AMBER Archive (2006)

Subject: AMBER: PBSA calculation fail ....

From: Changge Ji (jcg_at_itcc.nju.edu.cn)
Date: Thu Oct 05 2006 - 08:42:39 CDT

hi, Folks.

I did some MM_PBSA analysis with my dynamic traj.

 But it paused with the following error message : " PB Warning in epsbnd(): No neighbor found for boundary grids total: 61
 "

parameters used in mm_pbsa.in are

"
PROC 2
REFE 0
INDI 1.0
EXDI 80.0
SCALE 3
LINIT 3000
PRBRAD 1.4
"

I found out that this error message comes from pb_exmol.f ,but I don't know what it really means ?

And how can I fixed it .

By the way ,my system is very large , the protein contains about 16000 atoms .
but some parameters were already changed according to my protein ,(such as MAXMUM NUMBER OF ATOMS )

   Thank you very much for your sincerely help.

　　　　　　　　
Best wished ,
                                 
                     Yours ,
　　　　　　　　Changge Ji
　　　　　　　　jcg_at_itcc.nju.edu.cn
　　　　　　　　　　2006-10-05
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