I use this command:
$AMBERHOME/exe/mm_pbsa.pl binding_energy.mmpbsa > binding_energy.log
This is the binding_energy.mmpbsa file:
.GENERAL
PREFIX snapshot
PATH ./
#
COMPLEX 1
RECEPTOR 1
LIGAND 1
#
COMPT ./com_vac.prmtop
RECPT ./ricin.prmtop
LIGPT ./antibody_vac.prmtop
#
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
LINIT 1000
PRBRAD 1.4
ISTRNG 0.0
RADIOPT 0
NPOPT 1
CAVITY_SURFTEN 0.0072
CAVITY_OFFSET 0.00
#
SURFTEN 0.0072
SURFOFF 0.00
#
.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 0.0
#
.PROGRAMS
In mm_pbsa_readinput.pm, the line 76 is:
print " Found $key => $value\n";
Line 260 is:
$r_pro->{$key} = $value; # Overwriting of entries allowed here since
# default is set in &init_data()
________________________________
From: Bill Miller III <brmilleriii.gmail.com>
To: AMBER Mailing List <amber.ambermd.org>
Sent: Fri, October 29, 2010 11:09:03 AM
Subject: Re: [AMBER] Error message from binding_energy.mmpbsa
Can you show your input? And what is on lines 76 and 260 of
mm_pbsa_readinput.pm?
-Bill
On Fri, Oct 29, 2010 at 10:50 AM, bin wang <wang_p_z.yahoo.com.cn> wrote:
> Hello,
> I use the binding_energy.mmpbsa from the tutorial A3 to calculate binding
> energy. But I got these error messages:
> Use of uninitialized value in concatenation (.) or string at
> /usr/local/amber10/src/mm_pbsa/mm_pbsa_readinput.pm line 76, <IN> line 59.
> Use of uninitialized value in hash element at
> /usr/local/amber10/src/mm_pbsa/mm_pbsa_readinput.pm line 260, <IN> line
> 59.
> /usr/local/amber10/exe/sander -O -i pbsa_com.in -o pbsa_com.1.out
> -c
> ./snapshot_com.crd.1 -p ./com_vac.prmtop not successful
>
> I checked the mm_pbsa_readinput.pm, but don't know what I should do.
> Could
> anibody help me? Thank you.
>
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Bill Miller III
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-6715
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Received on Fri Oct 29 2010 - 09:00:03 PDT
