Hi Sinjini,
Is the system already simulated somehow, and that's why you want to replace a single chain? Otherwise, repacking everything would be probably easier.
This method could be a bit hacky, but here it goes (and seems more complicated than it is). It could also help someone else to get creative with such cases:
If you want to do this, it is probably easier done with packmol itself. Pdbremix gives you information regarding the volume of the protein in the different sections of your system. You can get this information by making a dummy run of packmol-memgen with the chain you want to remove.
Make a folder and place a pdb with the chain extracted from your packed system. Run it with something like --solvate --notrun, and see the volume in the packmol-memgen.log logfile. From there you can get how many water molecules you'd have to add (you can roughly estimate 0.033 waters per cubic angstrom), and a packmol.inp template file. Edit the template packmol.inp, change the number of waters for what you calculated, the coordinates in "inside box" to cover the simulation system where you want to replace the protein chain, and replace PROT0.pdb with your system without the chain you want to replace. You might want to check if you need to add ions for the removed charges of the protein chain you erased. Run packmol with "packmol < packmol.inp", it should be rather fast (make sure to run charmmlipid2amber -i packedpdb -o packedpdb, I think I still use a non-amber TIP3P pdb, and that should replace it). Check the packed structure, but all (or most) water molecules should have been added to the pocket that was left. Then you can load the generated system in leap to reparametrize it (without solvating of course). Just consider setting the PBC with "set XXX box {X Y Z}" according to the size of the original system, where XXX is the name of the loaded pdb object.
Hope it helps somehow,
Stephan Schott Verdugo
Biochemist
Computational Biophysical Chemistry
Institut für Bio- und Geowissenschaften / Bioinformatik (IBG-4)
Forschungszentrum Jülich GmbH
Wilhelm-Johnen-Straße, 52425 Jülich
Germany
---------------------------------------------------------------------------------------------
---------------------------------------------------------------------------------------------
Forschungszentrum Jülich GmbH
52425 Jülich
Sitz der Gesellschaft: Jülich
Eingetragen im Handelsregister des Amtsgerichts Düren Nr. HR B 3498
Vorsitzender des Aufsichtsrats: MinDir Stefan Müller
Geschäftsführung: Prof. Dr. Astrid Lambrecht (Vorsitzende),
Karsten Beneke (stellv. Vorsitzender), Dr. Ir. Pieter Jansens
---------------------------------------------------------------------------------------------
---------------------------------------------------------------------------------------------
El vie, 8 mar 2024 a la(s) 3:09 p.m., Bhattacharjee, Sinjini via AMBER (amber.ambermd.org<mailto:amber.ambermd.org>) escribió:
Dear Amber users,
I want to replace a single protein chain with extra TIP3P waters, in a protein-lipid-bilayer box (generated using packmol-memgen).
Can this be done using tleap without affecting the the original lipids?
Any help or suggestions will be appreciated.
Best ,
—
Sinjini Bhattacharjee
PhD Student
Molecular Theory and Spectroscopy
Max-Planck-Institut für Kohlenforschung
45470 Mülheim an der Ruhr, Germany
email: bhattacharjee.kofo.mpg.de<mailto:bhattacharjee.kofo.mpg.de><mailto:bhattacharjee.kofo.mpg.de<mailto:bhattacharjee.kofo.mpg.de>>
---
_______________________________________________
AMBER mailing list
AMBER.ambermd.org<mailto:AMBER.ambermd.org>
http://lists.ambermd.org/mailman/listinfo/amber
------------------------------------------------------------------------------------------------
------------------------------------------------------------------------------------------------
Forschungszentrum Jülich GmbH
52425 Jülich
Sitz der Gesellschaft: Jülich
Eingetragen im Handelsregister des Amtsgerichts Düren Nr. HR B 3498
Vorsitzender des Aufsichtsrats: MinDir Stefan Müller
Geschäftsführung: Prof. Dr. Astrid Lambrecht (Vorsitzende),
Karsten Beneke (stellv. Vorsitzender), Dr. Ir. Pieter Jansens
------------------------------------------------------------------------------------------------
------------------------------------------------------------------------------------------------
------------------------------------------------------------------------------------------------
------------------------------------------------------------------------------------------------
Forschungszentrum Jülich GmbH
52425 Jülich
Sitz der Gesellschaft: Jülich
Eingetragen im Handelsregister des Amtsgerichts Düren Nr. HR B 3498
Vorsitzender des Aufsichtsrats: MinDir Stefan Müller
Geschäftsführung: Prof. Dr. Astrid Lambrecht (Vorsitzende),
Karsten Beneke (stellv. Vorsitzender), Dr. Ir. Pieter Jansens
------------------------------------------------------------------------------------------------
------------------------------------------------------------------------------------------------
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Mar 08 2024 - 08:00:02 PST
