AMBER Archive (2008)

Subject: Re: AMBER: mm_pbsa problem: bad atom type: IP

From: David A. Case (case_at_scripps.edu)
Date: Thu May 08 2008 - 12:27:22 CDT


On Thu, May 08, 2008, mori_at_cerm.unifi.it wrote:

[converted from html; please post in plain text!]

"I'm trying to apply MM_PBSA to calculate the binding energy of my system
composed by two protein. I'm following the advanced tutorial n3 but when
I run mm_pbsa.pl for binding energy calculation I get this error: bad atom
type: IP Looking at the amberarchive, it seems that this problem is related to
the Na+ ions added to equilibrate the charge in .prmtop file. How can I solve
this problem without modifying mdread.f file with LCPO parameters? Or, anyway,
Where I have to modify this file?"

Basically, with MM-PBSA you are supposed to strip water and ions before
carrying out the calculation, so you should not have any sodium ions to worry
about.

Aside from the problem of making modifications to mdread, there aren't any
values to put in for LCPO parameters for ions. So, if you really want to
compute surface areas of systems that have ions, you would need to use some
other program. But I doubt that this is really what you want to do.

...dac

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