DAVID DE SANCHO wrote:
Dear all
I 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 ZN
HISE 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?
Yes. Chain identifiers must be continuous, per the way pdb2gmx now works.
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?
This is no trivial task. Instead of using formal bonds via specbond.dat, why
not try using simple distance restraints, which can be added to the topology
after pdb2gmx? See manual section 4.3.4.
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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