Dear Bill,
Thank you for the information,
I have redo the calculation with keep_files=2. but I did not find any file called _MMPBSA_complex_entropy.out,
_MMPBSA_receptor_entropy.out, and _MMPBSA_ligand_entropy.out.
I only found _MMPBSA_ptraj_entropy.out , which contains:
\-/
-/- PTRAJ: a utility for processing trajectory files
/-\
\-/ Version: "AMBER 11.0 integrated" (4/2010)
-/- Executable is: "/opt/amber11p15/bin/ptraj"
/-\ Running on 1 processor(s)
\-/ Residue labels:
LYS HIE ILE CYX ALA ILE CYX GLY ASP ARG
SER SER GLY LYS HIE TYR GLY VAL TYR SER
CYX GLU GLY CYX LYS GLY PHE PHE LYS ARG
THR VAL ARG LYS ASP LEU THR TYR THR CYX
ARG ASP ASN LYS ASP CYX LEU ILE ASP LYS
ARG GLN ARG ASN ARG CYX GLN TYR CYX ARG
TYR GLN LYS CYX LEU ALA MET GLY MET LYS
ARG GLU ALA VAL GLN GLU GLU ARG GLN ARG
GLY LYS ASP ARG ASN GLU ASN GLU VAL GLU
SER THR SER SER ALA ASN GLU ASP MET PRO
VAL GLU ARG ILE LEU GLU ALA GLU LEU ALA
VAL GLU PRO LYS THR GLU THR TYR VAL GLU
ALA ASN MET GLY LEU ASN PRO SER SER PRO
ASN ASP PRO VAL THR ASN ILE CYX GLN ALA
ALA ASP LYS GLN LEU PHE THR LEU VAL GLU
TRP ALA LYS ARG ILE PRO HIE PHE SER GLU
LEU PRO LEU ASP ASP GLN VAL ILE LEU LEU
ARG ALA GLY TRP ASN GLU LEU LEU ILE ALA
SER PHE SER HIE ARG SER ILE ALA VAL LYS
ASP GLY ILE LEU LEU ALA THR GLY LEU HIE
VAL HIE ARG ASN SER ALA HIE SER ALA GLY
VAL GLY ALA ILE PHE ASP ARG VAL LEU THR
GLU LEU VAL SER LYS MET ARG ASP MET GLN
MET ASP LYS THR GLU LEU GLY CYX LEU ARG
ALA ILE VAL LEU PHE ASN PRO ASP SER LYS
GLY LEU SER ASN PRO ALA GLU VAL GLU ALA
LEU ARG GLU LYS VAL TYR ALA SER LEU GLU
ALA TYR CYX LYS HIE LYS TYR PRO GLU GLN
PRO GLY ARG PHE ALA LYS LEU LEU LEU ARG
LEU PRO ALA LEU ARG SER ILE GLY LEU LYS
CYX LEU GLU HIE LEU PHE PHE PHE LYS LEU
ILE GLY ASP THR PRO ILE ASP THR PHE LEU
MET GLU MET LEU GLU ALA PRO HIE GLN MET
THR ALA ILE GLU CYX ARG VAL CYX GLY ASP
LYS ALA SER GLY PHE HIE TYR GLY VAL HIE
ALA CYX GLU GLY CYX LYS GLY PHE PHE ARG
ARG THR ILE ARG LEU LYS LEU ILE TYR ASP
ARG CYX ASP LEU ASN CYX ARG ILE HIE LYS
LYS SER ARG ASN LYS CYX GLN TYR CYX ARG
PHE GLN LYS CYX LEU ALA VAL GLY MET SER
HIE ASN ALA ILE ARG PHE GLY ARG MET PRO
GLN ALA GLU LYS GLU LYS LEU LEU ALA GLU
ILE SER SER ASP ILE ASP GLN LEU ASN PRO
GLU SER ALA ASP LEU ARG ALA LEU ALA LYS
HIE LEU TYR ASP SER TYR ILE LYS SER PHE
PRO LEU THR LYS ALA LYS ALA ARG ALA ILE
LEU THR GLY LYS THR THR ASP LYS SER PRO
PHE VAL ILE TYR ASP MET ASN SER LEU MET
MET GLY GLU ASP LYS ILE LYS PHE LYS HIE
ILE THR PRO LEU GLN GLU GLN SER LYS GLU
VAL ALA ILE ARG ILE PHE GLN GLY CYX GLN
PHE ARG SER VAL GLU ALA VAL GLN GLU ILE
THR GLU TYR ALA LYS SER ILE PRO GLY PHE
VAL ASN LEU ASP LEU ASN ASP GLN VAL THR
LEU LEU LYS TYR GLY VAL HIE GLU ILE ILE
TYR THR MET LEU ALA SER LEU MET ASN LYS
ASP GLY VAL LEU ILE SER GLU GLY GLN GLY
PHE MET THR ARG GLU PHE LEU LYS SER LEU
ARG LYS PRO PHE GLY ASP PHE MET GLU PRO
LYS PHE GLU PHE ALA VAL LYS PHE ASN ALA
LEU GLU LEU ASP ASP SER ASP LEU ALA ILE
PHE ILE ALA VAL ILE ILE LEU SER GLY ASP
ARG PRO GLY LEU LEU ASN VAL LYS PRO ILE
GLU ASP ILE GLN ASP ASN LEU LEU GLN ALA
LEU GLU LEU GLN LEU LYS LEU ASN HIE PRO
GLU SER SER GLN LEU PHE ALA LYS LEU LEU
GLN LYS MET THR ASP LEU ARG GLN ILE VAL
THR GLU HIE VAL GLN LEU LEU GLN VAL ILE
LYS LYS THR GLU THR ASP MET SER LEU HIE
PRO LEU LEU GLN GLU ILE TYR LYS ASP LEU
TYR DC5 DA DA DA DC DT DA DG DG
DT DC DA DA DA DG DG DT DC DA
DG3 DC5 DT DG DA DC DC DT DT DT
DG DA DC DC DT DA DG DT DT DT
DG3 Zn Zn Zn Zn
PTRAJ: Processing input from file _MMPBSA_ptrajentropy.in
PTRAJ: trajin _MMPBSA_complex.mdcrd
Checking coordinates: _MMPBSA_complex.mdcrd
and the the input file "_MMPBSA_ptrajentropy.in" contains :
trajin _MMPBSA_complex.mdcrd
reference _MMPBSA_avgcomplex.pdb
rms mass reference :1-745
matrix mwcovar name comp.matrix :1-745
analyze matrix comp.matrix out _MMPBSA_complex_entropy.out thermo reduce
rms mass reference :1-331:744-745
matrix mwcovar name rec.matrix :1-331:744-745
analyze matrix rec.matrix out _MMPBSA_receptor_entropy.out thermo reduce
rms mass reference :332-743
matrix mwcovar name lig.matrix :332-743
analyze matrix lig.matrix out _MMPBSA_ligand_entropy.out thermo reduce
I still got Entropy value = 0
regards
________________________________
From: Bill Miller III <brmilleriii.gmail.com>
To: belal najjar <belalnajjar.yahoo.com>; AMBER Mailing List <amber.ambermd.org>
Sent: Tuesday, August 2, 2011 6:30 AM
Subject: Re: [AMBER] QUASI-HARMONIC APPROXIMATION
Were any GB of PB calculations performed? For the entropy calculations in
particular, you should check out the _MMPBSA_complex_entropy.out,
_MMPBSA_receptor_entropy.out, and _MMPBSA_ligand_entropy.out files. Those
files are the corresponding output files for the entropy calculation.
Ideally there will be helpful information in those files that would point to
the source of the problem.
-Bill
On Tue, Aug 2, 2011 at 12:25 AM, belal najjar <belalnajjar.yahoo.com> wrote:
> Hi all,
>
> I have done MD simulation using AMBER11. and now I am trying to calculate
> the Protein-Protein binding energy
> using MMPBSA method.
> Also i have enabled the entropy calculation (QUASI-HARMONIC APPROXIMATION).
> But unfortunately, the entropy values were zero. what was the problem?
> the command is:
> MMPBSA.MPI -O -i mmpbsa_2.in -o Apo_MMPBSA_19_DS.dat -sp
> complex_wat.prmtop -cp complex_nowat.prmtop -rp protein1_nowat.prmtop -lp
> protein2_nowat.prmtop -y
> ../../md19.mdcrd.gz > mmpbsa.log &
>
> the Input file and the results are:
>
> |Input file:
> |--------------------------------------------------------------
> |Input file for running PB and GB
> |&general
> | endframe=50, verbose=1, receptor_mask= :1-331:744-745,
> ligand_mask=:332-743, entropy=1,
> |/
> |&gb
> | igb=2, saltcon=0.100
> |/
> |&pb
> | istrng=0.100,
> |/
> |
> |--------------------------------------------------------------
> |Solvated complex topology file: complex_wat.prmtop
> |Complex topology file: complex_nowat.prmtop
> |Receptor topology file: protein1_nowat.prmtop
> |Ligand topology file: protein2_nowat.prmtop
> |Initial mdcrd(s): ../../md18.mdcrd.gz
> |
> |Best guess for receptor mask: ":1-331:744-745"
> |Best guess for ligand mask: ":332-743"
>
> |Calculations performed using 50 frames.
> |Poisson Boltzmann calculations performed using internal PBSA solver in
> sander.
> |
> |All units are reported in kcal/mole.
> |All entropy results have units kcal/mole (Temperature is 298.15 K).
>
> -------------------------------------------------------------------------------
>
> -------------------------------------------------------------------------------
> ENTROPY RESULTS (QUASI-HARMONIC APPROXIMATION) CALCULATED WITH PTRAJ:
>
> Translational Rotational Vibrational Total
> Complex: 0.0000 0.0000 0.0000 0.0000
>
> -------------------------------------------------------------------------------
>
> -------------------------------------------------------------------------------
>
> why it gave an Entropy = 0 ?
>
> I can provide the crd and prmtop files for you if it is necessary.
>
> thank u
>
> regards
> BELAL OMAR AL NAJJAR
> H/P: 0147462707
> Pharmaceutical Design and Simulation Lab (PhDS)
> Pharmaceutical Technology Department
> School of Pharmaceutical Sciences
> University of Science Malaysia
> Penang
> _______________________________________________
> 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 Aug 03 2011 - 18:30:02 PDT
