Hello –


I would recommend using the input file parameters generated by PDB2PQR as a starting point.  In general, it is a good idea to have grid spacings at 0.5 A or smaller for visualization and at 0.25 A or smaller for energy calculations.





Nathan Baker

Laboratory Fellow

Pacific Northwest National Laboratory




From: sunyeping [mailto:sunyeping@aliyun.com]
Sent: Monday, November 25, 2013 7:07 PM
To: apbs-users@lists.sourceforge.net
Subject: [apbs-users] solvation energy


Dear all,


I want to calculate solvation energy of proteins. But I have no idea how to set the parameters dime and grid in the input file. There is an example for  solvation energy: the Born ion. The dime and grid parameter given by the example are 97,97,97 and 0.33,0.33,0.33. Could anyone explain that how these values were set and how to set there parameters in the case of proteins. Thanks in advance.



Yeping Sun

Institute of Microbiology, Chinese Academy of Sciences