madhumita das wrote:
Dear Justin,
I could solve that perticular error but another problem has come, After
running energy minimization, the sulphur and mercury(GG)atoms (present
in the modified residue of cysteine named CYP at 182 position) break the
bonds.
Bonds don't break and form during molecular mechanical processes. Likely
whatever you're seeing is simply extreme instability in the system. Most likely
your topology is wrong. You haven't said what parameters you're using, but as I
know I have indicated previously, deriving good parameters for such an exotic
species will be extremely challenging for the biomolecular force fields present
in Gromacs. My guess is that you haven't yet obtained proper parameters.
-Justin
On Thu, Nov 10, 2011 at 7:28 PM, madhumita das
<[email protected] <mailto:[email protected]>> wrote:
Dear Justin,
I could resolve that perticular error but another problem has come,
After running energy minimization, the sulphur and mercury(GG)atoms
(present in the modified residue of cysteine named CYP at 182
position) break the bonds and become freely moving atoms. I have
attached my prepared gromacs(aqp_newbox) topology(topol.top) and
file obtained after energy mimization(em.gro).
Please help me.
Madhumita
On Tue, Nov 8, 2011 at 5:03 PM, madhumita das
<[email protected] <mailto:[email protected]>>
wrote:
Hi GROMACS users,
i am in the midst of simulating a protein in water. I have
modified a residue in my pdb file at position 182, using
amber and then acpype.py. But after running the energy
minimization step,using em.mdp file generated from acpype ,
following error comes.
Steepest Descents:
Tolerance (Fmax) = 1.00000e+03
Number of steps = 5000
Step= 17, Dmax= 1.5e-06 nm, Epot= 9.89827e+17 Fmax=
inf, atom= 2700
Stepsize too small, or no change in energy.
Converged to machine precision,
but not to the requested precision Fmax < 1000
Double precision normally gives you higher accuracy.
writing lowest energy coordinates.
Steepest Descents converged to machine precision in 18 steps,
but did not reach the requested Fmax < 1000.
Potential Energy = 9.8982703e+17
Maximum force = inf on atom 2700
Norm of force = 1.7474532e+19
The mdp file is attached.
Please help.
Madhumita Das
--
========================================
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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