[gmx-users] CHOL still not recognised

[Mark Abraham]

Hi,

You should follow the error message instructions "... they should not have
the same chain ID as the adjacent protein chain" which you know is that X.
Make the protein have a different chain ID from the rest.

Mark

On Mon, 26 Aug 2019 at 19:27, Ayesha Fatima <ayeshafatima.69 at gmail.com>
wrote:

> Dear Justin,
> Thank you for your earlier response. I opened the file in vmd and it
> returned me with a 3 letter residue name and an X identifier for the whole
> molecule.
>
> CRYST1    0.000    0.000    0.000  90.00  90.00  90.00 P 1           1
> ATOM      1  C3  CHL X   1      -1.678   2.702  17.328  1.00  0.00
>  MEMB C
> ATOM      2  H3  CHL X   1      -0.722   3.268  17.289  1.00  0.00
>  MEMB H
> ATOM      3  O3  CHL X   1      -2.187   2.686  18.672  1.00  0.00
>  MEMB O
> ATOM      4  H3' CHL X   1      -1.369   2.855  19.145  1.00  0.00
>  MEMB H
> ..
> ATOM   9473  OH2 TIP X   1       0.049   2.793  20.554  1.00  0.00
>  TIP3 O
> ATOM   9474  H1  TIP X   1       0.881   2.777  20.081  1.00  0.00
>  TIP3 H
> ATOM   9475  H2  TIP X   1       0.235   2.351  21.383  1.00  0.00
>  TIP3 H
> ATOM   9476  OH2 TIP X   2      -1.458  -2.368  19.953  1.00  0.00
>  TIP3 O
> ATOM   9477  H1  TIP X   2      -2.185  -2.795  20.406  1.00  0.00
>  TIP3 H
>
> now when i run pdb2gmx, the error is
> Fatal error:
> The residues in the chain CHL1--TIP3130 do not have a consistent type. The
> first residue has type 'Other', while residue TIP1 is of type 'Water'.
> Either
> there is a mistake in your chain, or it includes nonstandard residue names
> that have not yet been added to the residuetypes.dat file in the GROMACS
> library directory. If there are other molecules such as ligands, they
> should
> not have the same chain ID as the adjacent protein chain since it's a
> separate
> molecule.
>
> i cant find the solution to the error online.
> would you or anyone one the list guide?
> Thank you
> regards
> --
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