Hi,
If you are using Molsurf (from your script it seems so) to calculate the
non polar solavtion free energy you should go to the
"mm_pbsa_calceneent.pm" Perl Module in your mm_pbsa directory ( mine is:
"/usr/local/amber9-x86_64/src/mm_pbsa") and add the Zn Bondi radius here:
# 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
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,
"Zn" => you know it + 1.400
"Na+" => 1.200 + 1.400,
"Cl-" => 1.700 + 1.400,
"MG" => 1.180 + 1.400,
);
Hope it helps
Angelo fro Nottingham
Varsha Goyal wrote:
>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
>
>__________________________________________________
>Do You Yahoo!?
>Tired of spam? Yahoo! Mail has the best spam protection around
>http://mail.yahoo.com
>-----------------------------------------------------------------------
>The AMBER Mail Reflector
>To post, send mail to amber.scripps.edu
>To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
>
>
>
This message has been checked for viruses but the contents of an attachment
may still contain software viruses, which could damage your computer system:
you are advised to perform your own checks. Email communications with the
University of Nottingham may be monitored as permitted by UK legislation.
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Sun Oct 29 2006 - 06:07:18 PST
