Dear Amber users !
I am working on the preparation of the model for the GPCR protein using
pack-mol memgen utility of amber tools for creation of the membrane and the
parametrization of the complex.
The initial structure was taken from the pdb, which has some missed loops.
Since I decided not to restore these missed fragments I removed all
hydrogens and then pre-processed the model using
pdb4amber -i ./input.pdb -o ./output_ambpro.pdb -y -p --add-missing-atoms
These re-added missed hydrogens and some of the missed heavy atoms.
Then, on the final step of the creation of the membrane complex I got the
error during the tleap parametrization of the embedded model:
There is a bond of 9.221 angstroms between C and N atoms:
------- .R<ASP 798>.A<C 11> and .R<ARG 799>.A<N 1>
FATAL: Atom .R<ASN 338>.A<OXT 15> does not have a type.
FATAL: Atom .R<GLU 339>.A<H1 16> does not have a type.
FATAL: Atom .R<GLU 339>.A<H2 17> does not have a type.
FATAL: Atom .R<GLU 339>.A<H3 18> does not have a type.
FATAL: Atom .R<SER 372>.A<H1 12> does not have a type.
FATAL: Atom .R<SER 372>.A<H2 13> does not have a type.
FATAL: Atom .R<SER 372>.A<H3 14> does not have a type.
FATAL: Atom .R<ASN 420>.A<H1 15> does not have a type.
FATAL: Atom .R<ASN 420>.A<H2 16> does not have a type.
FATAL: Atom .R<ASN 420>.A<H3 17> does not have a type.
FATAL: Atom .R<LYS 462>.A<H1 23> does not have a type.
FATAL: Atom .R<LYS 462>.A<H2 24> does not have a type.
FATAL: Atom .R<LYS 462>.A<H3 25> does not have a type.
FATAL: Atom .R<ASP 477>.A<H1 13> does not have a type.
FATAL: Atom .R<ASP 477>.A<H2 14> does not have a type.
FATAL: Atom .R<ASP 477>.A<H3 15> does not have a type.
FATAL: Atom .R<VAL 511>.A<H1 17> does not have a type.
FATAL: Atom .R<VAL 511>.A<H2 18> does not have a type.
FATAL: Atom .R<VAL 511>.A<H3 19> does not have a type.
FATAL: Atom .R<LEU 538>.A<OXT 20> does not have a type.
FATAL: Atom .R<SER 539>.A<H1 12> does not have a type.
FATAL: Atom .R<SER 539>.A<H2 13> does not have a type.
FATAL: Atom .R<SER 539>.A<H3 14> does not have a type.
FATAL: Atom .R<LYS 595>.A<OXT 23> does not have a type.
FATAL: Atom .R<TRP 596>.A<H1 25> does not have a type.
FATAL: Atom .R<TRP 596>.A<H2 26> does not have a type.
FATAL: Atom .R<TRP 596>.A<H3 27> does not have a type.
FATAL: Atom .R<ARG 799>.A<H1 25> does not have a type.
FATAL: Atom .R<ARG 799>.A<H2 26> does not have a type.
FATAL: Atom .R<ARG 799>.A<H3 27> does not have a type.
/opt/site/ubuntu_22.04/amber/22b/bin/teLeap: Fatal Error!
Failed to generate parameters
Exiting LEaP: Errors = 1; Warnings = 860; Notes = 1.
So I carefully examined the structure of the complex created by packmol and
found that the TER records (in the gaps corresponded to the missing
fragments) were removed so tleap did not recognize it correctly. For
simplicity I added TER records and in other cases (where there is no gap) I
just removed H1,H2,H3 atoms that were added in the wrong way. After this I
could parametrize the complex.
What could be the best way to overcome such issue ? I enclose the initial
PDB without hydrogen atoms (before processing by amber-tools) as a template.
Many thanks in advance!
Enrico
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Received on Fri Mar 22 2024 - 09:00:02 PDT
