AMBER Archive (2008)

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

From: mori_at_cerm.unifi.it
Date: Thu May 08 2008 - 06:59:12 CDT


Dear amber user,
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?

Thanks

mat

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**-**-**-**-**-**-**-**-**-**-**-**-**
 
Mattia Mori, PhD Student
CERM - Centro di Risonanze Magnetiche
via L. Sacconi 6,,
50019 Sesto Fiorentino, FI
fax (+39) 055 4573914
tel (+39) 055 4573912
www.cerm.unifi.it
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