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
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Received on Wed Nov 03 2010 - 10:30:03 PDT
