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 您在来信中写道：=======
>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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致
礼！
emilia wu
emiliawu.dicp.ac.cn
2007-01-20
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Received on Sun Jan 21 2007 - 06:07:43 PST
