AMBER Archive (2006)

Subject: Re: AMBER: mm_pbsa: binding energy calculation

From: Varsha Goyal (vgusp_at_yahoo.ca)
Date: Sat Oct 28 2006 - 16:41:02 CDT

Thanks Angelo,
It solved my problem but now when I am running
binding_energy.mmpbsa evertime it causes some problem
with my ligand file.
Error looks like this:

/usr/local/amber8/exe/pbsa -O -i pbsa.in -o
pbsa_lig.1.out -c ./extract_coord/snapshot_lig.crd.1
-p ./prmtop.ets not successful

I am not sure where should I look because when I look
at the structure for this trajectory in VMd it looks
fine to me.
Can you or someone else please suggest solution to
this problem?

Thanks in advance,
Varsha

--- Angelo <angelo_at_holmes.cancres.nottingham.ac.uk>
wrote:

> 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
> >
> >__________________________________________________
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>
=== message truncated ===

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