AMBER Archive (2008)

Subject: AMBER: MM-PBSA problem : Missing PBCAV for PB

From: Carra, Claudio (JSC-SK)[USRA] (Claudio.Carra-1_at_nasa.gov)
Date: Tue Sep 30 2008 - 11:49:26 CDT

Dear All,
I got the following error in the MM-PBSA calculation

[...]
=>> Reading files
    Reading snapshot_com.all.out
    WARNING: Missing PBCAV for PB in 0 -> Taken from -1
    WARNING: Missing PBDIS for PB in 0 -> Taken from -1
    WARNING: Missing SURF for MS in 0 -> Taken from -1
    WARNING: Missing PBCAV for PB in 1 -> Taken from 0
    WARNING: Missing PBDIS for PB in 1 -> Taken from 0
    WARNING: Missing SURF for MS in 1 -> Taken from 0
    WARNING: Missing PBCAV for PB in 2 -> Taken from 1
    WARNING: Missing PBDIS for PB in 2 -> Taken from 1
    WARNING: Missing SURF for MS in 2 -> Taken from 1
    WARNING: Missing PBCAV for PB in 3 -> Taken from 2
    WARNING: Missing PBDIS for PB in 3 -> Taken from 2
    WARNING: Missing SURF for MS in 3 -> Taken from 2
   [...]

and I don't get the final results. The same script works
perfectly for a system of smaller dimension.
do you have any idea on the origin of this and how to fix the problem?
thanks a lot
regards
claudio

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
      to majordomo_at_scripps.edu