AMBER Archive (2006)

Subject: Re: AMBER: one question about mm_pbsa

From: 杜永春 (duyongchun_at_mail.nankai.edu.cn)
Date: Thu Apr 13 2006 - 21:26:49 CDT

Yes

在您的来信中曾经提到:
>From: "Ray Luo" <rluo_at_uci.edu>
>Reply-To: amber_at_scripps.edu
>To: amber_at_scripps.edu
>Subject: Re: AMBER: one question about mm_pbsa
>Date:Thu, 13 Apr 2006 08:39:53 -0700
>
>Were you able to run the examples under src/mm_pbsa?
>
> Ray
>
> 售沏盐 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：
> >
> >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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> >.
> >
> >
> >
>
> --

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