AMBER Archive (2009)

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

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Wed Dec 23 2009 - 10:46:59 CST

we need more detail, this is unclear. please provide input files that worked
and did not, and output from addles so we can see what it did.

On Wed, Dec 23, 2009 at 11:44 AM, xmzpzengs <xmzpzengs_at_gmail.com> wrote:

> 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 !
> >
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