Hi,
Could you send me off-list a topology file and a restart or trajectory
with a few frames that illustrates the problem you are having? It will
be easier for me to make recommendations if I can see exactly what is
going awry. Thanks!
-Dan
On Sun, Oct 18, 2015 at 4:33 PM, Romero, Raquel
<raquel.romero.12.ucl.ac.uk> wrote:
>
>
> 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
--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Mon Oct 19 2015 - 13:00:02 PDT
