AMBER Archive (2006)

Subject: AMBER: mm_pbsa: binding energy calculation

From: Varsha Goyal (vgusp_at_yahoo.ca)
Date: Wed Oct 25 2006 - 13:51:57 CDT

Dear Amber Developers and Users,

I am trying to calculate Binding energy of protein and
Ligand. I was following the tutorial writeen by Dr.
Holger Gohlke. In my case I have a "ZN" ion in the
active site. When I prepared my topology files for
protein and complex I loaded parameters for Zn and
also lib file for Zn. During simulations it never
raised any error, but now when I am trying to estimate
binding energy it is giving me following error:

" No radius found for Zn 4042 in residue ZNC 259"
where ZNC is name of residue for Zn ion.

Here is my binding_energy.log file

=>> Init data
    Presuming executables of amber suite to be in
/usr/local/amber8/exe

=>> Reading input parameters
    Found PREFIX => snapshot
    Found PATH => ./extract_coord
    Found COMPLEX => 1
    Found RECEPTOR => 1
    Found LIGAND => 1
    Found COMPT => ./prmtop.com
    Found RECPT => ./prmtop.prot
    Found LIGPT => ./prmtop.ets
    Found GC => 0
    Found AS => 0
    Found DC => 0
    Found MM => 1
    Found GB => 1
    Found PB => 1
    Found MS => 1
    Found NM => 0
    Found PROC => 2
    Found REFE => 0
    Found INDI => 1.0
    Found EXDI => 80.0
    Found SCALE => 2
    Found LINIT => 1000
    Found PRBRAD => 1.4
    Found ISTRNG => 0.0
    Found RADIOPT => 0
    Found NPOPT => 1
    Found CAVITY_SURFTEN => 0.0072
    Found CAVITY_OFFSET => 0.00
    Found SURFTEN => 0.0072
    Found SURFOFF => 0.00
    Found DIELC => 1.0
    Found IGB => 2
    Found GBSA => 1
    Found SALTCON => 0.00
    Found EXTDIEL => 80.0
    Found INTDIEL => 1.0
    Found SURFTEN => 0.0072
    Found SURFOFF => 0.00
    Found PROBE => 0.0
    Found SANDER =>
/usr/local/amber8/exe-serial/sander

=>> Checking sanity
    Checking GENERAL
    Checking MM
    Checking PB
    Checking GB
    Checking MS

=>> Creating input
    Sander input
    PBSA input

=>> Calculating energy / entropy contributions
    Calc contrib for
./extract_coord/snapshot_com.crd.1
        Calc MM/GB/SAS
        Generate PDB
        Center PDB
        Calc PBSA
        Generate PQR
        No radius found for Zn 4042 in residue ZNC
259

Can someone please help me out in thir problem because
I am not sure where can i define radius of Zn now.

Here is files related to Zn, which i used while
creating topology files and coordinate files.
 ##############ZNC.lib###############################
!!index array str
 "ZNC"
!entry.ZNC.unit.atoms table str name str type int
typex int resx int flags int seq int elmnt dbl
chg
 "Zn" "Zn" 0 1 131075 1 30 0.866000
!entry.ZNC.unit.atomspertinfo table str pname str
ptype int ptypex int pelmnt dbl pchg
 "Zn" "Zn" 0 -1 0.0
!entry.ZNC.unit.boundbox array dbl
 -1.000000
 0.0
 0.0
 0.0
 0.0
!entry.ZNC.unit.childsequence single int
 263
!entry.ZNC.unit.connect array int
 0
 0
!entry.ZNC.unit.hierarchy table str abovetype int
abovex str belowtype int belowx
 "U" 0 "R" 1
 "R" 1 "A" 1
!entry.ZNC.unit.name single str
 ""
!entry.ZNC.unit.positions table dbl x dbl y dbl z
 -6.788000 -1.621000 15.381000
!entry.ZNC.unit.residueconnect table int c1x int c2x
 int c3x int c4x int c5x int c6x
 0 0 0 0 0 0
!entry.ZNC.unit.residues table str name int seq int
childseq int startatomx str restype int imagingx
 "ZNC" 262 2 1 "?" 0
!entry.ZNC.unit.residuesPdbSequenceNumber array int
 1
!entry.ZNC.unit.solventcap array dbl
 -1.000000
 0.0
 0.0
 0.0
 0.0
!entry.ZNC.unit.velocities table dbl x dbl y dbl z
 0.0 0.0 0.0
#################################################
------------------------------------------------------
##############frcmod.znc###########################
This frcmod file is for ZNC (zinc 2+ ion).
MASS
ZNC 65.4

NONB
ZNC 1.10 0.0125

Thanks in advance,
Varsha Gupta

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