Dear Mr Bill,
Thank you very much for your help.
I will try to solve this problem.
Kindest Regards
BELAL
________________________________
From: Bill Miller III <brmilleriii.gmail.com>
To: belal najjar <belalnajjar.yahoo.com>
Sent: Wednesday, August 10, 2011 10:59 PM
Subject: Re: [AMBER] QUASI-HARMONIC APPROXIMATION
Belal,
So I didn't initially realize how large your system was before I got your files. Entropy calculations are very memory intensive and you were running out of memory. Based on some test calculations I ran on your system you will need a minimum of 9-10 GB in order to run the quasi-harmonic entropy calculation. I was able to get it to work on a computer with 8 GB of memory and using ~1 GB of swap memory.
I hope that helps. Let me know if you have any other questions.
-Bill
On Mon, Aug 8, 2011 at 9:45 PM, belal najjar <belalnajjar.yahoo.com> wrote:
enclosed is the second part
>
>
>Regards
>BELAL
>
>
>
>________________________________
>From: belal najjar <belalnajjar.yahoo.com>
>To: Bill Miller III <brmilleriii.gmail.com>
>Sent: Monday, August 8, 2011 9:44 PM
>
>Subject: Re: [AMBER] QUASI-HARMONIC APPROXIMATION
>
>
>
>Dear Bill,
>sorry for late reply, I was trying to prepare the files for you.
>I separate the inputs into 2 email, because of the attachment size limits for the email.
>
>
>enclosed is the first part
>
>
>Regards
>BELAL
>
>
>
>________________________________
>From: Bill Miller III <brmilleriii.gmail.com>
>To: belal najjar <belalnajjar.yahoo.com>; AMBER Mailing List <amber.ambermd.org>
>Sent: Saturday, August 6, 2011 8:38 AM
>Subject: Re: [AMBER] QUASI-HARMONIC APPROXIMATION
>
>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
>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
Received on Wed Aug 10 2011 - 18:00:04 PDT
