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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Received on Sun Oct 29 2006 - 06:07:09 PST
