i have encounter the same problem with Amber 10. my system is 40807 atoms.
when i chose the whole system, the severe(174) is coming 。
when i shorten my systems to 1-6041(just contains protein), th output gave out severe(71) error because integer divide by zero.
looking forward to reponse.
------------------
Name：Zeng Zhi-Ping Ph.D
Email：zengzhiping.xmu.edu.cn
interest: organic phosphorus chemistry and drug design
software：DOCK6.2;AUTODOCK4.0;AMBER10;
address：Department of Chemistry, Xiamen University,
the Key Laboratory for Chemical Biology of Fujian Province,
Xiamen 361005, People’s Republic of China
2009-12-24
-------------------------------------------------------------
发件人：Carlos Simmerling
发送日期：2009-12-24 00:12:28
收件人：AMBER Mailing List
抄送：
主题：Re: [AMBER] NEB-error
is it possible to try amber10? amber9 is quite old by now. I looked at
amber10 addles and the default sizes should be plenty for your system.
if you can't try amber10, email me the input prmtop and crd file and I will
try it.
On Wed, Dec 23, 2009 at 11:04 AM, balaji nagarajan <balaji_sethu.hotmail.com
> wrote:
>
> dear amber !
>
>
> I have a two different DNA structures of 20 base pairs ,
> I would like to do NEB , I have already posted the error
> of segmentation fault regarding this ,
>
> It has totaly 1260 atoms , I have edited the SIZE.h file as said in earlier
> mails ,
> Now the addles.in is running without any error for 4 copies
> I was not able to do more than that , if i do more than 4 copies it is
> saying the same error (segmentation fault )
>
> I have attached all the files,
> I would like to generate more copies ,
> could any one help me regarding this
>
> thanks in advance !
>
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Received on Wed Dec 23 2009 - 09:00:03 PST
