[gmx-users] Linking MYR residue to N-terminus using pdb2gmx

[Justin Lemkul]

On 3/14/20 1:59 AM, Billy Williams-Noonan wrote:
> Hi Experts,
>
> This is a long-ish e-mail so thank you very much for your time
>
> I am using the GROMACS compatible charmm36 forcefield for
> betapeptides described here:
> https://gitlab.com/awacha/charmm-beta.ff
>
> In merged.rtp I have redefined the MYR residue hoping I could link it to
> the N-terminus of my b-peptide
>
>
> [ MYR ]
>    [ atoms ]
>             O1   OCL   -0.546  1
>             C1    CL    0.542  2
>             C2    CA   -0.280  3
>            H2R  HAL2    0.090  4
>            H2S  HAL2    0.090  5
>             C3  CTL2   -0.180  6
>            H3R  HAL2    0.090  7
>            H3S  HAL2    0.090  8
>             C4  CTL2   -0.180  9
>            H4R  HAL2    0.090 10
>            H4S  HAL2    0.090 11
>             C5  CTL2   -0.180 12
>            H5R  HAL2    0.090 13
>            H5S  HAL2    0.090 14
>             C6  CTL2   -0.180 15
>            H6R  HAL2    0.090 16
>            H6S  HAL2    0.090 17
>             C7  CTL2   -0.180 18
>            H7R  HAL2    0.090 19
>            H7S  HAL2    0.090 20
>             C8  CTL2   -0.180 21
>            H8R  HAL2    0.090 22
>            H8S  HAL2    0.090 23
>             C9  CTL2   -0.180 24
>            H9R  HAL2    0.090 25
>            H9S  HAL2    0.090 26
>            C10  CTL2   -0.180 27
>           H10R  HAL2    0.090 28
>           H10S  HAL2    0.090 29
>            C11  CTL2   -0.180 30
>           H11R  HAL2    0.090 31
>           H11S  HAL2    0.090 32
>            C12  CTL2   -0.180 33
>           H12R  HAL2    0.090 34
>           H12S  HAL2    0.090 35
>            C13  CTL2   -0.180 36
>           H13R  HAL2    0.090 37
>           H13S  HAL2    0.090 38
>            C14  CTL3   -0.270 39
>           H14R  HAL3    0.090 40
>           H14S  HAL3    0.090 41
>           H14T  HAL3    0.090 42
>    [ bonds ]
>             O1    C1
>             C1    C2
>             C1    +N
>             C2   H2R
>             C2   H2S
>             C2    C3
>             C3   H3R
>             C3   H3S
>             C3    C4
>             C4   H4R
>             C4   H4S
>             C4    C5
>             C5   H5R
>             C5   H5S
>             C5    C6
>             C6   H6R
>             C6   H6S
>             C6    C7
>             C7   H7R
>             C7   H7S
>             C7    C8
>             C8   H8R
>             C8   H8S
>             C8    C9
>             C9   H9R
>             C9   H9S
>             C9   C10
>            C10  H10R
>            C10  H10S
>            C10   C11
>            C11  H11R
>            C11  H11S
>            C11   C12
>            C12  H12R
>            C12  H12S
>            C12   C13
>            C13  H13R
>            C13  H13S
>            C13   C14
>            C14  H14R
>            C14  H14S
>            C14  H14T
>    [ impropers ]
>              C1   C2    +N     O1
>
>
> In ffnonbonded.itp I have added the following dihedral types:
>
>       C2       C1        +N        C     9     0.000000     7.531200     1
>       C2       C1        +N       HN     9     0.000000     7.531200     1
>
>
>
>
> Running pdb2gmx I get the following error:
>
> *gmx pdb2gmx -f outpdb.pdb -o pep.pdb -p pep.top -ter*
>
> Processing chain 1 'A' (105 atoms, 4 residues)
> Identified residue MYR1 as a starting terminus.
> Identified residue B3K4 as a ending terminus.
> 8 out of 8 lines of specbond.dat converted successfully
> Select start terminus type for MYR-1
>   0: Beta3NH3+
>   1: Beta2NH3+
>   2: Beta23NH3+
>   3: B3_NH2
>   4: B2_NH2
>   5: B23_NH2
>   6: 5TER
>   7: None
> 7
> Start terminus MYR-1: None
> Select end terminus type for B3K-4
>   0: BetaCOO-
>   1: BetaCOOH
>   2: BetaCT2
>   3: 3TER
>   4: None
> 0
> End terminus B3K-4: BetaCOO-
> Opening force field file ./charmm36_betapep.ff/betaaminoacids.arn
> Opening force field file ./charmm36_betapep.ff/cyclicbeta.arn
> Opening force field file ./charmm36_betapep.ff/merged.arn
> Checking for duplicate atoms....
> Generating any missing hydrogen atoms and/or adding termini.
> Now there are 4 residues with 106 atoms
> Making bonds...
> Number of bonds was 105, now 105
> Generating angles, dihedrals and pairs...
> Before cleaning: 288 pairs
>
> -------------------------------------------------------
> Program:     gmx pdb2gmx, version 2018.2
> Source file: src/gromacs/gmxpreprocess/pgutil.cpp (line 148)
>
> Fatal error:
> Residue 2 named MYR of a molecule in the input file was mapped
> to an entry in the topology database, but the atom C used in
> an interaction of type improper in that entry is not found in the
> input file. Perhaps your atom and/or residue naming needs to be
> fixed.
>
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> -------------------------------------------------------
>
> It seems to be having a problem recognising the link between C1 of Myr and
> the N-terminus of the next residue (B3K) - is there a file where I can
> explicitly mention this?
>
> Any help would be appreciated - how do I fix this?

The issue comes from whatever the amino acid is; the [impropers] and 
[cmap] entries specify that -C is needed to impose these bonded 
interactions. Your MYR residue does not have an atom named C, so you get 
an error.

The cleanest solution is probably to create a complete residue for a 
custom residue already linked to MYR (merge MYR with the amino acid). 
You likely don't want a CMAP on that residue, anyway.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Assistant Professor
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jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

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