Dear all,
I have run four simulations containing one protein (two of them) and a complex of two proteins (the other two) anchored to a lipid membrane. I used PBC in a rectangular box. I have had imaging issues that I have solved in two of them using the following cpptraj input file:
parm x.prmtop
trajin x.mdcrd
centre :1-77 # Amino acids of the protein
image
centre :1-827 # Aa plus lipids of the membrane
image
strip :WAT
strip :Na+
trajout y.binpos
However in the other two (one with one protein and the other with the complex) keep giving imaging problems. Some of the membrane lipids appear on the one the other side of the box or the two proteins get apart instantaneously and one of them jump to the other side of the lipid membrane.
I have tried to solve this using autoimage and other combinations of image as well as unwrap the system protein-membrane.
Any advise is welcomed.
Thanks a lot!
Raquel Romero
Department of Pharmaceutical and Biological Chemistry
UCL School of Pharmacy, University College London
29/39 Brunswick Square
London
WC1N 1AX
T: 0207 753 5972
E: raquel.romero.12.ucl.ac.uk
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sun Oct 18 2015 - 16:00:03 PDT
