AMBER Archive (2006)

Subject: Re: AMBER: one question about mm_pbsa

From: Ray Luo (rluo_at_uci.edu)
Date: Thu Apr 13 2006 - 10:39:53 CDT

Were you able to run the examples under src/mm_pbsa?

Ray

ÊÛÆãÑÎ wrote:

>hi,Amber,
> I use mm_pbsa programe to compute binding energy.The mm_pbsa input file is as
>flows:
>#
>################################################################################
>@GENERAL
>#
>PREFIX ablpse
>PATH ./
>#
>COMPLEX 1
>RECEPTOR 1
>LIGAND 1
>#
>COMPT ./ablpsenw.top
>RECPT ./ablnw.top
>LIGPT ./psenw.top
>#
>GC 0
>AS 0
>DC 0
>#
>MM 1
>GB 1
>PB 1
>MS 1
>#
>NM 0
>#
>################################################################################
>@PB
>#
>PROC 2
>REFE 0
>INDI 1.0
>EXDI 80.0
>SCALE 2.0
>LINIT 500
>PRBRAD 1.4
>#
>RADIOPT 1
>#
>FOCUS 0
>PERFIL 80.0
>CHARGE ./my_amber94_delphi.crg
>SIZE ./my_parse_delphi.siz
>#
>SURFTEN 0.005
>SURFOFF 0.0
>#
>################################################################################
>@MM
>DIELC 1.0
>################################################################################
>@GB
>IGB 2
>GBSA 1
>SALTCON 0.00
>EXTDIEL 80.0
>INTDIEL 1.0
>#
>SURFTEN 0.0072
>SURFOFF 0.00
>#
>################################################################################
>@MS
>PROBE 0
>#
>################################################################################
>@PROGRAMS
>#
># Program executables
>#
>DELPHI /nfs/s07r2p1/phoebusdu/delphiexe/delphi
>#
>################################################################################
>
>When I run ,it shows£º
>
>Use of uninitialized value in hash element at
>/nfs/s07r2p1/phoebusdu/amber8/amber8/src/mm_pbsa/mm_pbsa_readinput.pm line 260,
><IN> line 74.
>Use of uninitialized value in hash element at
>/nfs/s07r2p1/phoebusdu/amber8/amber8/src/mm_pbsa/mm_pbsa_readinput.pm line 260,
><IN> line 74.
>Use of uninitialized value in multiplication (*) at
>/nfs/s07r2p1/phoebusdu/amber8/amber8/src/mm_pbsa/mm_pbsa_statistics.pm line 1328.
>Use of uninitialized value in multiplication (*) at
>/nfs/s07r2p1/phoebusdu/amber8/amber8/src/mm_pbsa/mm_pbsa_statistics.pm line 1327.
>Use of uninitialized value in multiplication (*) at
>/nfs/s07r2p1/phoebusdu/amber8/amber8/src/mm_pbsa/mm_pbsa_statistics.pm line 1327.
>Use of uninitialized value in multiplication (*) at
>/nfs/s07r2p1/phoebusdu/amber8/amber8/src/mm_pbsa/mm_pbsa_statistics.pm line 1327.
> No data for 0+2 PB PB 0
>and in the mm_pbsa log file it shows :
>Reading ablpse_lig.all.out
> WARNING: Missing PB for PB in 0 -> Taken from -1
> WARNING: Missing PB for PB in 1 -> Taken from 0
> WARNING: Missing PB for PB in 2 -> Taken from 1
> WARNING: Missing PB for PB in 3 -> Taken from 2
>Is there any body know why and how can I modify it?
>Thanks!
> Yongchun Du
> 2006.4.13
>
>
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>.
>
>
> 

-- 
====================================================
Ray Luo, Ph.D.
Department of Molecular Biology and Biochemistry
University of California, Irvine, CA 92697-3900
Office: (949)824-9528         Lab: (949)824-9562
Fax: (949)824-8551          e-mail: rluo_at_uci.edu
Home page: http://rayl0.bio.uci.edu/rayl/
====================================================

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