i have Fe2S2 cluster linked to two histidines and two cysteines. i tried editing the topology file and i changed the name of HIS, CYS and the cluster to FES. i edited the topology file. but after running psfgen, the hydrogens are not being added properly, hey are being added with the coordinate 0.00 and it is distorting the other HIS and CYS. i dont know what am i doing wrong.
It is not very clear from your question, what are you trying to do exactly. Are you using any packages? What is your aim? Every package has its own grammar. That name changing part is not understood. Do you know if that changed name is identified the corresponding package??
If possible please share some more details, I am sure someone can help you out.
Thanks
hi Sayantan,
i solved that error. i was trying to say i made the four amino acids and the cluster as one molecule. the psfgen was not able to understand the naming terminology of atomnames. some format related error. thanks anyway!
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