[CP2K:109] Re: psf problems
Jadzia
c.gor... at gmail.com
Mon Jan 1 14:18:10 UTC 2018
Happy new year to everyone,
I have a closely related problem to the one above. I get the error message:
> FORCEFIELD| Missing Angle (NG2R,CG2R,OG2R)
> FORCEFIELD| Missing Angle (CG2R,CG2R,OG2R)
> FORCEFIELD| Missing Angle (OG2R,CG2R,HGR5)
>
> *******************************************************************************
> * ___
> *
> * / \
> *
> * [ABORT]
> *
> * \___/ Missing critical ForceField parameters!
> *
> * |
> *
> * O/|
> *
> * /| |
> *
> * / \
> force_fields_util.F:387 *
>
> *******************************************************************************
But in my PSF file I do not have any atoms of the type these types (e.g.
NG2R), only longer types (e.g. NG2R50). These are the default CGenFF atom
types.
PSF
1 !NTITLE
REMARKS VMD-generated NAMD/X-Plor PSF structure file
1821 !NATOM
1 LIG 1 LIG N1Q NG2S1 -0.495000 14.0067
0
2 LIG 1 LIG C1Q CG2O1 0.464000 12.0107
0
3 LIG 1 LIG O1Q OG2D1 -0.509000 15.9994
0
4 LIG 1 LIG C2Q CG331 -0.269000 12.0107
0
5 LIG 1 LIG C3Q CG311 0.150000 12.0107
0
6 LIG 1 LIG C4Q CG2R61 0.005000 12.0107
0
7 LIG 1 LIG C5Q CG2R61 -0.111000 12.0107
0
8 LIG 1 LIG C6Q CG2R61 -0.114000 12.0107
0
9 LIG 1 LIG C7Q CG2R67 -0.004000 12.0107
0
10 LIG 1 LIG C8Q CG2R61 -0.114000 12.0107
0
11 LIG 1 LIG C9Q CG2R61 -0.111000 12.0107
0
12 LIG 1 LIG C10Q CG2R67 -0.004000 12.0107
0
13 LIG 1 LIG C11Q CG2R61 -0.114000 12.0107
0
14 LIG 1 LIG C12Q CG2R61 -0.114000 12.0107
0
15 LIG 1 LIG C13Q CG2R61 -0.115000 12.0107
0
16 LIG 1 LIG C14Q CG2R61 -0.114000 12.0107
0
17 LIG 1 LIG C15Q CG2R61 -0.114000 12.0107
0
18 LIG 1 LIG C16Q CG321 -0.136000 12.0107
0
19 LIG 1 LIG S1Q SG311 -0.076000 32.0650
0
20 LIG 1 LIG C17Q CG2R53 0.562000 12.0107
0
21 LIG 1 LIG N2Q NG2R50 -0.355000 14.0067
0
22 LIG 1 LIG N3Q NG2R50 -0.249000 14.0067
0
23 LIG 1 LIG C18Q CG2R57 0.545000 12.0107
0
24 LIG 1 LIG O2Q OG2R50 -0.465000 15.9994
0
25 LIG 1 LIG C19Q CG2R57 0.247000 12.0107
0
26 LIG 1 LIG C20Q CG2R51 -0.179000 12.0107
0
27 LIG 1 LIG C21Q CG2R51 -0.276000 12.0107
0
And for all atom types I do have parameters in the prm file.
I have already tried to shift the position of the columns, in vain. In the
cp2k input file I have specified: CONN_FILE_FORMAT upsf
Any help is highly appreciated. I use cp2k version 5.1.
Thank you very much,
Jadzia
On Friday, June 1, 2007 at 4:59:26 PM UTC+2, Teo wrote:
>
> Thanks for the files Toon,
>
> it needs a COORD section mostly because the conversion to the new
> input was not fully
> completed for the MC module.
>
> Teo
> On 1 Jun 2007, at 15:18, Toon wrote:
>
> >
> > My apologies for the inconveinience. This is a more complete
> > description of the problem: I'm now running a cp2k compilation checked
> > out this morning. I have a problem that seems to be related to these
> > two input lines:
> >
> > COORDINATE XYZ
> > COORD_FILE_NAME geometry.xyz
> >
> > The error given by cp2k looks like this:
> >
> > ...
> > MC| The moves will not be biased,
> > MC| A full energy calculation will be done at every step.
> > MC| 4 swap insertions will be attempted per molecular swap move
> >
> > File name mc.inp
> >
> >
> > ************************************************
> > *** ERROR in mc_types.F/mc_input_file_create ***
> > ************************************************
> >
> > *** Could not find &END after &COORD (make sure & is the first in the
> > ***
> > *** same column after &COORD)
> > ***
> >
> >
> > ===== Routine Calling Stack =====
> >
> > 1 CP2K
> >
> > CP2K| Stopped by process
> > number 0
> > CP2K| Abnormal program termination
> >
> > Aborted
> >
> >
> > It appears that the MC code requires the COORD section to be used
> > instead of other means of defining the molecular geometry. These are
> > all the input files:
> >
> > mc.inp:
> >
> > &FORCE_EVAL
> >
> > METHOD Quickstep
> > &DFT
> > &QS
> > METHOD PM3
> > EPS_DEFAULT 1.0E-12
> > EPS_GVG 1.0E-6
> > EPS_PGF_ORB 1.0E-6
> > &END QS
> > &SCF
> > EPS_SCF 1.0E-6
> > MAX_SCF 150
> > SCF_GUESS atomic
> > &END SCF
> > &END DFT
> >
> > &SUBSYS
> > &CELL
> > ABC 7.800000 7.800000 7.800000
> > UNIT ANGSTROM
> > &END CELL
> > &TOPOLOGY
> > COORDINATE XYZ
> > COORD_FILE_NAME init.xyz
> > CONNECTIVITY MOL_SET
> > &MOL_SET
> > &MOLECULE
> > NMOL 8
> > CONN_FILE_NAME single.psf
> > CONNECTIVITY UPSF
> > &END
> > &END
> > &END TOPOLOGY
> > &PRINT
> > &TOPOLOGY_INFO
> > EACH 1
> > PSF_INFO T
> > &END TOPOLOGY_INFO
> > &END PRINT
> > &END SUBSYS
> > &END FORCE_EVAL
> >
> > &GLOBAL
> > FFT_LIB FFTSG
> > PROJECT mc
> > RUN_TYPE MC
> > &END GLOBAL
> >
> > &MOTION
> > &MC
> > IUPTRANS 100
> > IUPVOLUME 100
> > LBIAS no
> > LSTOP no
> > NMOVES 1
> > NSTEP 10
> > PMSWAP 0.0
> > PMSWAP_MOL 1.0
> > PMTRAION 0.00
> > PMTRAION_MOL 1.0
> > PMTRANS 0.5
> > PMTRANS_MOL 1.0
> > PMROT_MOL 1.0
> > PMVOLUME 0.2
> > PMVOL_BOX 1.0
> > PRESSURE 1.013
> > ENSEMBLE traditional
> > RESTART no
> > RESTART_FILE_NAME mc_restart_1
> > RMDIHEDRAL 1.0
> > RMANGLE 3.0
> > RMBOND 0.074
> > RMROT 26.0
> > RMTRANS 0.38
> > RMVOLUME 1.0
> > TEMPERATURE 298.0
> > IPRINT 1
> > AVBMC_ATOM 1
> > NSWAPMOVES 4
> > PMAVBMC 0.5
> > PMAVBMC_MOL 1.0
> > AVBMC_RMIN 2.0
> > AVBMC_RMAX 4.0
> > PBIAS 0.5
> > VIRIAL_TEMPS 300.0
> > &END MC
> > &PRINT
> > &TRAJECTORY
> > EACH 5
> > &END TRAJECTORY
> > &END PRINT
> > &END MOTION
> >
> > This is single.psf
> >
> > PSF
> >
> > 1 !NTITLE
> > None
> >
> > 5 !NATOM
> > 1 NAME 1 NAME C C 0.0 12.010700 0
> > 2 NAME 1 NAME H H 0.0 1.007940 0
> > 3 NAME 1 NAME H H 0.0 1.007940 0
> > 4 NAME 1 NAME H H 0.0 1.007940 0
> > 5 NAME 1 NAME H H 0.0 1.007940 0
> >
> > 4 !NBOND
> > 2 1 3 1 4 1 5 1
> >
> > 6 !NTHETA
> > 4 1 2 5 1 2 3 1 2
> > 5 1 4 4 1 3 5 1 3
> >
> > 0 !NPHI
> >
> > 0 !NIMPHI
> >
> > 0 !NDON
> >
> > 0 !NACC
> >
> > 0 !NNB
> >
> >
> > This is init.xyz
> >
> > 40
> > i = 200, E = 22.6433415965
> > C 6.9039075582 2.2556748672 0.6684090906
> > H 7.5807042939 2.9514646584 0.1778234170
> > H 6.4359114825 1.6148018511 -0.0751255788
> > H 6.1411834553 2.8077213762 1.2123856443
> > H 7.4649087760 1.6437421117 1.3661103663
> > C 6.9115470203 6.1425921064 2.1589360246
> > H 7.6276416557 6.8618026951 2.5486690023
> > H 7.4061522809 5.4950308617 1.4429986121
> > H 6.1001618632 6.6677780946 1.6615302422
> > H 6.5170086641 5.5418353691 2.9752995498
> > C 0.8124559617 6.2174060423 6.1085385115
> > H 0.9682759157 6.3527520522 5.0415332216
> > H -0.0050460555 6.8521178205 6.4438165561
> > H 1.7204472263 6.4844467269 6.6359163451
> > H 0.5776741793 5.1779744893 6.3188571695
> > C 4.6568183079 8.5306984679 4.5589000442
> > H 5.4014171220 8.0383130247 5.1798098710
> > H 4.0720357993 7.7856805661 4.0247749152
> > H 5.1510519252 9.1888538100 3.8480745892
> > H 3.9962925018 9.1156867542 5.1893066759
> > C 3.0026367985 4.6804958145 2.1341762406
> > H 2.5872117262 5.3961909512 2.8398055744
> > H 3.5973758287 3.9441956718 2.6702281645
> > H 3.6343783322 5.2012588593 1.4230404511
> > H 2.1983186479 4.1851221980 1.5958594440
> > C 3.0357598254 8.6354879819 8.5015934277
> > H 2.2355644284 8.1192114793 9.0268620523
> > H 3.7132001125 7.9084963590 8.0584302518
> > H 3.5842911872 9.2497091821 9.2067104274
> > H 2.6159490587 9.2689729491 7.7228475826
> > C 8.5668539873 2.2952643674 4.5588139458
> > H 9.3584593729 2.7884860822 5.1172331341
> > H 9.0003049169 1.6000473260 3.8438410104
> > H 7.9715191708 3.0389332591 4.0342037810
> > H 7.9309384985 1.7492402764 5.2468924719
> > C 4.7102978422 4.6594015643 6.0167776096
> > H 5.5013143603 4.2000713116 5.4279574197
> > H 5.1427927774 5.3339687406 6.7519655838
> > H 4.1333208145 3.8893804981 6.5228756168
> > H 4.0540983796 5.2195783822 5.3595115407
> >
> >
> >
> >
> > >
>
>
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