AMBER Archive (2009)

Subject: [AMBER] MMPBSA: No radius found for F

From: Jeff Yeo (weekiang_at_live.com)
Date: Sun Oct 04 2009 - 19:10:12 CDT

Hi,

I attempted to run mm-pbsa.pl

But it complains that "No radius found for F1 4424 in residue TOG 278"
 
Is it true that including the following line during the tleap session before the production run will avoid this problem?
set default PBradii bondi

Also, since the mm_pbsa_calceneent.pm file is located in a folder in which I do not have write access, how do I add the radius parameter for F ("F" => 1.470 + 1.400)?

The output file is pasted below:

=>> Init data
Presuming executables of amber suite to be in /app1/linux/amber10/exe
=>> Reading input parameters
Found PREFIX => snapshot
Found PATH => ./
Found COMPLEX => 1
Found RECEPTOR => 1
Found LIGAND => 1
Found COMPT => ./protein-ligand-complex.top
Found RECPT => ./protein-apo.top
Found LIGPT => ./ligand.top
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
=>> Checking sanity
Checking GENERAL
Setting START to default 1
Setting STOP to default 10e10
Setting OFFSET to default 1
Setting VERBOSE to default 0
Checking MM
Checking PB
Checking GB
Checking MS
=>> Creating input
Sander input
PBSA input
=>> Calculating energy / entropy contributions
Calc contrib for ./snapshot_com.crd.1
Calc MM/GB/SAS
Generate PDB
Center PDB
Calc PBSA
Generate PQR
No radius found for F1 4424 in residue TOG 278
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