Re: Biphasic box (fwd)

From: James W. Caldwell <>
Date: Tue 3 Dec 2002 15:15:50 -0800 (PST)

You need parameters for the Chloroform. Use


On Tue, 3 Dec 2002 wrote:

>---------- Forwarded message ----------
>Date: Tue, 3 Dec 2002 14:52:54 +0000 (GMT)
>From: Gemma Kinsella <>
>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,

James W. Caldwell                         (voice) 415-476-8603
Department of Pharmaceutical Chemistry    (fax)   415-502-1411  
Mail Stop 0446                            (email)
513 Parnassus Avenue                      
University of California                  
San Francisco, CA 94143-0446               
Received on Tue Dec 03 2002 - 15:15:50 PST
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