Re: [AMBER] MMPBSA

From: Daniel Roe <daniel.r.roe.gmail.com>
Date: Thu, 18 Sep 2014 13:19:23 -0600

Amber 9 is very old at this point. I recommend you upgrade to
AmberTools 14 (http://ambermd.org/AmberTools14-get.html), which is
freely available and includes everything except pmemd/pmemd.cuda.

-Dan

On Thu, Sep 18, 2014 at 12:39 PM, Asfa Ali <asfa.iisc.gmail.com> wrote:
> No Sir, it is Amber 9.
>
> On Fri, Sep 19, 2014 at 12:02 AM, Ray Luo, Ph.D. <ray.luo.uci.edu> wrote:
>
>> Is this from using Amber14?
>>
>> Ray
>> --
>> Ray Luo, Ph.D.
>> Professor,
>> Biochemistry, Molecular Biophysics, Chemical Physics,
>> Chemical and Biomedical Engineering
>> University of California, Irvine, CA 92697-3900
>>
>>
>> On Thu, Sep 18, 2014 at 11:26 AM, Asfa Ali <asfa.iisc.gmail.com> wrote:
>> > Yes, the message in pbsa_lig.77.out also indicates about fillratio.
>> > How to go about this and where exactly should I include the fillratio?
>> >
>> > Here is the out file:
>> >
>> > pbsa_lig.77.out
>> >
>> > -------------------------------------------------------
>> > Amber 9 PBSA Scripps/UCSF 2006
>> > -------------------------------------------------------
>> >
>> > | Run on 09/18/2014 at 19:20:32
>> > [-O]verwriting output
>> >
>> > File Assignments:
>> > | MDIN: pbsa.in
>> >
>> > | MDOUT:
>> > pbsa_lig.77.out
>> > |INPCRD:
>> > ./snapshot_lig.crd.77
>> > | PARM:
>> > ./lig_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,
>> > &end
>> >
>> > &pb
>> >
>> > epsin = 1.0, epsout =
>> > 80.0,
>> > istrng = 0, radiopt =
>> > 0,
>> > sprob = 1.4, space =
>> > 0.5,
>> > maxitn = 1000, npopt =
>> > 1,
>> > cavity_surften = 0.0072, cavity_offset =
>> > 0.00,
>> > npbverb=
>> > 1
>> > &end
>> >
>> >
>> >
>> --------------------------------------------------------------------------------
>> > 1. RESOURCE USE:
>> >
>> --------------------------------------------------------------------------------
>> >
>> > |
>> > Flags:
>> >
>> > | New format PARM file being parsed.
>> > | Version = 1.000 Date = 05/25/10 Time = 12:37:34
>> > NATOM = 90 NTYPES = 7 NBONH = 38 MBONA = 60
>> > NTHETH = 76 MTHETA = 88 NPHIH = 142 MPHIA = 144
>> > NHPARM = 0 NPARM = 0 NNB = 486 NRES = 1
>> > NBONA = 60 NTHETA = 88 NPHIA = 144 NUMBND = 19
>> > NUMANG = 36 NPTRA = 9 NATYP = 11 NPHB = 0
>> > IFBOX = 0 NMXRS = 90 IFCAP = 0 NEXTRA = 0
>> > NCOPY = 0
>> >
>> >
>> > | Memory Use Allocated
>> > | Real 3395
>> > | Hollerith 543
>> > | Integer 24315
>> > | Max Pairs 1
>> > | Max Rstack 1
>> > | Max Istack 1
>> > | Total 123 kbytes
>> > | Duplicated 0 dihedrals
>> > | Duplicated 0 dihedrals
>> >
>> >
>> --------------------------------------------------------------------------------
>> > 2. CONTROL DATA FOR THE RUN
>> >
>> --------------------------------------------------------------------------------
>> >
>> > LIG
>> >
>> >
>> > 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: 4051 4051 4051
>> >
>> > no. of atoms processed in PB initialization: 90
>> > NUM RESI NAME TYPE CHARGE ATM CRG/H GRP CRG PB RADI NP RADI
>> > 1 LIG C cc -0.123000 0.044000 0.045000 1.700000 1.700000
>> > 2 LIG C1 cd -0.257600 -0.091600 0.468300 1.700000 1.700000
>> > 3 LIG C2 cd 0.515900 0.515900 -0.394800 1.700000 1.700000
>> > 4 LIG N nc -0.619300 -0.619300 -0.010800 1.550000 1.550000
>> > 5 LIG C3 cf 0.081600 0.081600 0.135300 1.700000 1.700000
>> > 6 LIG C4 cc 0.092600 0.092600 -0.401100 1.700000 1.700000
>> > 7 LIG C5 cd -0.086100 -0.086100 0.268100 1.700000 1.700000
>> > 8 LIG C6 cc -0.146000 0.019000 -0.048100 1.700000 1.700000
>> > 9 LIG N1 na -0.089100 0.253600 0.081400 1.550000 1.550000
>> > 10 LIG C7 cc -0.146000 0.019000 -0.048100 1.700000 1.700000
>> > 11 LIG C8 cd -0.086100 -0.086100 0.268100 1.700000 1.700000
>> > 12 LIG H hn 0.342700 0.342700 0.342700 1.300000 1.300000
>> > 13 LIG C9 cf 0.081600 0.081600 0.135300 1.700000 1.700000
>> > 14 LIG C10 cc 0.092600 0.092600 -0.401100 1.700000 1.700000
>> > 15 LIG C11 cc -0.123000 0.044000 0.045000 1.700000 1.700000
>> > 16 LIG N2 nc -0.619300 -0.619300 -0.010800 1.550000 1.550000
>> > 17 LIG C12 cd -0.257600 -0.091600 0.468300 1.700000 1.700000
>> > 18 LIG C13 cd 0.515900 0.515900 -0.394800 1.700000 1.700000
>> > 19 LIG C14 cf -0.199800 -0.199800 0.508000 1.700000 1.700000
>> > 20 LIG C15 cd 0.098900 0.098900 0.081700 1.700000 1.700000
>> > 21 LIG C16 cc -0.123000 0.058000 0.214900 1.700000 1.700000
>> > 22 LIG N3 na -0.229100 0.124600 0.322400 1.550000 1.550000
>> > 23 LIG C17 cc -0.123000 0.058000 0.214900 1.700000 1.700000
>> > 24 LIG C18 cd 0.098900 0.098900 0.081700 1.700000 1.700000
>> > 25 LIG H1 hn 0.353700 0.353700 0.353700 1.300000 1.300000
>> > 26 LIG C19 cf -0.199800 -0.199800 0.508000 1.700000 1.700000
>> > 27 LIG C20 ca 0.047200 0.047200 0.277800 1.700000 1.700000
>> > 28 LIG C21 ca -0.131000 0.075000 0.324900 1.700000 1.700000
>> > 29 LIG C22 ca -0.023300 0.202700 0.325600 1.700000 1.700000
>> > 30 LIG N4 na 0.047900 0.047900 0.755000 1.550000 1.550000
>> > 31 LIG C23 ca -0.023300 0.201700 0.323600 1.700000 1.700000
>> > 32 LIG C24 c3 -0.042400 0.302700 0.350600 1.700000 1.700000
>> > 33 LIG C25 ca -0.132000 0.074000 0.322900 1.700000 1.700000
>> > 34 LIG C26 cc 0.093000 0.093000 0.000200 1.700000 1.700000
>> > 35 LIG C27 cc -0.143000 0.059000 0.459000 1.700000 1.700000
>> > 36 LIG C28 cd 0.084000 0.307000 0.018800 1.700000 1.700000
>> > 37 LIG N5 na -0.347200 -0.347200 0.748000 1.550000 1.550000
>> > 38 LIG C29 cd 0.087000 0.310000 0.010800 1.700000 1.700000
>> > 39 LIG C30 c3 0.137100 0.478200 0.131000 1.700000 1.700000
>> > 40 LIG C31 cc -0.151000 0.048000 0.451000 1.700000 1.700000
>> > 41 LIG C32 ca 0.047200 0.047200 0.277800 1.700000 1.700000
>> > 42 LIG C33 ca -0.131000 0.075000 0.324900 1.700000 1.700000
>> > 43 LIG C34 ca -0.023300 0.202700 0.325600 1.700000 1.700000
>> > 44 LIG N6 na 0.047900 0.047900 0.755000 1.550000 1.550000
>> > 45 LIG C35 ca -0.023300 0.201700 0.323600 1.700000 1.700000
>> > 46 LIG C36 c3 -0.042400 0.302700 0.350600 1.700000 1.700000
>> > 47 LIG C37 ca -0.132000 0.074000 0.322900 1.700000 1.700000
>> > 48 LIG C38 cc 0.093000 0.093000 0.000200 1.700000 1.700000
>> > 49 LIG C39 cc -0.151000 0.048000 0.451000 1.700000 1.700000
>> > 50 LIG C40 cd 0.087000 0.310000 0.010800 1.700000 1.700000
>> > 51 LIG N7 na -0.347200 -0.347200 0.748000 1.550000 1.550000
>> > 52 LIG C41 cd 0.084000 0.307000 0.018800 1.700000 1.700000
>> > 53 LIG C42 c3 0.137100 0.478200 0.131000 1.700000 1.700000
>> > 54 LIG C43 cc -0.143000 0.059000 0.459000 1.700000 1.700000
>> > 55 LIG H2 ha 0.167000 0.167000 0.167000 1.300000 1.300000
>> > 56 LIG H3 ha 0.166000 0.166000 0.166000 1.300000 1.300000
>> > 57 LIG H4 ha 0.165000 0.165000 0.165000 1.300000 1.300000
>> > 58 LIG H5 ha 0.165000 0.165000 0.165000 1.300000 1.300000
>> > 59 LIG H6 ha 0.167000 0.167000 0.167000 1.300000 1.300000
>> > 60 LIG H7 ha 0.166000 0.166000 0.166000 1.300000 1.300000
>> > 61 LIG H8 ha 0.181000 0.181000 0.181000 1.300000 1.300000
>> > 62 LIG H9 ha 0.181000 0.181000 0.181000 1.300000 1.300000
>> > 63 LIG H10 ha 0.206000 0.206000 0.206000 1.300000 1.300000
>> > 64 LIG H11 h4 0.226000 0.226000 0.226000 1.300000 1.300000
>> > 65 LIG H12 h4 0.225000 0.225000 0.225000 1.300000 1.300000
>> > 66 LIG H13 h1 0.114700 0.114700 0.114700 1.300000 1.300000
>> > 67 LIG H14 h1 0.115700 0.115700 0.115700 1.300000 1.300000
>> > 68 LIG H15 h1 0.114700 0.114700 0.114700 1.300000 1.300000
>> > 69 LIG H16 ha 0.206000 0.206000 0.206000 1.300000 1.300000
>> > 70 LIG H17 ha 0.202000 0.202000 0.202000 1.300000 1.300000
>> > 71 LIG H18 h4 0.223000 0.223000 0.223000 1.300000 1.300000
>> > 72 LIG H19 h4 0.223000 0.223000 0.223000 1.300000 1.300000
>> > 73 LIG H20 h1 0.113700 0.113700 0.113700 1.300000 1.300000
>> > 74 LIG H21 h1 0.114700 0.114700 0.114700 1.300000 1.300000
>> > 75 LIG H22 h1 0.112700 0.112700 0.112700 1.300000 1.300000
>> > 76 LIG H23 ha 0.199000 0.199000 0.199000 1.300000 1.300000
>> > 77 LIG H24 ha 0.206000 0.206000 0.206000 1.300000 1.300000
>> > 78 LIG H25 h4 0.226000 0.226000 0.226000 1.300000 1.300000
>> > 79 LIG H26 h4 0.225000 0.225000 0.225000 1.300000 1.300000
>> > 80 LIG H27 h1 0.114700 0.114700 0.114700 1.300000 1.300000
>> > 81 LIG H28 h1 0.115700 0.115700 0.115700 1.300000 1.300000
>> > 82 LIG H29 h1 0.114700 0.114700 0.114700 1.300000 1.300000
>> > 83 LIG H30 ha 0.206000 0.206000 0.206000 1.300000 1.300000
>> > 84 LIG H31 ha 0.199000 0.199000 0.199000 1.300000 1.300000
>> > 85 LIG H32 h4 0.223000 0.223000 0.223000 1.300000 1.300000
>> > 86 LIG H33 h4 0.223000 0.223000 0.223000 1.300000 1.300000
>> > 87 LIG H34 h1 0.113700 0.113700 0.113700 1.300000 1.300000
>> > 88 LIG H35 h1 0.114700 0.114700 0.114700 1.300000 1.300000
>> > 89 LIG H36 h1 0.112700 0.112700 0.112700 1.300000 1.300000
>> > 90 LIG H37 ha 0.202000 0.202000 0.202000 1.300000 1.300000
>> >
>> > total system charges (+/-) for PB 4.0030 9.4172
>> -5.4142
>> > cavity_surften = 0.0072 cavity_offset = 0.0000
>> >
>> > SAS Surface: surface dots generated: 366
>> >
>> >
>> --------------------------------------------------------------------------------
>> > 3. ATOMIC COORDINATES AND VELOCITIES
>> >
>> --------------------------------------------------------------------------------
>> >
>> >
>> >
>> > 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 3535
>> > NB-update: atom-based nb list 2292
>> >
>> >
>> > ======== Setting up Grid Parameters ========
>> > Using bounding box for grid setup
>> > Bounding Box Center: 64.000 43.000 18.000
>> > Xmin, Xmax, Xmax-Xmin: 59.729 68.710 8.981
>> > Ymin, Ymax, Ymax-Ymin: 32.255 53.504 21.249
>> > Zmin, Zmax, Zmax-Zmin: 7.106 28.945 21.839
>> > beginning box center at level 1 64.000 43.000 18.000
>> > beginning box center at level 2 64.000 43.000 18.000
>> > Grid dimension at level 1 5 13 13
>> > Grid origin corrected at level 1 52.000 15.000 -10.000
>> > Grid dimension at level 2 33 57 59
>> > Grid origin corrected at level 2 55.500 28.500 3.000
>> > PB Bomb in setgrd(): focusing grid too large 2
>> > reset fillratio to a larger number 2.000
>> >
>> > On Thu, Sep 18, 2014 at 8:12 PM, Jason Swails <jason.swails.gmail.com>
>> > wrote:
>> >
>> >> On Thu, 2014-09-18 at 19:40 +0530, Asfa Ali wrote:
>> >> > Hi,
>> >> >
>> >> > While running mm_pbsa.pl of a ligand-dna complex, I got the following
>> >> error
>> >> > message:
>> >> >
>> >> > /data/software/amber91/exe/pbsa -O -i pbsa.in -o pbsa_lig.77.out -c
>> >> > ./snapshot_lig.crd.77 -p ./lig_vac.prmtop not successful
>> >> >
>> >> > The snapshot_com.all.out and snapshot_rec.all.out are fine, only in
>> the
>> >> > case of lig, it is stopping at 77.
>> >> >
>> >> > I checked the ambermailing list and added the line "fillratio = 4.0"
>> in
>> >> the
>> >> > pbsa.in file generated but still the error persists.
>> >>
>> >> Look for the error message inside pbsa_lig.77.out. Try using that error
>> >> message as a starting point for an online search.
>> >>
>> >> HTH,
>> >> Jason
>> >>
>> >> --
>> >> Jason M. Swails
>> >> BioMaPS,
>> >> Rutgers University
>> >> Postdoctoral Researcher
>> >>
>> >>
>> >> _______________________________________________
>> >> AMBER mailing list
>> >> AMBER.ambermd.org
>> >> http://lists.ambermd.org/mailman/listinfo/amber
>> >>
>> >
>> >
>> >
>> > --
>> > Asfa Ali
>> > Prof. S. Bhattacharya's group,
>> > Dept. of Organic Chemistry,
>> > Indian Institute of Science,
>> > Bangalore-12
>> > _______________________________________________
>> > 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
>>
>
>
>
> --
> Asfa Ali
> Prof. S. Bhattacharya's group,
> Dept. of Organic Chemistry,
> Indian Institute of Science,
> Bangalore-12
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber



-- 
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Thu Sep 18 2014 - 12:30:04 PDT
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