Changge,
For small molecules, it is a normal behavior as discussed on the list
before ... please change "fillratio" to 4 or higher in "pbsa.in",
instead of changing "scale".
All the best,
Ray
Changge Ji wrote:
>Hi, Ray Luo!
>
>Thank you for your help.
>
>Originally , i used scale=2 , and it paused when calculating PB of the ligand . It says the grid spacing is too large .
>
>So i changed scale to 3 ,now it stops when calculating PB of the complex .
>
>Can I use different scales when calculating the ligand and the complex ?
>
>
>
>
>======= 2006-10-06 00:36:32 您在来信中写道：=======
>
>
>
>>Hi Changge,
>>
>>Have you tried to reduce the scale to see whether it works. You are
>>using a grid spacing of 0.333 A (scale=3), which is very fine for a
>>system of 16,000 atoms.
>>
>>Best,
>>Ray
>>
>>Changge Ji wrote:
>>
>>
>>
>>>hi, Folks.
>>>
>>>
>>>I did some MM_PBSA analysis with my dynamic traj.
>>>
>>>But it paused with the following error message : " PB Warning in epsbnd(): No neighbor found for boundary grids total: 61
>>>"
>>>
>>>parameters used in mm_pbsa.in are
>>>
>>>"
>>>PROC 2
>>>REFE 0
>>>INDI 1.0
>>>EXDI 80.0
>>>SCALE 3
>>>LINIT 3000
>>>PRBRAD 1.4
>>>"
>>>
>>>
>>>I found out that this error message comes from pb_exmol.f ,but I don't know what it really means ?
>>>
>>>And how can I fixed it .
>>>
>>>By the way ,my system is very large , the protein contains about 16000 atoms .
>>>but some parameters were already changed according to my protein ,(such as MAXMUM NUMBER OF ATOMS )
>>>
>>>
>>>
>>>
>>>
>>> Thank you very much for your sincerely help.
>>>
>>>
>>>
>>>Best wished ,
>>>
>>> Yours ,
>>> Changge Ji
>>> jcg.itcc.nju.edu.cn
>>> 2006-10-05
>>>-----------------------------------------------------------------------
>>>The AMBER Mail Reflector
>>>To post, send mail to amber.scripps.edu
>>>To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
>>>
>>>.
>>>
>>>
>>>
>>>
>>>
>>--
>>====================================================
>>Ray Luo, Ph.D.
>>Department of Molecular Biology and Biochemistry
>>University of California, Irvine, CA 92697-3900
>>Office: (949)824-9528 Lab: (949)824-9562
>>Fax: (949)824-8551 e-mail: rluo.uci.edu
>>Home page: http://rayl0.bio.uci.edu/rayl/
>>====================================================
>>
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>>
>>
>>__________ NOD32 1.1791 (20061005) Information __________
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>>
>>
>>
>
>= = = = = = = = = = = = = = = = = = = =
>
>
> 致
>礼！
>
>
> Changge Ji
> jcg.itcc.nju.edu.cn
> 2006-10-06
>
>-----------------------------------------------------------------------
>The AMBER Mail Reflector
>To post, send mail to amber.scripps.edu
>To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
>
>.
>
>
>
--
====================================================
Ray Luo, Ph.D.
Department of Molecular Biology and Biochemistry
University of California, Irvine, CA 92697-3900
Office: (949)824-9528 Lab: (949)824-9562
Fax: (949)824-8551 e-mail: rluo.uci.edu
Home page: http://rayl0.bio.uci.edu/rayl/
====================================================
-----------------------------------------------------------------------
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To post, send mail to amber.scripps.edu
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Received on Sun Oct 08 2006 - 06:07:30 PDT
