thanks felix you are right.both exist.but how can i tell gromacs to put MG ions in the standard vicinity of ATP? or maybe gromacs knows it already and i have to just type "MG-ATP" instead of "ADP"?
________________________________ From: "Rausch, Felix" <[email protected]> To: Discussion list for GROMACS users <[email protected]> Sent: Wed, April 27, 2011 1:33:52 PM Subject: [gmx-users] MG-ATP Hi. Looking at the list of building blocks available in GROMACS (http://www.gromacs.org/Documentation/File_Formats/Gromacs_Building_Blocks?highlight=building+blocks) you can find ATP as well as MG. So having a ATP-MG-complex in your simulation shouldn't be a problem. Regards, Felix ________________________________ Von: [email protected] im Auftrag von Sajad Ahrari Gesendet: Mi 27.04.2011 10:52 An: gromacs user forum Betreff: [gmx-users] MG-ATP dear users is "MG-ATP" known to gromacs ? in my pdb structure I have ADP and MG, apart from each other and not being crystallized in the right place. can i omit them and replace ADP's with MG-ATP? or I should introduce this topology to gromacs? regards sajad
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