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

From: emilia wu <emiliawu.dicp.ac.cn>
Date: Tue, 23 Jan 2007 10:45:46 +0800

Dear Ray,

thanks for all the help! it work when the GB option is turned off, but I need the GB result
to do the decomosition, could you please tell me which file should be use to add the parameters
for F atom?


emilia

        

======= 2007-01-23 10:37:01 艇壓栖佚嶄亟祇=======

>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.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: Monday, January 22, 2007 4:23 PM
>To: amber.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 艇壓栖佚嶄亟祇=======
>
>>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
>>撰
>>
>>
>>        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
>>
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>
>= = = = = = = = = = = = = = = = = = = =
>
>
>        崑
>撰
>
>
>        emilia wu
>        emiliawu.dicp.ac.cn
>          2007-01-22
>
>-----------------------------------------------------------------------
>The AMBER Mail Reflector
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= = = = = = = = = = = = = = = = = = = =
                        

        崑

 
                                 
        emilia wu
        emiliawu.dicp.ac.cn
          2007-01-23

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Received on Wed Jan 24 2007 - 06:07:30 PST
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