Re: PSF generated with PSFGEN [problem in CP2K] - Problem with CGenFF naming?

From: Christian Jorgensen (chrisjorg_at_gmail.com)
Date: Thu Feb 12 2015 - 13:01:13 CST

> Hello, I was merely trying to illustrate which atoms
> the CP2K indices corresponded to,
>
>
> the corresponding section of the PSF is
>
>
> 49885 ION 42 SOD SOD SOD 1.000000 22.9898 0
> 49886 ION 43 SOD SOD SOD 1.000000 22.9898 0
> 49887 ION 44 SOD SOD SOD 1.000000 22.9898 0
> 49888 ION 45 SOD SOD SOD 1.000000 22.9898 0
> 49889 ION 46 SOD SOD SOD 1.000000 22.9898 0
> 49890 ION 47 SOD SOD SOD 1.000000 22.9898 0
> 49891 ION 48 SOD SOD SOD 1.000000 22.9898 0
> 49892 ION 49 CLA CLA CLA -1.000000 35.4500 0
> 49893 ION 50 CLA CLA CLA -1.000000 35.4500 0
> 49894 ION 51 CLA CLA CLA -1.000000 35.4500 0
> 49895 ION 52 CLA CLA CLA -1.000000 35.4500 0
> 49896 ION 53 CLA CLA CLA -1.000000 35.4500 0
> 49897 ION 54 CLA CLA CLA -1.000000 35.4500 0
> 49898 ION 55 CLA CLA CLA -1.000000 35.4500 0
> 49899 ION 56 CLA CLA CLA -1.000000 35.4500 0
> 49900 ION 57 CLA CLA CLA -1.000000 35.4500 0
> 49901 ION 58 CLA CLA CLA -1.000000 35.4500 0
> 49902 ION 59 CLA CLA CLA -1.000000 35.4500 0
> 49903 ION 60 CLA CLA CLA -1.000000 35.4500 0
> 49904 ION 61 CLA CLA CLA -1.000000 35.4500 0
> 49905 ION 62 CLA CLA CLA -1.000000 35.4500 0
> 49906 ION 63 CLA CLA CLA -1.000000 35.4500 0
> 49907 ION 64 CLA CLA CLA -1.000000 35.4500 0
>
>
>
>
> I do have a CGenFF ligand too,
>
> 3780 U2 574 LEU HD23 HA 0.090000 1.0079 0
> 3781 U3 501 FE2 FE2 FE2 2.000000 55.8450 0
> 3782 AKG 1 AKG CG CG2O3 0.700000 12.0107 0
> 3783 AKG 1 AKG OG1 OG2D2 -0.823000 15.9994 0
> 3784 AKG 1 AKG OG2 OG2D2 -0.823000 15.9994 0
> 3785 AKG 1 AKG C CG2O5 0.257000 12.0107 0
> 3786 AKG 1 AKG O OG2D3 -0.497000 15.9994 0
> 3787 AKG 1 AKG CA CG321 0.105000 12.0107 0
> 3788 AKG 1 AKG CB CG321 -0.350000 12.0107 0
>
>
> This 5-space naming seems to cause problems because CP2K
> only parses 4 entries.
>
> On Thu, Feb 12, 2015 at 6:32 PM, Jim Phillips <jim_at_ks.uiuc.edu> wrote:
>
>>
>> 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
>>>
>>>
>
>
> --
> _______
>
> Christian Jørgensen
>

-- 
_______
Christian Jørgensen

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