Hi,
Visualize your structure using VMD or Tleap.
Maybe the unusually long bond is the primary reason for sander to fail.
Is that bond necessary or some artefact??
Best Regards
Elvis Martis
Ph.D. Student (Computational Chemistry)
at Bombay College of Pharmacy
A Kalina, Santacruz [E], Mumbai 400098, INDIA
W www.elvismartis.in
Skype. adrian_elvis12
-----Original Message-----
From: Andreas Tosstorff [mailto:andreas.tosstorff.cup.uni-muenchen.de]
Sent: Sunday, April 09, 2017 4:39 AM
To: amber.ambermd.org
Subject: [AMBER] Minimization fails when switching from steepest descent to conjugate gradient
>
> 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 - 22:30:03 PDT
