Hi every one.
I have a protein with a palmitoyl bound to it with a esteric bond(palmitoyl OH group bound to OH group of a amino acid serin). does any one have a similar experience? any help will appreciated.
Dear Najme
Use Antechamber which is a free module of AmberTool to generate palmitoyl Amber ff topology. Install AmberTool first. Then generate topology there.
Otherwise you can use ACPYPE, which is a python program available in below link
https://code.google.com/archive/p/acpype/
But this program also need preinstall AmberTool in your system.
Hope this will help.
dear Krishnendu Bera
thank you for your reply. I want use gromacs program for my run. if I make palmitoyl using Antechamber, can I do this?
You will get amber ff topology for palmitoyl using Antechamber. After that you have to modify it according to GROMACS format (you can follow already present ff files in your GROMACS and do the changes).
Dear Najme
Yes!! you can do it. There is a script in gromacs site, which can change amber format to gromacs format. Use that script.
Happy simulation!!
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