Dear users, I am trying to predict the position of metal binding sites in a
protein. The protein is known to contain three calcium ions in its crystal
structure, and I want to predict the position of the third Ca binding site
keeping two calcium ions as part of solute in the PDB. When I run 3drism
calculation it gives following error:
addstrand: strand A already in mol
My understanding behind this error is that an ion can not be part of the
solute and solvent both during 3drism run. I tried to change the name of
two Ca ions in solute PDB and in the prmtop file but still it gives the
same error (perhaps because parameter values do not change just by changing
the name).
Could you please suggest a way to deal with this problem where I want to
study the cooperativity of Ca ions binding?
Thanks in advance for your help.
*Rakesh Srivastava*
Postdoctoral Fellow
Center for Computational Natural Sciences and Bioinformatics (CCNSB)
International Institute of Information Technology, Hyderabad
India
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Received on Thu Feb 03 2022 - 07:00:02 PST
