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-- Mengjuei Hsieh, Molecular Biology & Biochem, Univ. of California Irvine. > From: Ray Luo <ray.luo.uci.edu> > Date: Fri, 08 Jan 2010 09:24:39 -0800 > To: xueqin pang <pangxueqintea.yahoo.com.cn> > Cc: MengJuei Hsieh <mengjueh.uci.edu> > Subject: Re: error when doing mm-pbsa > > This is the error message that the last mmpbsa bugfix was intended to > fix ... I'm emailing MJ on this, who compiled the bugfix. > > All the best, > Ray > > ========================================== > Ray Luo, Ph.D. > Associate Professor in Computational > Biochemistry and Molecular Biophysics > Dept of Molecular Biology and Biochemistry > Dept of Biomedical Engineering > University of California, Irvine, CA 92697-3900 > Email: rluo.uci.edu Phones: (949) 824-9528, 9562 > Web: http://rayl0.bio.uci.edu/rayl/ > ========================================== > > > > xueqin pang wrote: >> Prof. Ray Luo >> >> Thanks for your kind help >> >> I am using Amber10 now. I have down load the bugfix for ambertools >> version1.2(http://ambermd.org/bugfixesat.html) and bugfix for >> amber10(http://ambermd.org/bugfixes10.html). After patch them and >> recompiled amber10, it still can not get through for Examples in mm_pbsa. >> >> It stopped when *Calc delta from raw data*. And the out print is *No >> data for 0 + 0 PB ELRAELE 0.* >> >> There is little discuss on this and I find no answer for it. >> >> So, do you have any suggestions. Should I just use Amber9 for mm-pbsa? >> >> Thanks so much for your help >> >> Xueqin >> >> DICP CAS >> >> --- *10年1月8日，周五, Ray Luo /<ray.luo.uci.edu>/* 写道： >> >> >> 发件人: Ray Luo <ray.luo.uci.edu> >> 主题: Re: error when doing mm-pbsa >> 收件人: "xueqin pang" <pangxueqintea.yahoo.com.cn> >> 日期: 2010年1月8日,周五,上午2:40 >> >> Xueqin, >> >> This error message occurs without the bugfixes ... there is an >> extensive bug fix for Amber10 mmpbsa ... please patch all bugfixes >> and recompile to see whether you can pass all the mmpbsa examples >> within $AMBERHOME/src/mmpbsa first ... >> >> All the best, >> Ray >> >> ========================================== >> Ray Luo, Ph.D. >> Associate Professor in Computational >> Biochemistry and Molecular Biophysics >> Dept of Molecular Biology and Biochemistry >> Dept of Biomedical Engineering >> University of California, Irvine, CA 92697-3900 >> Email: rluo.uci.edu Phones: (949) 824-9528, 9562 >> Web: http://rayl0.bio.uci.edu/rayl/ >> ========================================== >> >> >> >> >> xueqin pang wrote: >>> Pro. Ray Luo >>> >>> Thanks for your previous suggestion on cutres. I have got it >>> following your suggestion. >>> >>> What is more, I have changed the cutres into 16, and the same >>> problem does not show up again. However the program exit when >>> "Calc delta from raw data". The output is:no data for 0+0 PB >>> ELRAELE 0. And there is no BOND VDWAALS and 1-4 VDW for both >>> receptor and complex. >>> So do you have any suggestions on this problem. >>> >>> Thanks for your kind help >>> >>> Pang Xueqin >>> >>> DICP CAS >>> >>> >>> ------------------------------------------------------------------------ >>> 好玩贺卡等你发，邮箱贺卡全新上线！ >>> >>> <http://cn.rd.yahoo.com/mail_cn/tagline/card/*http://card.mail.cn.yahoo.com/>>> > >> >> >> >> ------------------------------------------------------------------------ >> 好玩贺卡等你发，邮箱贺卡全新上线！ >> <http://cn.rd.yahoo.com/mail_cn/tagline/card/*http://card.mail.cn.yahoo.com/> > _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amberReceived on Sat Jan 09 2010 - 05:30:02 PST