AMBER Archive (2009)

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

From: xmzpzengs (
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
interest: organic phosphorus chemistry and drug design
address:Department of Chemistry, Xiamen University,
            the Key Laboratory for Chemical Biology of Fujian Province,
            Xiamen 361005, People’s Republic of China

发件人:Carlos Simmerling
发送日期:2009-12-24 00:12:28
收件人:AMBER Mailing List
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 <
> 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 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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