Dear amber members,
After i adding the print OUT " fillratio=3 \n"; to the line number 435 in
the file $AMBERHOME/src/mm_pbsa/mm_pbsa_createinput.pm
and then make
make install
I still got the same errors so what i did something wrong or this way might
not work ?
any suggestions would be great,
////////mm_pbsa_createinput.pm/////////////////
print OUT " &pb\n";
print OUT " epsin = ${epsin}, epsout = ${epsout},\n";
print OUT " istrng = ${istrng}, radiopt = ${radiopt},\n";
print OUT " sprob = ${sprob}, space = ${space},\n";
print OUT " fillratio=
4\n";
I
added this line here.
print OUT " maxitn = ${maxitn}, npopt = ${npopt},\n";
print OUT " cavity_surften = ${cavity_surften}, cavity_offset =
${cavity_offset},\n";
print OUT " npbverb= 1\n";
print OUT " &end\n";
Thanks,
Jitrayut
---------- Forwarded message ----------
From: Navnit Kumar Mishra <navnit.chemi.muni.cz>
Date: เม.ย. 23, 2007 9:04 หลังเที่ยง
Subject: Re: AMBER: MM-PBSA: Can't finish the binding energy process
To: amber.scripps.edu
jitrayut jitonnom wrote:
> Dear amber users,
>
> I have run the binding_energy.in in order to obtain the binding free
> energy in term of COM, LIG, REC. The output name
> "snapshot_statistics.out" should be generated but it stop at the
> process line below:
>
> pbsa_lig.14.out
>
> And, I also check the end of this file which its details show below:
>
> ======== Setting up Grid Parameters ========
> Using bounding box for grid setup
> Bounding Box Center: 43.000 33.500 40.000
> Xmin, Xmax, Xmax-Xmin: 34.354 51.926 17.572
> Ymin, Ymax, Ymax-Ymin: 20.466 46.695 26.229
> Zmin, Zmax, Zmax-Zmin: 35.378 44.181 8.803
> beginning box center at level 1 43.000 33.500 40.000
> beginning box center at level 2 43.000 33.500 40.000
> Grid dimension at level 1 11 15 5
> Grid origin corrected at level 1 19.000 1.500 28.000
> Grid dimension at level 2 49 67 33
> Grid origin corrected at level 2 30.500 16.500 31.500
> PB Bomb in setgrd(): focusing grid too large 2
> reset fillratio to a larger number 2.000
you need to increase the fillration to 3 or 4. simplest way to do it by
adding the
print OUT " fillratio=3 \n";
to the line number 435 in the file
$AMBERHOME/src/mm_pbsa/mm_pbsa_createinput.pm
good luck
Navnit
>
> Actually, i perform the same protocal for other similar system and i
> can obtain the output but why these errors
> still occurs.
>
> Therefore, anyone who can give me some suggestions would be appreciated.
>
> Jitrayut Jitonnom
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Sun May 13 2007 - 06:07:18 PDT
