Yes, if you could send me directly the necessary files to run this
calculation on a few frames that result in this problem, I will look into it
further.
-Bill
On Thu, Aug 4, 2011 at 9:24 PM, belal najjar <belalnajjar.yahoo.com> wrote:
> 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
> _______________________________________________
> 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
_______________________________________________
AMBER mailing list
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Received on Sat Aug 06 2011 - 06:00:03 PDT
