AMBER Archive (2008)

Subject: RE: AMBER: MM_PBSA problems in AMBER9

From: 欧阳德方 (ouyangdf1978_at_hotmail.com)
Date: Tue Oct 07 2008 - 00:19:54 CDT

Hi,

Thanks very for Ray and Alessandro's advice!

I try Alessandro's advice and add the following line to $AMBERHOME/src/mm_pbsa/mm_pbsa_createinput.pm to 435 lines:
print OUT " fillratio=3 \n";

However, a new problem comes out:
 The output file shows:
 "---
    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
 ---
 Calc delta from raw data"

 Also the command lines shows:
 " ---
 Use of uninitialized value in multiplication (*) at /usr/local/amber9/src/mm_pbsa/mm_pbsa_statistics.pm line 1336.
 Use of uninitialized value in multiplication (*) at /usr/local/amber9/src/mm_pbsa/mm_pbsa_statistics.pm line 1336.
   No data for 0+2 PB PB 0"
The new problem is same as that I change "SCALE" 2.0 to 3.0. But this time SCALE is 2.0
I search past posts and cannot get results.

Moreover, Ray, can u explain to me more details about how to add fillratio to 3.0? Which file I should correct in $AMBERHOME/src/mm_pbsa?
I read previous emails about this and cannot get detailed answers.

Thanks very much for your help,

Ouyang

School of Pharmacy
 The University of Queensland
 Brisbane, Australia
----------------------------------------
> Date: Mon, 6 Oct 2008 10:04:37 -0300
> From: al.s.nascimento_at_gmail.com
> To: amber_at_scripps.edu
> Subject: Re: AMBER: MM_PBSA problems in AMBER9
> CC: rluo_at_uci.edu
>
> Adding the following line to $AMBERHOME/src/mm_pbsa/mm_pbsa_createinput.pm:
> print OUT " fillratio=3 \n"; should solve the problem according to
>
> http://www.teokem.lu.se/~ulf/Methods/mm_pbsa.html
>
> HTH
>
> --alessandro
>
>
> 2008/10/6 Ray Luo :
>> The error message says that you should change fillratio NOT scale to a
>> larger number ...
>>
>> All the best,
>> Ray
>>
>> 2008/10/5 欧阳德方 :
>>>
>>> Hi, all,
>>>
>>> When I calculate the binding energy of RNA-small molecule interaction by MM_PBSA in AMBER9. Input file is as following:
>>>
>>> PREFIX snapshot
>>> PATH ./
>>> #
>>> COMPLEX 1
>>> RECEPTOR 1
>>> LIGAND 1
>>> #
>>> COMPT ./den4_complex_major_vac.prmtop
>>> RECPT ./rna_vac.prmtop
>>> LIGPT ./dendrimer4.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 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
>>> #
>>> 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
>>> #
>>>
>>> But it shows "---snapshot_lig.crd.17 not successful---"
>>> The output file shows
>>> "---PB Bomb in setgrd (): focusing grid too large 2
>>> reset fillratio to a large number 2.000"
>>>
>>> According previous post, I change SCALE 2.0 to 4.0 (or 3.0). But new problems appears.
>>> The output file shows:
>>> "---
>>> 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
>>> ---
>>> =>> Calc delta from raw data"
>>>
>>> Also the command lines shows:
>>> " ---
>>> Use of uninitialized value in multiplication (*) at /usr/local/amber9/src/mm_pbsa/mm_pbsa_statistics.pm line 1336.
>>> Use of uninitialized value in multiplication (*) at /usr/local/amber9/src/mm_pbsa/mm_pbsa_statistics.pm line 1336.
>>> No data for 0+2 PB PB 0"
>>>
>>> I cannot get the final statistical output file.
>>>
>>> Could u tell me the reasons and how to solve it?
>>>
>>> Thanks for your help,
>>>
>>> Ouyang
>>>
>>> School of Pharmacy
>>> The University of Queensland
>>> Brisbane, Australia
>>>
>>>
>>>
>>>
>>>
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>
>
>
> --
> [ ]s
>
> --alessandro
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