Dear Mr. Bill,
I visualized the complex using VMD, by uploading complex.prmtop and the _MMPBSA_complex.mdcrd files.
The structure looks OK with no errors or warnings.
do you need the files to check them?
thank you
________________________________
From: Bill Miller III <brmilleriii.gmail.com>
To: belal najjar <belalnajjar.yahoo.com>; AMBER Mailing List <amber.ambermd.org>
Sent: Friday, August 5, 2011 2:06 AM
Subject: Re: [AMBER] QUASI-HARMONIC APPROXIMATION
The calculation appears to be ending when ptraj is checking the trajectory
file _MMPBSA_complex.mdcrd made by MMPBSA.py It looks like something may be
wrong with trajectory _MMPBSA_complex.mdcrd. Have you visualized this
trajectory using your complex prmtop to make sure they are compatible?
-Bill
On Wed, Aug 3, 2011 at 9:16 PM, belal najjar <belalnajjar.yahoo.com> wrote:
> 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
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
> _______________________________________________
> 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 Thu Aug 04 2011 - 18:30:03 PDT
