AMBER Archive (2009)

Subject: Re: Re: [AMBER] NEB-error

From: xmzpzengs (xmzpzengs_at_gmail.com)
Date: Wed Dec 23 2009 - 10:44:36 CST

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_at_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_at_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 !
>
> _________________________________________________________________
> Windows 7: Find the right PC for you. Learn more.
> http://windows.microsoft.com/shop
> _______________________________________________
> AMBER mailing list
> AMBER_at_ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
>
_______________________________________________
AMBER mailing list
AMBER_at_ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber

_______________________________________________
AMBER mailing list
AMBER_at_ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber