Bill,
I fixed the problem in one section - calculation of binding energy -
but now I am encountering a new one.
I would like to conduct a energy decomposition in mm_pbsa of amber11
using the input pasted below.
But the program quits with a message:
bad atom type: Zn
/share/apps/amber11/bin/sander -O -i sander_com.in -o
sander_com.1.out -
c ../01_GenerateSnapshots/phd_dpfh3_com.crd.1 -p ../phd_dpfh3_anal.top
not succe
ssful
For details see: http://ambermd.org/Questions/mm_pbsa.html#mmgbsas_comma
nd_not_successful
Where should I introduce this atom type for the calculation?
Thanks for your help.
Rami
#
# Input parameters for mm_pbsa.pl
#
# Holger Gohlke
# 25.02.2010
#
################################################################################
.GENERAL
#
VERBOSE 0
PARALLEL 0
#
PREFIX phd_dpfh3
PATH ../01_GenerateSnapshots/
START 1
STOP 10
OFFSET 1
#
COMPLEX 1
RECEPTOR 1
LIGAND 1
#
COMPT ../phd_dpfh3_anal.top
RECPT ../phd_anal.top
LIGPT ../h3_anal.top
#
GC 0
AS 0
DC 1
#
MM 1
GB 1
PB 1
MS 0
#
NM 0
#
################################################################################
.DECOMP
#
DCTYPE 2
#
COMREC 21-138
COMLIG 1-20
COMPRI 1-138
RECRES 1-118
RECPRI 1-118
RECMAP 21-138
LIGRES 1-20
LIGPRI 1-20
LIGMAP 1-20
################################################################################
.PB
#
PROC 2
REFE 0
INDI 1.0
EXDI 80.0
SCALE 2
LINIT 1000
PRBRAD 1.4
ISTRNG 150.0
RADIOPT 1
INP 0
#
SURFTEN 0.04356
SURFOFF -1.008
#
IVCAP 0
CUTCAP -1.0
XCAP 0.0
YCAP 0.0
ZCAP 0.0
#
################################################################################
.MM
#
DIELC 1.0
#
################################################################################
.GB
#
IGB 5
GBSA 2
SALTCON 0.15
EXTDIEL 80.0
INTDIEL 1.0
#
SURFTEN 0.0072
SURFOFF 0.00
#
################################################################################
.PROGRAMS
#
# Additional program executables can be defined here
#
#
################################################################################
On Nov 3, 2010, at 1:02 PM, Bill Miller III wrote:
> Zn is not a pre-defined atom using mm_pbsa.pl. You will need to
> define the
> parameters for Zn atom in $AMBERHOME/src/mm_pbsa/
> mm_pbsa_calceneent.pm and
> then re-compile mm_pbsa.
>
> Good luck!
>
> -Bill
>
> On Wed, Nov 3, 2010 at 12:17 PM, Roman Osman <roman.osman.mssm.edu>
> wrote:
>
>> To Amber List
>> I would like to calculate the binding energy of a peptide to a
>> protein
>> that contains 4 Zn atoms. I have constructed the corresponding
>> topologies of the complex, receptor (both with Zn ions) and the
>> ligand. I am using the amber11 version of mm_pbsa.pl and I am
>> enclosing the input below:
>> I have set RADIOPT 0 and INP 1 according to the instructions to read
>> the radii from the topology file. I checked - they are there.
>> However the program reaches the point of creating a pqr file and
>> stops
>> at the first Zn atom because it cannot find the radius:
>> =>> Calculating energy / entropy contributions
>> Calc contrib for ../01_GenerateSnapshots/phd_dpf3_com.crd.1
>> Checking atom numbers
>> Calc MM/GB/SAS
>> Generate PDB
>> Center PDB
>> Calc PBSA
>> Generate PQR
>> No radius found for Zn 2019 in residue ZNB 135
>> I would be grateful if anyone knows how to fix this problem.
>> Thanks,
>> Rami
>>
>> Here is the mm_pbsa.in
>> # Input parameters for mm_pbsa.pl
>> #
>> # Holger Gohlke
>> # 25.02.2010
>> #
>>
>> ################################################################################
>> .GENERAL
>> #
>> VERBOSE 0
>> PARALLEL 0
>> #
>> PREFIX phd_dpf3
>> PATH ../01_GenerateSnapshots/
>> START 1
>> STOP 10
>> OFFSET 1
>> #
>> COMPLEX 1
>> RECEPTOR 1
>> LIGAND 1
>> #
>> COMPT ../phd_dpf3_anal.top
>> RECPT ../phd_anal.top
>> LIGPT ../h3k14_anal.top
>> #
>> GC 0
>> AS 0
>> DC 0
>> #
>> MM 1
>> GB 1
>> PB 1
>> MS 1
>> #
>> NM 0
>> #
>>
>> ################################################################################
>> .PB
>> #
>> PROC 2
>> REFE 0
>> INDI 1.0
>> EXDI 80.0
>> SCALE 2
>> LINIT 1000
>> PRBRAD 1.4
>> ISTRNG 150
>> RADIOPT 0
>> INP 1
>> #
>> SURFTEN 0.00542
>> SURFOFF 0.9200
>> #
>> IVCAP 0
>> CUTCAP -1.0
>> XCAP 0.0
>> YCAP 0.0
>> ZCAP 0.0
>> #
>>
>> ################################################################################
>> .MM
>> #
>> DIELC 1.0
>> #
>>
>> ################################################################################
>> .GB
>> #
>> IGB 5
>> GBSA 1
>> SALTCON 0.15
>> EXTDIEL 80.0
>> INTDIEL 1.0
>> #
>> SURFTEN 0.0072
>> SURFOFF 0.00
>> #
>>
>> ################################################################################
>> .MS
>> #
>> PROBE 0.0
>> #
>>
>> ################################################################################
>> Roman Osman
>> roman.osman.mssm.edu
>>
>>
>>
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
>
> --
> Bill Miller III
> Quantum Theory Project,
> University of Florida
> Ph.D. Graduate Student
> 352-392-6715
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
Roman Osman
roman.osman.mssm.edu
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Received on Mon Nov 08 2010 - 20:30:01 PST
