From: Bryan Roessler (roessler_at_uab.edu)
Date: Fri Sep 04 2015 - 00:07:49 CDT
Hello,
Could someone point out where I am going wrong here?
I'm getting the infamous unable to find bond parameter error, but the bond
is defined in a stream file with cgenff topology/paramters for a
carboxybenzyl (PHQ) bound to leucine. This bond is the peptide bond between
the two.
FATAL ERROR: UNABLE TO FIND BOND PARAMETERS FOR CG2O2 NH1 (ATOMS 2318 2335)
I'm reading in charmm36_prot.prm, and cgenff_prot.prm prior to the stream
file.
I manually added the C1 +N bond to the PHQ topology and then added a
typical peptide bond length and spring parameters for CG202 and NH1.
I'm guessing that the stream file is not being parsed correctly but I might
just be missing something obvious.
stream.str file
> * Toppar stream file generated by
> * CHARMM General Force Field (CGenFF) program version 1.0.0
> * For use with CGenFF version 3.0.1
> *
> read rtf card append
> * Topologies generated by
> * CHARMM General Force Field (CGenFF) program version 1.0.0
> *
> 36 1
> ! "penalty" is the highest penalty score of the associated parameters.
> ! Penalties lower than 10 indicate the analogy is fair; penalties between
> 10
> ! and 50 mean some basic validation is recommended; penalties higher than
> ! 50 indicate poor analogy and mandate extensive validation/optimization.
> DECL +N
> RESI B27 0.000 ! param penalty= 38.500 ; charge penalty= 34.016
> GROUP ! CHARGE CH_PENALTY
> ATOM N NG321 -0.594 ! 34.016
> ATOM CA CG311 -0.000 ! 22.203
> ATOM CB CG311 0.138 ! 15.419
> ATOM CG2 CG331 -0.273 ! 12.491
> ATOM OG1 OG311 -0.652 ! 14.058
> ATOM SG SG311 -0.243 ! 20.973
> ATOM CX CG321 -0.093 ! 22.601
> ATOM HN HGPAM2 0.254 ! 17.264
> ATOM HA HGA1 0.090 ! 0.520
> ATOM HB HGA1 0.090 ! 1.160
> ATOM HG HGP1 0.419 ! 0.000
> ATOM HG2 HGA3 0.090 ! 0.000
> ATOM AHG2 HGA3 0.090 ! 0.000
> ATOM BHG2 HGA3 0.090 ! 0.000
> ATOM HX HGA2 0.090 ! 0.810
> ATOM HXA HGA2 0.090 ! 0.810
> BOND N HN
> BOND N CA
> BOND CA HA
> BOND CA CB
> BOND CA CX
> BOND CB CG2
> BOND CB OG1
> BOND CB HB
> BOND CG2 HG2
> BOND CG2 AHG2
> BOND CG2 BHG2
> BOND OG1 HG
> BOND SG CX
> BOND CX HXA
> BOND CX HX
> RESI PHQ 0.000 ! param penalty= 108.000 ; charge penalty= 12.592
> GROUP ! CHARGE CH_PENALTY
> ATOM C1 CG2O2 0.557 ! 7.809
> ATOM O1 OG2D1 -0.456 ! 0.000
> ATOM O2 OG302 -0.461 ! 12.592
> ATOM C2 CG321 0.064 ! 9.576
> ATOM H21 HGA2 0.090 ! 0.000
> ATOM H22 HGA2 0.090 ! 0.000
> ATOM C3 CG2R61 -0.006 ! 10.071
> ATOM C8 CG2R61 -0.117 ! 5.324
> ATOM H81 HGR61 0.115 ! 0.000
> ATOM C7 CG2R61 -0.108 ! 0.000
> ATOM H71 HGR61 0.115 ! 0.000
> ATOM C6 CG2R61 -0.115 ! 0.000
> ATOM H61 HGR61 0.115 ! 0.000
> ATOM C5 CG2R61 -0.108 ! 0.000
> ATOM H51 HGR61 0.115 ! 0.000
> ATOM C4 CG2R61 -0.117 ! 5.324
> ATOM H41 HGR61 0.115 ! 0.000
> BOND C3 C4
> BOND H41 C4
> BOND C5 C4
> BOND H51 C5
> BOND C6 C5
> BOND H61 C6
> BOND C7 C6
> BOND H71 C7
> BOND C8 C7
> BOND H81 C8
> BOND C3 C8
> BOND C2 C3
> BOND H22 C2
> BOND H21 C2
> BOND O2 C2
> BOND C1 O2
> BOND C1 O1
> BOND C1 +N
> END
> read para card flex append
> * Parameters generated by analogy by
> * CHARMM General Force Field (CGenFF) program version 1.0.0
> *
> ! Penalties lower than 10 indicate the analogy is fair; penalties between
> 10
> ! and 50 mean some basic validation is recommended; penalties higher than
> ! 50 indicate poor analogy and mandate extensive validation/optimization.
> BONDS
> CG311 NG321 263.00 1.4740 ! B27 , from CG321 NG321, penalty= 4
> CG202 NH1 360.00 1.3450 ! Typical peptide bond length/strength
> ANGLES
> CG311 CG311 NG321 43.70 112.20 ! B27 , from CG331 CG321 NG311,
> penalty= 6.7
> CG321 CG311 NG321 43.70 112.20 ! B27 , from CG331 CG321 NG311,
> penalty= 6.1
> NG321 CG311 HGA1 32.40 109.50 50.00 2.14000 ! B27 , from
> NG321 CG321 HGA2, penalty= 4
> CG311 NG321 HGPAM2 41.00 112.10 ! B27 , from CG321 NG321 HGPAM2,
> penalty= 0.6
> OG302 CG2O2 HGR52 47.00 105.00 ! PHQ , from OG311 CG2O2 HGR52,
> penalty= 15
> DIHEDRALS
> CG321 CG311 CG311 CG331 0.5000 4 180.00 ! B27 , from CG321
> CG311 CG311 CG321, penalty= 0.9
> CG321 CG311 CG311 OG311 0.1400 3 0.00 ! B27 , from CG311
> CG311 CG311 OG311, penalty= 0.6
> CG331 CG311 CG311 NG321 0.2000 3 0.00 ! B27 , from CG331
> CG311 CG321 OG302, penalty= 37.5
> NG321 CG311 CG311 OG311 0.2000 3 0.00 ! B27 , from OG311
> CG311 CG321 OG303, penalty= 38.5
> NG321 CG311 CG311 HGA1 0.1600 3 0.00 ! B27 , from NG311
> CG321 CG331 HGA3, penalty= 16.2
> CG311 CG311 CG321 SG311 0.1950 3 0.00 ! B27 , from CG311
> CG321 CG321 SG311, penalty= 4
> NG321 CG311 CG321 SG311 0.2000 3 0.00 ! B27 , from NG3P3
> CG314 CG321 SG311, penalty= 37.9
> NG321 CG311 CG321 HGA2 0.1600 3 0.00 ! B27 , from NG311
> CG321 CG331 HGA3, penalty= 11.2
> CG311 CG311 NG321 HGPAM2 0.1000 3 0.00 ! B27 , from CG331
> CG321 NG311 HGP1, penalty= 17
> CG321 CG311 NG321 HGPAM2 0.1000 3 0.00 ! B27 , from CG331
> CG321 NG311 HGP1, penalty= 16.4
> HGA1 CG311 NG321 HGPAM2 0.0100 3 0.00 ! B27 , from HGA2 CG321
> NG321 HGPAM2, penalty= 4
> HGR52 CG2O2 OG302 CG321 2.0500 2 180.00 ! PHQ , from CG321
> CG2O2 OG302 CG321, penalty= 108
> IMPROPERS
> CG2O2 OG2D1 OG302 HGR52 75.0000 0 0.00 ! PHQ , from CG2O2
> OG2D1 OG311 HGR52, penalty= 1
>
> END
What am I missing here?
Thanks!
*Bryan Roessler | Graduate Research Assistant*
UAB | The University of Alabama at Birmingham
*uab.edu/cmdb <http://uab.edu/cmdb>*
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