Dear AMBER experts.
Applying AMBE14 and AmberTools15, I have simulated a protein in membrane by MD in periodic cell.
The next step is calculation of the average structure from
the fragment of the production trajectory that satisfies a desired protein
backbone RMSD condition.
Finally, to obtain a representative protein structure the latter step must be minimization.
The adequate minimization of a membarne protein can be conducted in
membrane environment only. That is why I have accounted in the averaging procedure
the whole soup in the periodic cell: protein, membrane, water, and counter ions.
In this purpose I have applied the following cpptraj script:
parm ../*.prmtop
trajin prod4.mdcrd 3000 10000
center :1-9308 mass origin
autoimage origin
rms first .C,CA,N
average average_prod4_3000-10000.pdb PDB
run
quit
The problem I faced is that despite the final pdb file contains also
solvent water molecules and counter ions their coordinates are corrupted.
Water molecules and counter ions are collapsed
in a very small condensed area in the center of periodic cell
like in a black hole.
What command lines should be added to the cpptraj script in order to resolve the problem?
Thank you,
Michael
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Received on Sat Mar 26 2016 - 12:00:03 PDT
