[gmx-users] how to set hetrodimer for MD Simulation

Erik Marklund erik.marklund at kemi.uu.se
Thu Nov 23 12:52:48 CET 2017

Dear Rana,

a) We are not (necessarily) Amber users. This is a gromacs mailing list.

b) If the separate structures are correctly positioned relative to each other, you basically just need to cut-and-paste the ATOM records from one pdb file into the other one.

Kind regards,
Erik Marklund, PhD, Marie Skłodowska Curie INCA Fellow
Department of Chemistry – BMC, Uppsala University
+46 (0)18 471 4539
erik.marklund at kemi.uu.se<mailto:erik.marklund at kemi.uu.se>

On 22 Nov 2017, at 22:15, Rana Rehan Khalid <rrkhalid at umich.edu<mailto:rrkhalid at umich.edu>> wrote:

Dear Amber users

My protein system consist of two subunit chains alpha and beta each chain
consist four domains. I predicted the structure of both subunit chains now
i want to combine both structure  subunits models, How i can combine them
in one pdb file.  so that i can run the simulation on complete structure.
Kindly guide me.

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