Re: Re: Re: [AMBER] error when running mmpbsa

From: pxq <pangxueqintea.yahoo.com.cn>
Date: Mon, 19 Apr 2010 10:49:37 +0800

Bill,

It works! Thanks very much

Best wishes

Xueqin

        

======= 2010-04-18 21:50:22 您在来信中写道:=======

>When you open $AMBERHOME/src/mm_pbsa/mm_pbsa_createinput.pm search for
>'Using PB.' The first match should be the line
>
> print OUT "File generated by mm_pbsa.pl. Using PB\n";
>
>This is the start of the input created by mm_pbsa.pl for PBSA calculations.
>Scroll down to the &pb section of the input file and add
>
>fillratio = 4
>
>to one of the print OUT lines in this section and re-compile mm_pbsa. This
>should make the desired change in mm_pbsa.pl.
>
>Good luck!
>
>-Bill
>
>2010/4/18 pxq <pangxueqintea.yahoo.com.cn>
>
>> Jason,
>>
>> Thanks for reply.
>>
>> I have not found the right line to add "fillratio" in. I tried every line
>> of 590-600 in my mm_pbsa_createinput.pm but failed. I have added "cutres"
>> in, thus maybe there is difference in line number.
>>
>> However, it works well with MMPBSA.py for my system.
>>
>> The error report is :Useless use of a constant in void context at
>> /home/pxq/software/amber10/src/mm_pbsa/mm_pbsa_readinput.pm line 590. and
>> so on.
>>
>> The line 590-600 of my mm_pbsa_createinput.pm are as follows:
>> &test_par(\.MS_PAR,[$r_mol]);
>> &test_fil(\.MS_FIL,[$r_mol,$r_pro]);
>> }
>> return;
>> }
>>
>> sub get_res_no(){
>> #################
>>
>> # Parameters: $str
>>
>> Do you have any suggestions modifying the mm_pbsa model.
>>
>> Thanks very much.
>>
>> Xueqin
>>
>>
>> ======= 2010-04-17 22:58:41 您在来信中写道:=======
>>
>> > Hello,
>> >
>> > If you are using mm_pbsa.pl, edit the file mm_pbsa_createinput.pm in
>> > $AMBERHOME/src/mm_pbsa around lines 590-600 and add fillratio to the pbsa
>> > input file.
>> >
>> > If you are using MMPBSA.py, you may specify it right in the mmpbsa input
>> > file in the &pb namelist.
>> >
>> > Good luck!
>> > Jason
>> >
>> > 2010/4/17 pxq < pangxueqintea.yahoo.com.cn>
>> >
>> > > Hello everyone,
>> > >
>> > > When running mmpbsa I get the error:
>> > > PB Bomb in setgrd(): focusing grid too large 2
>> > > reset fillratio to a larger number 2.000
>> > > and stopped.
>> > >
>> > > Ray has suggested changing fillratio in the list, but where to change
>> it?
>> > >
>> > > What is more, I have done mmpbsa calculation for this same system and
>> the
>> > > difference is that I changed some charge parameter for part of the
>> receptor
>> > > (which is not protein, and the new charge is come form a reference ).
>> And
>> > > then mmpbsa calculation stops at the same step when doing ligand
>> related
>> > > calculation (both receptor and complex related calculations are
>> passed)
>> > >
>> > > And the memory of my computer is 24G, so is it possible of laking of
>> > > memory?
>> > >
>> > > So do you have any suggestions?
>> > >
>> > > Thanks so much
>> > >
>> > > Best wishes
>> > >
>> > > Xueqin
>> > >
>> > >
>> > >
>> > >
>> =========================================================================================================
>> > > Pang Xueqin
>> > > State Key Laboratory of Molecular Reaction Dynamics
>> > > Dalian Institute of Chemical Physics
>> > > Chinese Academy of Sciences.
>> > > Tel: 0411-84379352 Fax: 0411-84675584
>> > >
>> > >
>>
>> =================================================================================================================================
>> =======
>> > > _______________________________________________
>> > > AMBER mailing list
>> > > AMBER.ambermd.org
>> > > http://lists.ambermd.org/mailman/listinfo/amber
>> > >
>> >
>> >
>> >
>> > --
>> > ---------------------------------------
>> > Jason M. Swails
>> > Quantum Theory Project,
>> > University of Florida
>> > Ph.D. Graduate Student
>> > 352-392-4032
>> > _______________________________________________
>> > AMBER mailing list
>> > AMBER.ambermd.org
>> > http://lists.ambermd.org/mailman/listinfo/amber
>>
>> = = = = = = = = = = = = = = = = = = = =
>>
>> 致
>> 礼!
>>
>>
>> pxq
>> pangxueqintea.yahoo.com.cn
>> 2010-04-18
>>
>> _______________________________________________
>> AMBER mailing list
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>>
>>
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        致
礼!
 
                                 
        pxq
        pangxueqintea.yahoo.com.cn
          2010-04-19

嗃i'櫒ド╤∈&

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Received on Sun Apr 18 2010 - 20:00:02 PDT
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