AMBER Archive (2009)

Subject: Re: [AMBER] MM_PBSA Problem (no radius for ion)

From: s. Bill (s_bill36_at_yahoo.co.uk)
Date: Fri Dec 18 2009 - 09:33:57 CST

Dear Brozell
Thanks for your reply.
But I still have some questions.
I used RADIOPT = 0 in my binding_energy.mmpbsa input file, which means

#   RADIOPT - Option to set up radii for PB calc:
#           0: uses the radii from the prmtop file. Default.

So, why the program didn't read it from prmtop file?
Also, I don't know the radius of Zinc and Calcium ion.
I need a help please.
Thanks in advance
Sincerely;
S. Bill
--- On Fri, 18/12/09, Scott Brozell <sbrozell_at_rci.rutgers.edu> wrote:

From: Scott Brozell <sbrozell_at_rci.rutgers.edu>
Subject: Re: [AMBER] MM_PBSA Problem (no radius for ion)
To: "AMBER Mailing List" <amber_at_ambermd.org>
Date: Friday, 18 December, 2009, 3:07

Hi,

Here's what i did to the mm_pbsa_calceneent.pm file a while back
for amber9:

sub generate_pqr(){
###################

  # This implementation uses bondi radii

  # Parameters: $pdb,$pqr,$r_mol
  my $pdb = shift;
  my $pqr = shift;
  my $r_mol = shift;

  # Bondi radii + 1.4A and probe radius of 0.0A yields SAS
  # Bondi radii + 0.0A and probe radius of 1.4A yields molecular surface
  # Bondi radii + 0.0A and probe radius of 0.0A yields vdW surface
# SRB Oct 3, 2008; add fluorine vdw radius; see ticket 18558
# SRB Oct 13, 2008; add zinc radius; see ticket 18993
  my %exp_rad = (
       "N"    => 1.550 + 1.400,
       "H"    => 1.200 + 1.400,
       "C"    => 1.700 + 1.400,
       "O"    => 1.500 + 1.400,
       "P"    => 1.800 + 1.400,
       "S"    => 1.800 + 1.400,
       "FE"   => 1.300 + 1.400,
       "Na+"  => 1.200 + 1.400,
       "Cl-"  => 1.700 + 1.400,
       "MG"   => 1.180 + 1.400,
       "F"    => 1.470 + 1.400,
       "Zn"   => 1.100 + 1.400,
      );

  print "        Generate PQR\n";
  print "          Warning:  the fluorine radius is 1.47 Angstroms.\n";
  print "          Warning:  the zinc radius is 1.10 Angstroms.\n";
  print "          These warning only applies to MS=1 calculations.\n";
  make_pqr_file($pdb,$pqr,\%exp_rad);
}

I also modified sander/mdread.f
diff mdread.f.original mdread.f
1209a1210,1218
>             else if (atype == 'ZN' .or. atype == 'Zn') then
>                ! SRB Oct 13, 2008.  See ticket 18993
>                write( 6,* ) 'Warning:  Non standard sander behavior!'
>                write( 6,* ) '    Using zinc radius of 1.10 Ang. for SA.'
>                x(l165-1+i) = 1.10d0 + 1.4d0
>                x(l170-1+i) = 0.00000d0
>                x(l175-1+i) = 0.00000d0
>                x(l180-1+i) = 0.00000d0
>                x(l185-1+i) = 0.00000d0
1233a1243,1251
>             else if (atype(1:1) == 'F' .or. atype(1:1) == 'f') then
>                ! SRB Sep 11, 2008.  See ticket 18558
>                write( 6,* ) 'Warning:  Non standard sander behavior!'
>                write( 6,* ) '    Using VDW radius of fluorine for SA.'
>                x(l165-1+i) = 1.47d0 + 1.4d0  ! VDW radius of fluorine + 1.4 Ang.
>                x(l170-1+i) = 0.00000d0
>                x(l175-1+i) = 0.00000d0
>                x(l180-1+i) = 0.00000d0
>                x(l185-1+i) = 0.00000d0

Naturally followed by rebuilding.
I did this for someone else and don't remember any details or gottchas.

good luck,
Scott

On Thu, Dec 17, 2009 at 07:39:49PM +0000, s. Bill wrote:
> Dear AMBER
> Today, I have encountered another problem during performing MM-PBSA for my system. My system contains Zinc ion and Calcium ion.
> During binding_energy.mmpbsa step, I got the following error:
>         No radius found for ZN    2647 in residue ZN  172
> I searched the AMBER archieve and I found that we should modify the mm_pbsa_calceneent.pm file.
> I did add the raidus for my ions, as following:
>
>  if(exists $r_del->{"IVCAP"} && ($r_del->{"IVCAP"} == 1 || $r_del->{"IVCAP"} == 5)){
>     # Prepare for calc of molecular surface
>     %exp_rad = (
>            "N"    => 1.550,
>            "H"    => 1.200,
>            "C"    => 1.700,
>            "O"    => 1.500,
>            "P"    => 1.800,
>            "S"    => 1.800,
>            "FE"   => 1.300,
>            "Na+"  => 1.200,
>            "Cl-"  => 1.700,
>            "MG"   => 1.180,
>            "ZN"   => 0.740,
>            "CA"   => 0.990,
>            );
> Unfortunately, I still have the same error.
> Could any body tell me what should I do? and also are these Radii values for Zinc (0.74) and Calcium (0.99) right?

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