From: Jim Phillips (jim_at_ks.uiuc.edu)
Date: Thu Feb 12 2015 - 12:32:42 CST
Those lines are from a PDB file, not a PSF file.
Jim
On Thu, 12 Feb 2015, Christian Jorgensen wrote:
> Hello,
> *I've been redirected from the CP2K user's list in relation
> to this question.
>
> I'm trying to run a QM/MM calculation on my system, built
> with PSFGEN and running smoothly with Namd 2.9.
>
>
> However, upon taking said PSF/PDB and running an MM
> calculation with CP2K I run into a topology problem that
> pertains the PSF.
>
>
> This is the part of the PSF concerned:
>
> ATOM 49880 SOD SOD I 37 21.151 0.526 -30.628 1.00 0.00 ION
> NA
> ATOM 49881 SOD SOD I 38 24.667 -35.051 19.114 1.00 0.00 ION
> NA
> ATOM 49882 SOD SOD I 39 -12.620 2.426 26.969 1.00 0.00 ION
> NA
> ATOM 49883 SOD SOD I 40 -10.705 -33.380 -11.158 1.00 0.00 ION
> NA
> ATOM 49884 SOD SOD I 41 -19.491 29.350 -34.679 1.00 0.00 ION
> NA
> ATOM 49885 SOD SOD I 42 40.802 -30.866 10.911 1.00 0.00 ION
> NA
> ATOM 49886 SOD SOD I 43 -21.411 -20.389 17.270 1.00 0.00 ION
> NA
> ATOM 49887 SOD SOD I 44 13.100 24.287 18.857 1.00 0.00 ION
> NA
> ATOM 49888 SOD SOD I 45 33.628 30.716 18.333 1.00 0.00 ION
> NA
> ATOM 49889 SOD SOD I 46 14.256 -31.556 -9.097 1.00 0.00 ION
> NA
> ATOM 49890 SOD SOD I 47 -1.600 38.825 28.079 1.00 0.00 ION
> NA
> ATOM 49891 SOD SOD I 48 26.911 -9.319 19.217 1.00 0.00 ION
> NA
> ATOM 49892 CLA CLA I 49 -21.849 -29.233 -4.389 1.00 0.00 ION
> CL
> ATOM 49893 CLA CLA I 50 -27.778 19.207 -8.907 1.00 0.00 ION
> CL
> ATOM 49894 CLA CLA I 51 -1.036 -18.525 -33.557 1.00 0.00 ION
> CL
> ATOM 49895 CLA CLA I 52 -37.955 23.751 -9.529 1.00 0.00 ION
> CL
> ATOM 49896 CLA CLA I 53 -15.636 -34.005 12.873 1.00 0.00 ION
> CL
> ATOM 49897 CLA CLA I 54 40.122 21.296 -26.349 1.00 0.00 ION
> CL
> ATOM 49898 CLA CLA I 55 32.593 -9.101 17.836 1.00 0.00 ION
> CL
> ATOM 49899 CLA CLA I 56 8.168 -24.215 8.246 1.00 0.00 ION
> CL
> ATOM 49900 CLA CLA I 57 -4.530 -32.691 -6.031 1.00 0.00 ION
> CL
> ATOM 49901 CLA CLA I 58 -14.998 37.422 2.603 1.00 0.00 ION
> CL
> ATOM 49902 CLA CLA I 59 -22.559 -24.866 -37.160 1.00 0.00 ION
> CL
> ATOM 49903 CLA CLA I 60 22.442 -17.653 -37.184 1.00 0.00 ION
> CL
> ATOM 49904 CLA CLA I 61 -31.657 0.756 -22.411 1.00 0.00 ION
> CL
> ATOM 49905 CLA CLA I 62 -25.707 4.569 26.200 1.00 0.00 ION
> CL
> ATOM 49906 CLA CLA I 63 9.816 21.844 -29.523 1.00 0.00 ION
> CL
> ATOM 49907 CLA CLA I 64 20.348 15.655 31.373 1.00 0.00 ION
> CL
> ATOM 49908 CLA CLA I 65 -33.471 28.927 25.816 1.00 0.00 ION
> CL
> ATOM 49909 CLA CLA I 66 -23.076 -36.320 -14.581 1.00 0.00 ION
> CL
> ATOM 49910 CLA CLA I 67 11.228 23.055 26.442 1.00 0.00 ION
> CL
> ATOM 49911 CLA CLA I 68 -31.967 -25.220 12.122 1.00 0.00 ION
> CL
> ATOM 49912 CLA CLA I 69 7.122 -32.163 -23.902 1.00 0.00 ION
> CL
> ATOM 49913 CLA CLA I 70 -30.542 -17.921 15.502 1.00 0.00 ION
> CL
> ATOM 49914 CLA CLA I 71 -35.163 -32.044 11.857 1.00 0.00 ION
> CL
> ATOM 49915 CLA CLA I 72 -1.340 -18.251 -21.790 1.00 0.00 ION
> CL
>
>
> In relation to the error in CP2K
>
>
> 49892 0
> Two molecules have been defined as identical molecules but atoms mismatch
> charges!!
> 49893 0
> Two molecules have been defined as identical molecules but atoms mismatch
> charges!!
> 49894 0
> Two molecules have been defined as identical molecules but atoms mismatch
> charges!!
> 49895 0
> Two molecules have been defined as identical molecules but atoms mismatch
> charges!!
> 49896 0
> Two molecules have been defined as identical molecules but atoms mismatch
> charges!!
> 49897 0
> Two molecules have been defined as identical molecules but atoms mismatch
> charges!!
> "
>
>
> I do have a CGENFF CHARMM 36 ligand naming in the PSF, which has previously
> been reported as causing problems due to the 6-character naming system.
>
> What do you suggest I might do to alleviate this?
>
> Managers of the CP2K list have kindly asked me to not ask
> this question on their list, and have told me to ask it to the NAMD
> list.
>
>
> Best
>
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