AMBER Archive (2007)

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

From: Ray Luo (rluo_at_uci.edu)
Date: Mon Jan 22 2007 - 20:35:06 CST

This comes from the GB radii assignment. So please also turn off GB unless
you know the radius parameters for atom type "f".

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_at_uci.edu
Web: http://rayl0.bio.uci.edu/
==========================================

-----Original Message-----
From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf Of
emilia wu
Sent: Monday, January 22, 2007 4:23 PM
To: amber_at_scripps.edu
Subject: Re: RE: RE: AMBER: PB Bomb in pb_aaradi(): No radius assigned for
atom 4474 F3 f

Hi, Ray

This time I set MS=0, radiopt=0, and npopt=1, but the job still can not
pass.
and the log file of mm_pbsa.pl gives out "
=>> Creating input
    Sander input
    PBSA input

=>> Calculating energy / entropy contributions
    Calc contrib for ../01/thrombin_cda_wat_com.crd.1
        Calc MM/GB/SAS
 bad atom type: f
        /home2/handicp/wuling/amber9/amber9/exe/sander -O -i sander_com.in
-o sander_com.1.out -c ../01/thrombin_cda_wat_com.crd.1 -p
../01/protein.prmtop not successful"

and the sander_com.1.out stop at "
Potential function:
     ntf = 1, ntb = 0, igb = 2, nsnb =
99999
     ipol = 0, gbsa = 1, iesp = 0
     dielc = 1.00000, cut = 999.00000, intdiel = 1.00000
     saltcon = 0.00000, offset = 0.09000, gbalpha= 0.80000
     gbbeta = 0.00000, gbgamma = 2.90912, surften = 1.00000
     rdt = 0.00000, rgbmax = 25.00000
     alpb = 0
     scnb = 2.00000, scee = 1.20000

Frozen or restrained atoms:
     ibelly = 0, ntr = 0

Energy minimization:
     maxcyc = 1, ncyc = 0, ntmin = 1
     dx0 = 0.01000, drms = 0.00010
"
how do I deal with it?
Thanks in advance!
        

emilia
======= 2007-01-21 02:50:58 ÄúÔÚÀ´ÐÅÖÐдµÀ£º=======

>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_at_uci.edu
>Web: http://rayl0.bio.uci.edu/
>==========================================
>
>
>-----Original Message-----
>From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf Of
>emilia wu
>Sent: Friday, January 19, 2007 5:54 PM
>To: amber_at_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 ÄúÔÚÀ´ÐÅÖÐдµÀ£º=======
>
>>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_at_uci.edu
>>Web: http://rayl0.bio.uci.edu/
>>==========================================
>>
>>
>>-----Original Message-----
>>From: owner-amber_at_scripps.edu [mailto:owner-amber_at_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_at_dicp.ac.cn
>>¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡2007-01-19
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>= = = = = = = = = = = = = = = = = = = =
>
>
>¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡ÖÂ
>Àñ£¡
>
>
>¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡emilia wu
>¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡emiliawu_at_dicp.ac.cn
>¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡2007-01-20
>
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¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡emilia wu
¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡emiliawu_at_dicp.ac.cn
¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡2007-01-22

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