Dear allI am trying to run a simulation of a dimer including a zinc finger
using Gromacs 4.5.3. I have gone through the documentation and searched the
forums but could not find a specific answer to my problem.
In order to produce the initial topology (top) and coordinate (gro) files for
the simulation I am running pdb2gmx using the PDB structure of the complex,
including the Zn ions. I realized that for them to be constrained in their
position, i.e. in the Zn finger, I should create bonds editing the specbond.dat
file. I introduced the following lines:
CYS SG 1 ZN Zn 1 0.23 CYS ZNHISE NE2
1 ZN Zn 1 0.21 HISE ZN
and updated the counter from 8 to 10. Needless to say, the Zn atoms are
coordinated to His and Cys residues in the first protein. The distances
correspond to what I measured using VMD. However pdb2gmx did not seem to be
linking the aforementioned residues. I then moved the Zn lines in the PDB to
the end of the section in the PDB file corresponding to chain A, the one with
the Zn fingers. Then the links were produced. So the first question is: should
one move the special atoms to the chain to which they supposedly correspond?
After successfully pdb2gmx-ing, I tried the Gromacs preprocessor (grompp). It
complained producing 138 errors like.
ERROR 132 [file PDBcode_forcefield_Protein_chain_A.itp, line 13663]: No
default Proper Dih. types / No default Angle types
By looking at the lines in the itp file for the chain A I found that the errors
referred to the lack of dihedrals or angles of the Zn atoms with their
partners. Could you give some suggestions on how to produce these missing
parameters?
Thank you very much,
David
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