Ok !Thank you !
At 2011-07-23 07:59:40,"Ray Luo, Ph.D." <ray.luo.uci.edu> wrote:
>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
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
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Received on Fri Jul 22 2011 - 17:30:03 PDT
