AMBER Archive (2002)

Subject: Re: Biphasic box (fwd)

From: James W. Caldwell (caldwell_at_heimdal.compchem.ucsf.edu)
Date: Tue Dec 03 2002 - 17:15:50 CST

You need parameters for the Chloroform. Use
amber7/dat/solvents/cform/frcmod.chcl3

jim

On Tue, 3 Dec 2002 amber_at_heimdal.compchem.ucsf.edu wrote:

>
>
>---------- 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
>
>
>
> 

-- 

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James W. Caldwell                         (voice) 415-476-8603
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