[gmx-users] CHOL still not recognised

Ayesha Fatima ayeshafatima.69 at gmail.com
Mon Aug 26 19:26:51 CEST 2019


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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