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.rci.rutgers.edu> wrote:
From: Scott Brozell <sbrozell.rci.rutgers.edu>
Subject: Re: [AMBER] MM_PBSA Problem (no radius for ion)
To: "AMBER Mailing List" <amber.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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Received on Fri Dec 18 2009 - 08:00:03 PST
