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
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Received on Tue May 08 2012 - 03:30:03 PDT
