From: Christian Jorgensen (chrisjorg_at_gmail.com)
Date: Thu Feb 12 2015 - 10:16:00 CST
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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