In my actual script says "center", sorry for the mistake.
Dan I will be sending the those frames soon, Thanks a lot!
Raquel
________________________________________
From: Hai Nguyen <nhai.qn.gmail.com>
Sent: 19 October 2015 20:59
To: AMBER Mailing List
Subject: Re: [AMBER] Membrane protein imagining problems
Hi
On Sun, Oct 18, 2015 at 6:33 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
>
Did you use exact command here in your real script? Because 'centre' is not
a valid word, should be 'center'.
> 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
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Oct 20 2015 - 05:00:05 PDT
