[gmx-users] cmap

[Justin Lemkul]

On 11/26/17 6:33 PM, MD wrote:
> 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?

Keep it in the working directory when running pdb2gmx. All GROMACS 
programs search the working directory first before looking in $GMXLIB.

-Justin

> 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
>> 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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-- 
==================================================

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

==================================================