Hi,
As you are discovering, tleap is not well-suited to creating membrane
systems. You'll likely have better luck using either CHARMM-GUI
(
http://www.charmm-gui.org, can produce Amber-compatible files) or the
new Packmol-MemGen tool bundled with more recent versions of
AmberTools.
Good luck,
-Dan
On Tue, Jun 18, 2019 at 2:40 AM xmgign.126.com <xmgign.126.com> wrote:
>
> Deal all,
>
> I have already asked a few questions and got patient answers, thank you very much. But I encounter new problems when doing membrane protein simulation. I followed the tutorial (http://ambermd.org/tutorials/advanced/tutorial16/index.html) to build the box with the command:
> "set POPC box { 63.180 63.436 140.466 }
> saveamberparm POPC popc.prmotp popc.inpcrd
> ”
> There is a contradiction between the tutorial and the manual here, because the tutorial mentions that the "set box" will build a periodic box, while the manual says that the "set box" only builds a box. But the manual does not mention what commands can add a specific periodic box. The command solvateoct/solvatebox is not suitable for membrane proteins.
> Therefore, I can only use the "set box" command to add a box to the established membrane-water system. At present, the system has been able to run, but in the production run, I have encountered problems, as follows:
> "ERROR: Calculation halted. Periodic box dimensions have changed too much from their initial values.
> Your system density has likely changed by a large amount, probably from starting the simulation from a structure a long way from equilibrium"
>
> It looks like the system ran out of the box. How should this problem be solved?
>
> Thanks!
> Qiao Xue
>
>
>
> xmgign.126.com
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Received on Tue Jun 18 2019 - 09:30:02 PDT
