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
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sun Apr 18 2010 - 07:00:02 PDT
