AMBER: mm_pbsa vertex atom mismatch

Date: Wed, 17 Jan 2007 01:10:35 +0200

Dear all,

I am trying to calculate the binding free energy of my receptor - ligand complex (both are protein chains) using MM-PB(GB)SA. When I run the mm_pbsa script I eventually get the results(statistics.out etc.), however I also get this message too,

vertex atom mismatch
       atom: 100
vertex atom: 91

I searched the list but I could not figure out the problem. Anybody have an idea?

Also I want to ask a second question,
Before extracting the snapshots from the explicit water trajectory for this calculation, do we have to strip away the waters and ions with ptraj? (I mean we already define where the receptor and ligand starts and ends in the script) If we do not, does this effect the final results?

Thanks for the help.


The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to
Received on Wed Jan 17 2007 - 06:08:36 PST
Custom Search