., 13 nov. 2018 a las 8:04, Momin Ahmad ()
escribió:
> Hi,
You should know how many atoms in each residue then how many residues of
XXX you have then you can see.
Suggestion, if possible use sperate pdb files then use solvation option to
produce your system .gro or pdb. This will help you in editing each pdb
then get your correct gromacs input files.
Best
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
build
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 a
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 anyth
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 wrote:
> Hi,
>
> is there a tool where i can use for example a .cif file (or .xyz) file
> to generate a .p
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