AMBER Archive (2002)

Subject: Biphasic box (fwd)

From: amber_at_heimdal.compchem.ucsf.edu
Date: Tue Dec 03 2002 - 16:13:10 CST

---------- Forwarded message ----------
Date: Tue, 3 Dec 2002 14:52:54 +0000 (GMT)
From: Gemma Kinsella <maynooth_at_maths.tcd.ie>
To: amber_at_heimdal.compchem.ucsf.edu
Subject: Biphasic box

Hi all,

I'm trying to simulate a membrane protein and would be interested in using
a biphasic solvent box to do this. I've played around with the solvatebox
option and have been able to save a pdb file of my protein which has the
layers of solvent as I wanted them. To do this I solvated the helical
bundle in one solvent and then added the loop regions in to the pdb
and solvated the top and bottom of the box with water. So far however I've
been unable to save a prmtop or prmcrd file. If I read it from the pdb
file I get the leap error

FATAL: Atom .R<CL3 355>.A<H1 1> does not have a type.
FATAL: Atom .R<CL3 355>.A<C1 2> does not have a type.
FATAL: Atom .R<CL3 355>.A<CL1 3> does not have a type.
FATAL: Atom .R<CL3 355>.A<CL2 4> does not have a type.
FATAL: Atom .R<CL3 355>.A<CL3 5> does not have a type.
Failed to generate parameters
Parameter file was not saved.

I can save the prmtop and prmcrd for a single solvent with no
difficulty. What do I need to do for two?? Where would I find/need to add
this information to be able to read it the CL3 res from a pdb file?? Does
anyone have experience with biphasic boxes??

Many thanks for all your help,

Gemma