I already have the ambertools1.5, are you suggesting the mmpbsa.py to
calculate the binding energy??
Thank you very much for your answer.
Sergio.
> I suggest that you download the latest ambertool (1.5). It's free and
> much better supported ...
>
> All the best,
> Ray
>
> On Mon, Aug 15, 2011 at 8:04 AM, <sribone.fcq.unc.edu.ar> wrote:
>> Dear all, Im writing because I've been trying to solve a problem with
>> the mm_pbsa for months but I can not do it. When I calculate the
>> binding energy for a ligand-enzime complex by mm_pbsa in amber10 using
>> the following input:
>>
>> PREFIX tr103-sr25
>> PATH ./
>> #
>> COMPLEX 1
>> RECEPTOR 1
>> LIGAND 1
>> #
>> COMPT complejo.prmtop
>> RECPT receptor.prmtop
>> LIGPT ligando.prmtop
>> #
>> GC 0
>> AS 0
>> DC 0
>> #
>> MM 1
>> GB 1
>> PB 1
>> MS 1
>> #
>> NM 0
>> PROC 2
>> REFE 0
>> INDI 1.0
>> EXDI 80.0
>> SCALE 1
>> 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
>>
>> DIELC 1.0
>>
>> IGB 2
>> GBSA 1
>> SALTCON 0.00
>> EXTDIEL 80.0
>> INTDIEL 1.0
>> #
>> SURFTEN 0.0072
>> SURFOFF 0.00
>>
>> PROBE 0.0
>>
>> I received the following problem:
>>
>> Use of uninitialized value in multiplication (*) at
>> /home/sergio/Programas/amber10/src/mm_pbsa/mm_pbsa_statistics.pm line
>> 1378.
>> No data for 0+2 PB PB 0
>>
>> The output file gave me some warnings:
>> Reading tr103-sr25_com.all.out
>> WARNING: Missing PBNONPOL for PB in 0 -> Taken from -1
>> WARNING: Missing ELRAELE for PB in 0 -> Taken from -1
>> WARNING: Missing EPB for PB in 0 -> Taken from -1
>> Reading tr103-sr25_rec.all.out
>> Checking CALC
>> WARNING: Missing PBNONPOL for PB in 0 -> Taken from -1
>> WARNING: Missing ELRAELE for PB in 0 -> Taken from -1
>> WARNING: Missing EPB for PB in 0 -> Taken from -1
>> Reading tr103-sr25_lig.all.out
>> Checking CALC
>> WARNING: Missing PBNONPOL for PB in 0 -> Taken from -1
>> WARNING: Missing PB for PB in 0 -> Taken from -1
>> WARNING: Missing ELRAELE for PB in 0 -> Taken from -1
>> WARNING: Missing EPB for PB in 0 -> Taken from -1
>>
>> The energy output for ligand, receptor and complex are:
>> ligand
>> MM
>> GB
>> PB
>> MS
>> 1
>> BOND = 6.4620 ANGLE = 9.0237 DIHED =
>> 15.3520
>> VDWAALS = -4.9297 EEL = 0.0000 EGB =
>> 0.0000
>> 1-4 VDW = 16.1895 1-4 EEL = 0.0000 RESTRAINT =
>> 0.0000
>> surface area = 594.734
>> ECAVITY = 594.734
>> EDISPER = 0.0000
>>
>> receptor
>> MM
>> GB
>> PB
>> MS
>> 1
>> BOND = 3076.6042 ANGLE = 8300.7106 DIHED =
>> 9726.1992
>> VDWAALS = -7614.1238 EEL = -73971.1573 EGB =
>> -12444.1021
>> 1-4 VDW = 3708.5404 1-4 EEL = 47222.5091 RESTRAINT =
>> 0.0000
>> corrected reaction field energy: -20517.454143
>> surface area = 52994.258
>> ECAVITY = 52994.258
>> EDISPER = 0.0000
>>
>> complex
>> MM
>> GB
>> PB
>> MS
>> 1
>> BOND = 3083.0662 ANGLE = 8309.7344 DIHED =
>> 9741.5536
>> VDWAALS = -7655.2357 EEL = -73971.1573 EGB =
>> -12436.3100
>> 1-4 VDW = 3724.7299 1-4 EEL = 47222.5091 RESTRAINT =
>> 0.0000
>> corrected reaction field energy: -20505.425856
>> surface area = 52811.495
>> ECAVITY = 52811.495
>> EDISPER = 0.0000
>>
>> I patched the bugfixes for amber. I've been running mm_pbsa for others
>> very similar ligands, but I never had this problem before.
>> I appreciate any kind of help or explanation about this problem.
>> Thank you very much for your time.
>>
>> Sergio Ribone.
>>
>>
>> Dept Pharmacy, Science Chemistry Phaculty
>> National University of Córdoba
>>
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Received on Tue Aug 16 2011 - 05:30:04 PDT
