While he BOND energy is concerning, I'd resolve the van der Waals term first
In my experience, when you see energies outside the display bounds *****.
BOND = 258342.4685 ANGLE = 1028.6606 DIHED = 3160.9109
VDWAALS = ************* <<<!!!
on step 1, the next geometry is exploded far away from the start coordinates (along the few bad contacts) - and things go from bad to worse for step 2.
Good luck.
Chris
On 4/9/2017 12:43 AM, Hai Nguyen wrote:
> 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 Sun Apr 09 2017 - 14:30:02 PDT
