If possible, try the latest AmberTool (1.5) with your mmpbsa projects
... it's free ...
All the best,
Ray
On Fri, Jul 22, 2011 at 1:40 AM, 刘金峰 <liujinfeng.1119.163.com> wrote:
> Dear all,
> I'm trying to use MM_PBSA to calculate a protein-ligand binding energy,but unluckily,I received a message like this:
> Use of uninitialized value in multiplication (*) at /apps/amber11/src/mm_pbsa/mm_pbsa_statistics.pm line 1457.
> Use of uninitialized value in multiplication (*) at /apps/amber11/src/mm_pbsa/mm_pbsa_statistics.pm line 1457.
> Use of uninitialized value in multiplication (*) at /apps/amber11/src/mm_pbsa/mm_pbsa_statistics.pm line 1457.
> Use of uninitialized value in multiplication (*) at /apps/amber11/src/mm_pbsa/mm_pbsa_statistics.pm line 1457.
> Use of uninitialized value in multiplication (*) at /apps/amber11/src/mm_pbsa/mm_pbsa_statistics.pm line 1457.
> Use of uninitialized value in multiplication (*) at /apps/amber11/src/mm_pbsa/mm_pbsa_statistics.pm line 1457.
> Use of uninitialized value in multiplication (*) at /apps/amber11/src/mm_pbsa/mm_pbsa_statistics.pm line 1457.
> Use of uninitialized value in multiplication (*) at /apps/amber11/src/mm_pbsa/mm_pbsa_statistics.pm line 1457.
> No data for 0+0 NM SROT 0
> For details see: http://ambermd.org/Questions/mm_pbsa.html#calc_delta_no_data_plus_zero
> It has produced the output files:snapshot_com.all.out,snapshot_rec.all.out,snapshot_lig.all.out,but not "snapshot_statistics.out " file.I don't know how to work it out .My input file is like this :
> .GENERAL
> PREFIX snapshot
> PATH ./snapshot
> COMPLEX 1
> RECEPTOR 1
> LIGAND 1
> COMPT ./comp_ini.prmtop
> RECPT ./protein.prmtop
> LIGPT ./ind.prmtop
> GC 0
> AS 0
> DC 0
> MM 1
> GB 1
> PB 1
> MS 1
> NM 1
> .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
> .NM
> PROC 2
> DIELC 4
> MAXCYC 10000
> DRMS 0.1
> IGB 0
> .PROGRAMS
>
>
> Many thanks !
> jinfengliu
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>
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Received on Fri Jul 22 2011 - 17:00:08 PDT
