AMBER Archive (2006)

Subject: Re: Re: AMBER: PBSA calculation fail ....

From: Changge Ji (jcg_at_itcc.nju.edu.cn)
Date: Thu Oct 05 2006 - 21:36:34 CDT

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 ÄúÔÚÀ´ÐÅÖÐдµÀ£º=======

>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_at_itcc.nju.edu.cn
>>¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡2006-10-05
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>>
>>.
>>
>>
>>
>
>--
>====================================================
>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_at_uci.edu
>Home page: http://rayl0.bio.uci.edu/rayl/
>====================================================
>
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= = = = = = = = = = = = = = = = = = = =
                        

¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡ÖÂ
Àñ£¡
 
                                 
¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡Changge Ji
¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡jcg_at_itcc.nju.edu.cn
¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡2006-10-06

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