>
> 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.
>
> 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 - 17:00:02 PDT
