RE: RE: AMBER: PB Bomb in pb_aaradi(): No radius assigned for atom 4474 F3 f

From: Ray Luo <rluo.uci.edu>
Date: Sat, 20 Jan 2007 10:45:36 -0800

Emilia,

I forgot to mention ... if you use radiopt=0, you also need to set npopt=1
(the default is 2). See PB manual pages for more info.

Best,
Ray

==========================================
Ray Luo, Ph.D.
Dept Molecular Biology & Biochemistry
University of California, Irvine, CA 92697
USPS: PO Box 3900
Phone: (949) 824-9528
Email: rluo.uci.edu
Web: http://rayl0.bio.uci.edu/
==========================================


-----Original Message-----
From: owner-amber.scripps.edu [mailto:owner-amber.scripps.edu] On Behalf Of
emilia wu
Sent: Friday, January 19, 2007 5:54 PM
To: amber.scripps.edu
Subject: Re: RE: AMBER: PB Bomb in pb_aaradi(): No radius assigned for atom
4474 F3 f

Hi, Ray

Thanks for your reply. I already try radiopt=0, but it still can not pass,
and
the output file of pbsa_com.1.out gives out "PB Bomb in pb_read(): use of
radi other than vdw sigma for
                       np solvation dispersion/cavity is not supported!".
so what should I do?


emilia

        

======= 2007-01-20 03:58:18 艇壓栖佚嶄亟祇=======

>Emilia,
>
>Since you are using gaff force field, as indicated by lower-case atom
types,
>please set radiopt = 0 to use the radii in your prmtop file.
>
>Best,
>Ray
>
>==========================================
>Ray Luo, Ph.D.
>Dept Molecular Biology & Biochemistry
>University of California, Irvine, CA 92697
>USPS: PO Box 3900
>Phone: (949) 824-9528
>Email: rluo.uci.edu
>Web: http://rayl0.bio.uci.edu/
>==========================================
>
>
>-----Original Message-----
>From: owner-amber.scripps.edu [mailto:owner-amber.scripps.edu] On Behalf Of
>emilia wu
>Sent: Friday, January 19, 2007 5:16 AM
>To: amber
>Subject: AMBER: PB Bomb in pb_aaradi(): No radius assigned for atom 4474 F3
>f
>
>Dear amber users,
>
> I try to calculate the binding free energy of an inhibitor and a protein
>with MM/PBSA using Amber9,
>but it stopped and the output tell me that"PB Bomb in pb_aaradi(): No
radius
>assigned for atom
> 4474 F3 f". and there is a fluorin atom in the inhibitor, so how to fix
>it, if I should add some
>radius parameters for fluorin, which file should be modified, and what
>parameter should I use?
>
>thanks in advance!
>
>        emilia wu
>        emiliawu.dicp.ac.cn
>          2007-01-19
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= = = = = = = = = = = = = = = = = = = =
                        

        崑

 
                                 
        emilia wu
        emiliawu.dicp.ac.cn
          2007-01-20

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Received on Sun Jan 21 2007 - 06:07:49 PST
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