[gmx-users] cmap

[Justin Lemkul]

On 11/26/17 6:06 PM, MD wrote:
> Hi,
>
> I had to repost this cause of the size of the previous thread.
>
> I had another error after grompp, "ERROR 1 [file topol_Protein_chain_E.itp,
> line 52165]:
>    Unknown cmap torsion between atoms 3022 3024 3026 3046 3049"
>
> The 3022 3024 3026 3046 3049 in the itp files referred to the backbone
> (C-N-CA-C-N) of three connected residues R-W-T..
>
> I found out it is the W that causing issue. I am not sure why it has one
> CC, two OT1 instead of one  C and O like the rest of the Trp residues in
> the protein. This is the only Trp that has these parameters.
>   Any suggestions?

This is the C-terminal Trp residue, hence the carbonyl becomes a 
carboxylate.  There should not be a CMAP generated for a C-terminal 
residue and pdb2gmx should have removed that interaction.

If this is the residue preceding CSO, then you are getting a false chain 
termination because you haven't added CSO to residuetypes.dat.

-Justin

> residue 196 TRP rtp TRP  q -1.0
>    3024        NH1    196    TRP      N   3024      -0.47     14.007   ;
> qtot 8.53
>    3025          H    196    TRP     HN   3025       0.31      1.008   ;
> qtot 8.84
>    3026        CT1    196    TRP     CA   3026       0.07     12.011   ;
> qtot 8.91
>    3027        HB1    196    TRP     HA   3027       0.09      1.008   ;
> qtot 9
>    3028        CT2    196    TRP     CB   3028      -0.18     12.011   ;
> qtot 8.82
>    3029        HA2    196    TRP    HB1   3029       0.09      1.008   ;
> qtot 8.91
>    3030        HA2    196    TRP    HB2   3030       0.09      1.008   ;
> qtot 9
>    3031         CY    196    TRP     CG   3031      -0.03     12.011   ;
> qtot 8.97
>    3032         CA    196    TRP    CD1   3032      -0.15     12.011   ;
> qtot 8.82
>    3033         HP    196    TRP    HD1   3033       0.22      1.008   ;
> qtot 9.04
>    3034         NY    196    TRP    NE1   3034      -0.51     14.007   ;
> qtot 8.53
>    3035          H    196    TRP    HE1   3035       0.37      1.008   ;
> qtot 8.9
>    3036        CPT    196    TRP    CE2   3036       0.24     12.011   ;
> qtot 9.14
>    3037        CPT    196    TRP    CD2   3037       0.11     12.011   ;
> qtot 9.25
>    3038        CAI    196    TRP    CE3   3038      -0.25     12.011   ;
> qtot 9
>    3039         HP    196    TRP    HE3   3039       0.17      1.008   ;
> qtot 9.17
>    3040         CA    196    TRP    CZ3   3040       -0.2     12.011   ;
> qtot 8.97
>    3041         HP    196    TRP    HZ3   3041       0.14      1.008   ;
> qtot 9.11
>    3042        CAI    196    TRP    CZ2   3042      -0.27     12.011   ;
> qtot 8.84
>    3043         HP    196    TRP    HZ2   3043       0.16      1.008   ;
> qtot 9
>    3044         CA    196    TRP    CH2   3044      -0.14     12.011   ;
> qtot 8.86
>    3045         HP    196    TRP    HH2   3045       0.14      1.008   ;
> qtot 9
>    3046         CC    196    TRP      C   3046       0.34     12.011   ;
> qtot 9.34
>    3047         OC    196    TRP    OT1   3047      -0.67    15.9994   ;
> qtot 8.67
>    3048         OC    196    TRP    OT2   3048      -0.67    15.9994   ;
> qtot 8

-- 
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

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