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
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Received on Tue May 08 2012 - 10:00:02 PDT
