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

From: emilia wu <emiliawu.dicp.ac.cn>
Date: Sat, 20 Jan 2007 09:54:27 +0800

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
>-----------------------------------------------------------------------
>The AMBER Mail Reflector
>To post, send mail to amber.scripps.edu
>To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
>
>-----------------------------------------------------------------------
>The AMBER Mail Reflector
>To post, send mail to amber.scripps.edu
>To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu

= = = = = = = = = = = = = = = = = = = =
                        

        崑

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

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Sun Jan 21 2007 - 06:07:43 PST
Custom Search