Use the LATEST release not Amber11 ... Make sure you have patched all the bug fixes and passed all tests before trying again.
Ray Luo, Ph.D.
On May 9, 2012, at 7:57 AM, Jyotsna Bhat <bhat.jyotsna.yahoo.com> wrote:
> Is there any solution for MMPBSA calculation of large proteins. I have 579 residues in my protein. Also zn ca ions are present in this protein
>
> --- On Wed, 5/9/12, Jyotsna Bhat <bhat.jyotsna.yahoo.com> wrote:
>
> From: Jyotsna Bhat <bhat.jyotsna.yahoo.com>
> Subject: Re: [AMBER] MMPBSA calculation of large proteins
> To: "AMBER Mailing List" <amber.ambermd.org>
> Date: Wednesday, May 9, 2012, 5:05 AM
>
> I tried with python scripts of Amber11 but I got the same error
>
> --- On Tue, 5/8/12, Ray Luo, Ph.D. <ray.luo.uci.edu> wrote:
>
> From: Ray Luo, Ph.D. <ray.luo.uci.edu>
> Subject: Re: [AMBER] MMPBSA calculation of large proteins
> To: "AMBER Mailing List" <amber.ambermd.org>
> Date: Tuesday, May 8, 2012, 4:39 PM
>
> It won't matter which sander did you use to simulate the system ...
> I'm keeping my fingers crossed, :).
>
> Ray
>
> On Tue, May 8, 2012 at 3:02 AM, Jyotsna Bhat <bhat.jyotsna.yahoo.com> wrote:
>>
>> To Ray Luo,
>>
>> I have used amber10 while simulation run, will it affect the binding energy result if I use mmpbsa python scripts installed with amber11 version. There may be different parameters applied in amber11 which will give different results with amber10 simulation systems
>>
>> --- On Mon, 5/7/12, Ray Luo, Ph.D. <ray.luo.uci.edu> wrote:
>>
>> From: Ray Luo, Ph.D. <ray.luo.uci.edu>
>> Subject: Re: [AMBER] MMPBSA calculation of large proteins
>> To: "AMBER Mailing List" <amber.ambermd.org>
>> Date: Monday, May 7, 2012, 5:15 PM
>>
>> Why not upgrade to the latest AmberTools? It's free and should resolve
>> the issue.
>>
>> All the best,
>> Ray
>>
>> Ray
>>
>> On Mon, May 7, 2012 at 9:31 AM, Jyotsna Bhat <bhat.jyotsna.yahoo.com> wrote:
>>> I have used Amber10 for MD run and further calculations. I am using perl scripts for mmpbsa.INPUT files
>>> for extraction of coordinates as follows:
>>> .GENERAL
>>> PREFIX snapshot
>>> PATH ./
>>> COMPLEX 1
>>> RECEPTOR 1
>>> LIGAND 1
>>> COMPT
>>> ../prmtop/complex_vac.prmtop
>>> RECPT ../prmtop/prot_vac.prmtop
>>> LIGPT ../prmtop/BIM.prmtop
>>> GC 1
>>> AS 0
>>> DC 0
>>> MM 0
>>> GB
>>> 0
>>> PB 0
>>> MS 0
>>> NM 0
>>> .MAKECRD
>>> BOX YES
>>> NTOTAL 9249
>>> NSTART 1
>>> NSTOP 999
>>> NFREQ
>>> 100
>>> NUMBER_LIG_GROUPS 1
>>> LSTART 9188
>>> LSTOP 9249
>>> NUMBER_REC_GROUPS 1
>>> RSTART 1
>>> RSTOP 9187
>>> .TRAJECTORY
>>> TRAJECTORY ../strip_mdcrd/2mBIM_nowat.mdcrd
>>> .PROGRAMS
>>> for binding energy calculation:
>>> .GENERAL
>>> PREFIX
>>> snapshot
>>> PATH ./
>>> #
>>> COMPLEX 1
>>> RECEPTOR 1
>>> LIGAND 1
>>> #
>>> COMPT ../prmtop/complex_vac.prmtop
>>> RECPT ../prmtop/prot_vac.prmtop
>>> LIGPT ../prmtop/BIM.prmtop
>>> #
>>> 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
>>> 0.0
>>> RADIOPT 0
>>> NPOPT 1
>>> CAVITY_SURFTEN 0.0072
>>> CAVITY_OFFSET 0.00
>>> #
>>> SURFTEN 0.0072
>>> SURFOFF 0.00
>>> #
>>> ################################################################################
>>> .MM
>>> DIELC 1.0
>>> .GB
>>> IGB 2
>>> GBSA 1
>>> SALTCON 0.00
>>> EXTDIEL 80.0
>>> INTDIEL
>>> 1.0
>>> #
>>> SURFTEN 0.0072
>>> SURFOFF 0.00
>>> #
>>> ################################################################################
>>> .MS
>>> PROBE 0.0
>>> .
>>> Extraction occurs with no problems but after running binding energy script it gives error as follows:
>>> /opt/amber10/exe/sander
>>> -O -i pbsa_com.in -o pbsa_com.1.out -c ./snapshot_com.crd.1 -p
>>> ../prmtop/complex_vac.prmtop not successful
>>>
>>> log file of binding energy calculation:
>>>
>>> =>> Init data
>>> Presuming executables of amber suite to be in /opt/amber10/exe
>>>
>>> =>> Reading input parameters
>>> Found PREFIX => snapshot
>>> Found PATH => ./
>>> Found COMPLEX => 1
>>> Found RECEPTOR => 1
>>> Found LIGAND => 1
>>> Found COMPT => ../prmtop/complex_vac.prmtop
>>> Found RECPT =>
>>> ../prmtop/prot_vac.prmtop
>>> Found LIGPT => ../prmtop/BIM.prmtop
>>> Found GC => 0
>>> Found AS => 0
>>> Found DC => 0
>>> Found MM => 1
>>> Found GB => 1
>>> Found PB => 1
>>> Found MS => 1
>>> Found NM => 0
>>> Found PROC => 2
>>> Found REFE => 0
>>> Found INDI => 1.0
>>> Found EXDI => 80.0
>>> Found SCALE => 2
>>> Found LINIT => 1000
>>> Found PRBRAD => 1.4
>>> Found ISTRNG => 0.0
>>> Found RADIOPT => 0
>>> Found NPOPT => 1
>>> Found CAVITY_SURFTEN => 0.0072
>>> Found CAVITY_OFFSET => 0.00
>>> Found
>>> SURFTEN => 0.0072
>>> Found SURFOFF => 0.00
>>> Found DIELC => 1.0
>>> Found IGB => 2
>>> Found GBSA => 1
>>> Found SALTCON => 0.00
>>> Found EXTDIEL => 80.0
>>> Found INTDIEL => 1.0
>>> Found SURFTEN => 0.0072
>>> Found SURFOFF => 0.00
>>> Found PROBE => 0.0
>>>
>>> =>> Checking sanity
>>> Checking GENERAL
>>> Setting START to default 1
>>> Setting STOP to default 10e10
>>> Setting OFFSET to default 1
>>> Setting VERBOSE to default 0
>>> Checking MM
>>> Checking PB
>>> Checking GB
>>> Checking MS
>>>
>>> =>> Creating input
>>> Sander
>>> input
>>> PBSA input
>>>
>>> =>> Calculating energy / entropy contributions
>>> Calc contrib for ./snapshot_com.crd.1
>>> Calc MM/GB/SAS
>>> Generate PDB
>>> Center PDB
>>> Calc PBSA
>>>
>>> pbsa_com.1.out:
>>>
>>> File Assignments:
>>> | MDIN: pbsa_com.in
>>> | MDOUT: pbsa_com.1.out
>>> |INPCRD:
>>> ./snapshot_com.crd.1
>>> | PARM: ../prmtop/complex_vac.prmtop
>>> |RESTRT:
>>> restrt
>>> | REFC: refc
>>> | MDVEL:
>>> mdvel
>>> | MDEN: mden
>>> | MDCRD:
>>> mdcrd
>>> |MDINFO: mdinfo
>>> |INPDIP:
>>> inpdip
>>> |RSTDIP: rstdip
>>>
>>>
>>> Here is the input file:
>>>
>>> File generated by mm_pbsa.pl. Using
>>> PB
>>> &cntrl
>>> ntf = 1, ntb =
>>> 0,
>>> igb = 10, dielc = 1.0,
>>> cut = 999.0, nsnb =
>>> 99999,
>>> scnb = 2.0, scee = 1.2,
>>> imin = 1, maxcyc = 0, ntmin = 2,
>>> ivcap =
>>> 0, cutcap = -1,
>>> xcap = 0, ycap = 0, zcap = 0
>>> idecomp=
>>> 0,
>>> &end
>>>
>>> &pb
>>> epsin = 1.0, epsout = 80.0,
>>> istrng = 0.0, radiopt =
>>> 0,
>>> sprob = 1.4, space = 0.5,
>>> maxitn = 1000, npopt = 1, dbfopt = 1,
>>> cavity_surften = 0.0072, fillratio = 4.00,
>>> cavity_offset = 0.00,
>>> npbverb= 1
>>> &end
>>>
>>>
>>> --------------------------------------------------------------------------------
>>> 1. RESOURCE USE:
>>> --------------------------------------------------------------------------------
>>>
>>> | Flags:
>>> | New format PARM file being parsed.
>>> | Version = 1.000 Date = 08/09/11 Time = 22:39:42
>>> NATOM = 9249 NTYPES = 18 NBONH = 4578 MBONA = 4783
>>> NTHETH =
>>> 10490 MTHETA = 6457 NPHIH = 19824 MPHIA = 15978
>>> NHPARM = 0 NPARM = 0 NNB = 51187 NRES = 579
>>> NBONA = 4783 NTHETA = 6457 NPHIA = 15978 NUMBND = 66
>>> NUMANG = 132 NPTRA = 49 NATYP = 47 NPHB = 0
>>> IFBOX = 0 NMXRS = 62 IFCAP = 0 NEXTRA = 0
>>> NCOPY = 0
>>>
>>> Implicit solvent radii are modified Bondi radii
>>> (mbondi)
>>>
>>> | Memory Use Allocated
>>> | Real 592745
>>> | Hollerith 56075
>>> | Integer 500704
>>> | Max Pairs 1
>>> | nblistReal
>>> 0
>>> | nblist Int 0
>>> | Total 6805 kbytes
>>> | Duplicated 0 dihedrals
>>> | Duplicated 0 dihedrals
>>>
>>> --------------------------------------------------------------------------------
>>> 2. CONTROL DATA FOR THE
>>> RUN
>>> --------------------------------------------------------------------------------
>>>
>>>
>>>
>>> General flags:
>>> imin = 1, nmropt = 0
>>>
>>> Nature and format of input:
>>> ntx = 1, irest = 0, ntrx
>>> = 1
>>>
>>> Nature and format of output:
>>> ntxo = 1, ntpr = 50, ntrx = 1, ntwr = 500
>>> iwrap = 0, ntwx = 0, ntwv = 0, ntwe = 0
>>> ioutfm = 0, ntwprt = 0, idecomp = 0, rbornstat= 0
>>>
>>> Potential function:
>>> ntf
>>> = 1, ntb = 0, igb = 10, nsnb = 99999
>>> ipol = 0, gbsa = 0, iesp = 0
>>> dielc = 1.00000, cut = 999.00000, intdiel = 1.00000
>>> scnb = 2.00000, scee = 1.20000
>>>
>>> Frozen or restrained atoms:
>>> ibelly = 0, ntr = 0
>>>
>>> Energy minimization:
>>> maxcyc
>>> = 0, ncyc = 10, ntmin = 2
>>> dx0 = 0.01000, drms = 0.00010
>>>
>>> ======== Implicit Solvent Initialization ========
>>>
>>> Max Nonbonded Pairs: 10405125 2247507 42772001
>>>
>>> no. of atoms processed in PB initialization: 9249
>>> NUM RESI NAME TYPE CHARGE ATM CRG/H GRP CRG PB RADI NP RADI
>>> 1 LYS N N3 0.096600 0.746100 0.862600 1.550000 1.550000
>>> 2 LYS H1 H 0.216500
>>> 0.000000 0.000000 1.300000 1.300000
>>> 3 LYS H2 H 0.216500 0.000000 0.000000 1.300000 1.300000
>>> 4 LYS H3 H 0.216500 0.000000 0.000000 1.300000 1.300000
>>> 5 LYS CA CT -0.001500 0.116500 1.661800 1.700000 1.700000
>>> 6 LYS HA HP 0.118000 0.000000 0.000000 1.300000 1.300000
>>> 7 LYS CB CT 0.021200 0.077800 0.213700 1.700000 1.700000
>>> 8 LYS HB2 HC 0.028300 0.000000
>>> 0.000000 1.300000 1.300000
>>> .
>>> .
>>> .
>>> 246 BIM C20 ca -0.101600 0.043300 -0.012800 1.700000 1.700000
>>> 9247 BIM H12 ha 0.144900 0.144900 0.144900 1.300000 1.300000
>>> 9248 BIM C21 ca -0.191300 -0.065000 -0.108300 1.700000 1.700000
>>> 9249 BIM H13 ha 0.126300 0.126300 0.126300 1.300000 1.300000
>>>
>>> total system charges (+/-) for PB -2.9998 1123.8366 -1126.8364
>>> cavity_surften = 0.0072 cavity_offset =
>>> 0.0000
>>>
>>> SAS Surface: surface dots generated: 366
>>> | INFO: Old style inpcrd file read
>>> --------------------------------------------------------------------------------
>>> 3. ATOMIC COORDINATES AND VELOCITIES
>>> --------------------------------------------------------------------------------
>>>
>>> trajectory generated by ptraj
>>> begin time read from input coords = 0.000 ps
>>>
>>> Number of triangulated 3-point waters found:
>>> 0
>>>
>>> --------------------------------------------------------------------------------
>>> 4. RESULTS
>>> --------------------------------------------------------------------------------
>>>
>>> NB-update: residue-based nb list 4087009
>>> NB-update: atom-based nb list 905095
>>>
>>>
>>> ======== Setting up Grid Parameters ========
>>> Using bounding box for grid setup
>>> Bounding Box Center: 67.500 73.000 67.500
>>> Xmin, Xmax, Xmax-Xmin: 20.518 114.427 93.909
>>> Ymin, Ymax, Ymax-Ymin: 17.394 128.517 111.123
>>> Zmin, Zmax, Zmax-Zmin: 26.562 108.482 81.920
>>> beginning box center at level 1
>>> 67.500 73.000 67.500
>>> beginning box center at level 2 67.500 73.000 67.500
>>> Grid dimension at level 1 95 113 83
>>> Grid origin corrected at level 1 -124.500 -155.000 -100.500
>>> Grid dimension at level 2 203 237 179
>>> Grid origin corrected at level 2 16.500 13.500 22.500
>>> SA surface: setting up working radii
>>> SA surface: found nonzero radii 9249
>>> Number of SA srf points exposed133796
>>> SA Bomb in sa_arc(): Allocation
>>> aborted 0 0 0
>>> 0 41
>>>
>>> I
>>> tried same process by removing calcium zinc ions which are present in
>>> respective system but error remains the same. I also tried considering
>>> ions as ligand, as receptor but no positive result. I also reduced the
>>> protein size by abducting regulatory domain and keeping only active
>>> domain but I could not form the neccessary topology files as removal of
>>> part of protein cause imbalance of hydrogens due to loss of peptide
>>> bond. tleap adds some extra hydrogens on its own but they are not
>>> present in original mdcrd trjectory file so i could not use such
>>> topology files for calculations.
>>>
>>> Than you so much for your consideration.
>>> Regards,
>>> Jyotsna
>>>
>>>
>>>
>>> --- On Mon, 5/7/12, Jason Swails <jason.swails.gmail.com> wrote:
>>>
>>> From: Jason Swails <jason.swails.gmail.com>
>>> Subject: Re: [AMBER] MMPBSA calculation of large proteins
>>> To: "AMBER Mailing List" <amber.ambermd.org>
>>> Date: Monday, May 7, 2012, 2:14 PM
>>>
>>> We need more information.
>>>
>>> What version of Amber/AmberTools are you using? Which MM/PBSA script are
>>> you using? What is your input file? What is your *exact* error (not just
>>> part of your error). Based on the provided information it's impossible to
>>> debug any further.
>>>
>>> All the best,
>>> Jason
>>>
>>> On Mon, May 7, 2012 at 2:58 AM, Jyotsna Bhat <bhat.jyotsna.yahoo.com> wrote:
>>>
>>>> Dear AMBER users,
>>>> I am trying to run MMPBSA script on 10 ns simulation trajectory.( My
>>>> protein-ligand complex system has 579 residues. It is a multidomain
>>>> protein; active domain and regulatory domain are situated far away from
>>>> each other, but linked by a large loop. Ligand is present in an active
>>>> domain). Extraction of coordinates is done successfully but during binding
>>>> energy calculation job gets aborted at first coordinate only with the error
>>>> "complex_vac.prmtop not successful".I have tried the adjustment with
>>>> fillratio (2,3 or 4) but it didn't help. Waiting for suggestions
>>>> Thank you.Jyotsna
>>>>
>>>> _______________________________________________
>>>> AMBER mailing list
>>>> AMBER.ambermd.org
>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>>
>>>
>>>
>>>
>>> --
>>> Jason M. Swails
>>> Quantum Theory Project,
>>> University of Florida
>>> Ph.D. Candidate
>>> 352-392-4032
>>> _______________________________________________
>>> 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
>>
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Received on Wed May 09 2012 - 10:00:03 PDT
