Re: [AMBER] mmpbsa conflict with Ca2+ ?

From: Bill Ross <>
Date: Wed, 11 Mar 2015 08:40:00 -0700

The errors look like a stack trace. So I would look at each file+line and see if that gives a clue.


<div>-------- Original message --------</div><div>From: Jinfeng Huang <> </div><div>Date:03/11/2015 7:52 AM (GMT-08:00) </div><div>To: amber mailist <> </div><div>Subject: [AMBER] mmpbsa conflict with Ca2+ ? </div><div>
</div>Dear amber users,
     I need to calculate the bingding free energy with a structure containing Ca2+ ions. But when I using mmpbsa of amber14,there is some erros as follows.
calculating complex contribution...
  File "/share/apps/", line 96, in <module>
  File "/share/apps/", line 218, in run_mmpbsa, self.stdout)
  File "/share/apps/", line 79, in run, stdout=stdout, stderr=stderr)
  File "/share/apps/", line 148, in run
CalcError: /share/apps/ failed with prmtop!
    How should I deal with the problem?

Any help is greatly appreciated. Thank you!

Jingfeng Huang
AMBER mailing list
AMBER mailing list
Received on Wed Mar 11 2015 - 09:00:05 PDT
Custom Search