[gmx-users] how to add potassium ions correctly?
zhongqiao_hu at nus.edu.sg
Thu Nov 23 02:41:02 CET 2006
I want to add both sodium and potassium to a protein solution. But there
is always error information about potassium after I used genion to add
K(K+) and set right no of molecules at the bottom of .top file:
No such moleculetype K (or K+)
no matter I use K or K+ as potassium name and no matter I used g43a1 or
By the way, I used v3.3 and selected gromos 43a1 force fields. I have
searched the mailing list and found some confusing information. For
example, somebody said the 43a1 can recognize potassium, but someone
else said it can not and suggested to use OPLS-AA instead. So can
anybody who have experiences give an authoritative explanation and
solution for using potassium?
Further, is there any reference which provides a general description for
all force fieds in Gmx v3.3, which is expected to be more detailed than
something showing in brackets after the ff names when using the command
pdb2gmx, so that users can know their advantages and disadvantages and
select a suitable one according to different aims?
Thanks in advance
Department of Chemical and Biomolecular Engineering
National University of Singapore
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