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
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Received on Sun Apr 18 2010 - 05:00:02 PDT
