As far as I can remember (or check), every Amber prep file has 3 dummy
atoms named like that (but it may just be those with internal coordinates,
since that would allow every _real_ atom to be defined with a distance,
angle, and dihedral).
If you are having issues, I don't think it's because of the dummy atoms.
Check the
http://ambermd.org/formats.html for information about the prep
format (at the very bottom is an example -- the documentation is a bit
verbose for my tastes).
HTH,
Jason
On Tue, Nov 15, 2011 at 4:57 AM, Andrew Voronkov <drugdesign.yandex.ru>wrote:
> Hello everyone,
> is it ok to get dummy atoms in parametrzation using MCPB, I am getting
> errors while saving parameters while using this prep file and I am trying
> to understand what might be the problem.
> There is some confusion that there are dummy atoms with DU type in prep
> file below.
>
> Is that normal?
>
> Best regards,
> Andrew
>
> 1 1 2
> Zn-CCCH fragment set created by MTK++/MCPB
> CYSTEINE with negative charge
>
> CY2 INT 1
> CORR OMIT DU BEG
> 0.00000
> 1 DUMM DU M 0 -1 -2 0.000 .0 .0 .00000
> 2 DUMM DU M 1 0 -1 1.449 .0 .0 .00000
> 3 DUMM DU M 2 1 0 1.522 111.1 .0 .00000
> 4 N N M 3 2 1 1.335 116.600 180.000 -0.46300
> 5 HN H E 4 3 2 1.010 119.800 0.000 0.25200
> 6 CA CT M 4 3 2 1.449 121.900 180.000 0.03500
> 7 HA H1 E 6 4 3 1.090 109.500 300.000 0.04800
> 8 CB CT 3 6 4 3 1.525 111.100 60.000 -0.32484
> 9 HB3 H1 E 8 6 4 1.090 109.500 60.000 0.17553
> 10 HB2 H1 E 8 6 4 1.090 109.500 300.000 0.17553
> 11 SG S2 E 8 6 4 1.810 116.000 180.000 -0.47287
> 12 C C M 6 4 3 1.522 111.100 180.000 0.61600
> 13 O O E 12 6 4 1.229 120.500 0.000 -0.50400
>
> DONE
> HISTIDINE EPSILONH
>
> HE1 INT 1
> CORR OMIT DU BEG
> 0.00000
> 1 DUMM DU M 0 -1 -2 0.000 .0 .0 .00000
> 2 DUMM DU M 1 0 -1 1.449 .0 .0 .00000
> 3 DUMM DU M 2 1 0 1.522 111.1 .0 .00000
> 4 N N M 3 2 1 1.335 116.600 180.000 -0.41570
> 5 H H E 4 3 2 1.010 119.800 0.000 0.27190
> 6 CA CT M 4 3 2 1.449 121.900 180.000 -0.05810
> 7 HA H1 E 6 4 3 1.090 109.500 300.000 0.13600
> 8 CB CT 3 6 4 3 1.525 111.100 60.000 -0.39023
> 9 HB2 HC E 8 6 4 1.090 109.500 300.000 0.17670
> 10 HB3 HC E 8 6 4 1.090 109.500 60.000 0.17670
> 11 CG CC S 8 6 4 1.510 115.000 180.000 0.17220
> 12 ND1 N1 S 11 8 6 1.390 122.000 180.000 -0.21863
> 13 CE1 CR B 12 11 8 1.320 108.000 180.000 0.02565
> 14 HE1 H5 E 13 12 11 1.090 120.000 180.000 0.12545
> 15 NE2 NA B 13 12 11 1.310 109.000 0.000 -0.13860
> 16 HE2 H E 15 13 12 1.010 125.000 180.000 0.30074
> 17 CD2 CW S 15 13 12 1.360 110.000 0.000 -0.24025
> 18 HD2 H4 E 17 15 13 1.090 120.000 180.000 0.16438
> 19 C C M 6 4 3 1.522 111.100 180.000 0.59730
> 20 O O E 19 6 4 1.229 120.500 0.000 -0.56790
>
> LOOP
> CG CD2
>
> IMPROPER
> CA N H
> CE1 CD2 NE2 HE2
> CG NE2 CD2 HD2
> ND1 NE2 CE1 HE1
>
> DONE
> Zinc(II) Ion
>
> ZN2 INT 1
> CORR OMIT DU BEG
> 0.00000
> 1 DUMM DU M 0 -1 -2 0.000 .0 .0 .00000
> 2 DUMM DU M 1 0 -1 1.449 .0 .0 .00000
> 3 DUMM DU M 2 1 0 1.522 111.1 .0 .00000
> 4 ZN ZN M 3 2 1 1.000 90.000 180.000 0.50194
>
> DONE
> STOP
>
> _______________________________________________
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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Wed Nov 16 2011 - 12:30:03 PST
