[gmx-users] cmap

[MD]

Hi Justin,
I added the CSO to residuetypes.dat in my local computer and it worked now.
I then tried to copy the modified "residuetypes.dat" to the ff  folder on
the server computer, but the server computer gromacs wouldn't give option
to choose which residuetypes.dat to use. Do you know how to let it choose
instead of using its original one by default?
Thanks,
Ming

On Sun, Nov 26, 2017 at 6:11 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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
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> Blacksburg, VA 24061
>
> jalemkul at vt.edu | (540) 231-3129
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>
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