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
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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.uci.edu
>Home page: http://rayl0.bio.uci.edu/rayl/
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= = = = = = = = = = = = = = = = = = = =
致
礼！
Changge Ji
jcg.itcc.nju.edu.cn
2006-10-06
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Received on Sun Oct 08 2006 - 06:07:25 PDT
