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Dear GROMACS users,
Though these problems have been discussed earlier, I would like to raise this topic again as the solutions seem confusing to me. I am new to GROMACS and facing multiple issues while preparing a system of protein in
spce water, much like the lysozyme tutorial, but using the GROMOS54a7 force field
(instead of OPLS/AA).
- For step 1: While using pdb2gmx to generate a .gro file, I get the following
warnings-
Duplicate line found in or between hackblock and rtp entries.
I came across an archived mail that says these warnings arise due to some
typo in the ff.itp file. However, I have not tampered with the files that are
present in the gromacs library so any explanation as to what can be the source
of these warnings will be most helpful.
- The pdb2gmx step terminates with “successful” creation of the topology file.
However on closer inspection, I found out that certain fields corresponding to
bonds, angles and dihedrals are empty.
For bonds: The field corresponding to parameter c0 is missing for the 4 S-S bonds
present in my protein.
For angles: The field corresponding to parameter c0 is missing for the 4
CH2-S-S bond angles.
For dihedrals: The field c0 is absent for
CH1-C-N-H (PRO-PRO-THR-THR)
C-N-CH1-CH2 (ILE-CYS-CYS-CYS)
CH2-NE-C-NZ (ARG-ARG-ARG-ARG)
H-NE-C-NZ (ARG-ARG-ARG-ARG)
C-CH1-CH2-S (CYS-CYS-CYS-CYS)
The next two steps involving solvation proceeds smoothly but the ion addition
step terminates with the following error:
No default Proper Dih. types
I tried the same process with the lysozyme tutorial which is well documented
but instead of OPLS/AA I opted for the GROMOS54a7 force field and ended up
with the same kind of errors. Previous solutions suggest to fill the empty fields
by hand but I am not sure as to how to obtain these parameters, specially for the
dihedrals where two amino acids are involved.Any suggestion regarding this is most
welcome.