[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
More information about the gromacs.org_gmx-users
mailing list