On Sat, Apr 8, 2017 at 7:08 PM, Andreas Tosstorff <
andreas.tosstorff.cup.uni-muenchen.de> wrote:
>
> >
> > Hi all,
> >
> > I am having trouble with minimizing a structure I generated with MCPB.py.
> >
> > The minimization always fails after ncyc steps, apparently independently
> of what ncyc actually is and without any specific error message. I tried
> setting ntpr=1 but also here no specific error.
> >
> > I run the minimization with pmemd and sander. See below for an excerpt
> of the output. I tried sending it with the complete file attached but the
> mail bounced back.
> >
> >
>
> > I checked my structure with cpptraj check, and there are some close
> contacts, and a bond that is too long. However I was hoping to fix this by
> minimization. If required I can provide the topology and coordinates file.
>
Hi,
I think in this case, you need to see the WARNING from tleap about long
(usually incorrect) bond.
If the bond was created wrongly, don't mind about fixing by minimization at
all.
Hai
> >
> > I would really appreciate your help!
> >
> >
> > Best,
> >
> > Andy
> -------------------------------------------------------
> Amber 16 PMEMD 2016
> -------------------------------------------------------
>
> | PMEMD implementation of SANDER, Release 16
>
> | Run on 04/07/2017 at 12:53:51
>
> | Executable path: pmemd
> | Working directory: /state/partition2/home/local/
> andtos-loc/Dropbox/PhD/MCP/MCP_05
> | Hostname: kemi-steno.win.dtu.dk
>
> [-O]verwriting output
>
> File Assignments:
> | MDIN: min.in
> | MDOUT: fixed.HY133_solv_spc_min.out
> | INPCRD: fixed.restart.HY133_solv_spc.inpcrd
> | PARM: fixed.HY133_solv_spc.prmtop
> | RESTRT: fixed.HY133_solv_spc_min.rst
> | REFC: refc
> | MDVEL: mdvel
> | MDEN: mden
> | MDCRD: mdcrd
> | MDINFO: mdinfo
> | MDFRC: mdfrc
>
>
> Here is the input file:
>
>
> &cntrl
> imin=1, maxcyc=10000, ncyc=6000, ntpr=1,
> &end
>
>
> Note: ig = -1. Setting random seed to 409910 based on wallclock time in
> microseconds.
>
>
> | Conditional Compilation Defines Used:
> | PUBFFT
> | BINTRAJ
> | EMIL
>
> | Largest sphere to fit in unit cell has radius = 36.488
>
> | New format PARM file being parsed.
> | Version = 1.000 Date = 04/07/17 Time = 10:28:32
>
> | Note: 1-4 EEL scale factors are being read from the topology file.
>
> | Note: 1-4 VDW scale factors are being read from the topology file.
> | Duplicated 0 dihedrals
>
> | Duplicated 0 dihedrals
>
> ------------------------------------------------------------
> --------------------
> 1. RESOURCE USE:
> ------------------------------------------------------------
> --------------------
>
> getting new box info from bottom of inpcrd
> NATOM = 81317 NTYPES = 21 NBONH = 79101 MBONA = 2265
> NTHETH = 4859 MTHETA = 3097 NPHIH = 10115 MPHIA = 9652
> NHPARM = 0 NPARM = 0 NNB = 126684 NRES = 25954
> NBONA = 2265 NTHETA = 3097 NPHIA = 9652 NUMBND = 81
> NUMANG = 192 NPTRA = 191 NATYP = 46 NPHB = 1
> IFBOX = 1 NMXRS = 24 IFCAP = 0 NEXTRA = 0
> NCOPY = 0
>
> | Coordinate Index Table dimensions: 22 16 28
> | Direct force subcell size = 4.6501 4.5610 4.6290
>
> BOX TYPE: RECTILINEAR
>
> ------------------------------------------------------------
> --------------------
> 2. CONTROL DATA FOR THE RUN
> ------------------------------------------------------------
> --------------------
>
> default_name
>
> General flags:
> imin = 1, nmropt = 0
>
> Nature and format of input:
> ntx = 1, irest = 0, ntrx = 1
>
> Nature and format of output:
> ntxo = 2, ntpr = 1, ntrx = 1, ntwr =
> 1
> iwrap = 0, ntwx = 0, ntwv = 0, ntwe =
> 0
> ioutfm = 1, ntwprt = 0, idecomp = 0, rbornstat=
> 0
>
> Potential function:
> ntf = 1, ntb = 1, igb = 0, nsnb =
> 25
> ipol = 0, gbsa = 0, iesp = 0
> dielc = 1.00000, cut = 8.00000, intdiel = 1.00000
>
> Frozen or restrained atoms:
> ibelly = 0, ntr = 0
>
> Energy minimization:
> maxcyc = 10000, ncyc = 6000, ntmin = 1
> dx0 = 0.01000, drms = 0.00010
>
> | Intermolecular bonds treatment:
> | no_intermolecular_bonds = 1
>
> | Energy averages sample interval:
> | ene_avg_sampling = 1
>
> Ewald parameters:
> verbose = 0, ew_type = 0, nbflag = 1, use_pme =
> 1
> vdwmeth = 1, eedmeth = 1, netfrc = 0
> Box X = 102.302 Box Y = 72.976 Box Z = 129.612
> Alpha = 90.000 Beta = 90.000 Gamma = 90.000
> NFFT1 = 108 NFFT2 = 75 NFFT3 = 135
> Cutoff= 8.000 Tol =0.100E-04
> Ewald Coefficient = 0.34864
> Interpolation order = 4
>
> ------------------------------------------------------------
> --------------------
> 3. ATOMIC COORDINATES AND VELOCITIES
> ------------------------------------------------------------
> --------------------
>
> Cpptraj Generated Restart
> begin time read from input coords = 0.000 ps
>
>
> Number of triangulated 3-point waters found: 25653
>
> Sum of charges from parm topology file = -0.00002930
> Forcing neutrality...
>
> | Dynamic Memory, Types Used:
> | Reals 1914841
> | Integers 2157536
>
> | Nonbonded Pairs Initial Allocation: 13581971
>
> ------------------------------------------------------------
> --------------------
> 4. RESULTS
> ------------------------------------------------------------
> --------------------
>
> ---------------------------------------------------
> APPROXIMATING switch and d/dx switch using CUBIC SPLINE INTERPOLATION
> using 5000.0 points per unit in tabled values
> TESTING RELATIVE ERROR over r ranging from 0.0 to cutoff
> | CHECK switch(x): max rel err = 0.2738E-14 at 2.422500
> | CHECK d/dx switch(x): max rel err = 0.8332E-11 at 2.782960
> ---------------------------------------------------
> |---------------------------------------------------
> | APPROXIMATING direct energy using CUBIC SPLINE INTERPOLATION
> | with 50.0 points per unit in tabled values
> | Relative Error Limit not exceeded for r .gt. 2.47
> | APPROXIMATING direct force using CUBIC SPLINE INTERPOLATION
> | with 50.0 points per unit in tabled values
> | Relative Error Limit not exceeded for r .gt. 2.89
> |---------------------------------------------------
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 1 5.0426E+08 3.8287E+07 1.0554E+10 HA3 2568
>
> BOND = 258342.4685 ANGLE = 1028.6606 DIHED =
> 3160.9109
> VDWAALS = ************* EEL = -284621.7195 HBOND =
> 0.0000
> 1-4 VDW = 1565.2178 1-4 EEL = 13661.6160 RESTRAINT =
> 0.0000
>
> > --
> > M.Sc. Andreas Tosstorff
> > Lehrstuhl für Pharmazeutische Technologie und Biopharmazie
> > Department Pharmazie
> > LMU München
> > Butenandtstr. 5-13 ( Haus B)
> > 81377 München
> > Germany
> > Tel.: +49 89 2180 77059
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Received on Sat Apr 08 2017 - 23:00:02 PDT
