Xueqin,
I still think you did not patch the bugfixes correctly. Could you start
from a fresh Amber10 installation and check again?
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 and MengJuei Hsieh,
>
> Thanks so much for your kind help.
>
> I am working on a 8-processor AMD x86_64 Linux system
>
> Amber is compiled with icc for amber tools and ifort for amber10
>
> To recompile Amber10 I deleted the files of bin exe lib and include in the old Amber. Does cause the errors?
>
> I just test the examples by: mm_pbsa.pl mm_pbsa.in > mm_pbsa.log &
>
> When test 01_GenerateSnapshots nothing went wrong.
>
> But when test 02_MMPBSA_Stability I get the following:
> No skew or curtosis when zero variance in moment
> Use of uninitialized value in addition (+) at /home/pxq/program/amber10/src/mm_pbsa/mm_pbsa_statistics.pm line 1836.
> Use of uninitialized value in subtraction (-) at /home/pxq/program/amber10/src/mm_pbsa/mm_pbsa_statistics.pm line 1848.
>
> And when test 03_MMPBSA_Binding, I get the massage:
> No data for 0+0 PB ELRAELE 0
> in the output field there are warnings:
> Reading ras_raf_II_wt_com.all.out
> WARNING: Missing PBNONPOL for PB in 0 -> Taken from -1
> WARNING: Missing ELRAELE for PB in 0 -> Taken from -1
> WARNING: Missing EPB for PB in 0 -> Taken from -1
> Reading ras_raf_II_wt_rec.all.out
> Checking CALC
> WARNING: Missing PBNONPOL for PB in 0 -> Taken from -1
> WARNING: Missing ELRAELE for PB in 0 -> Taken from -1
> WARNING: Missing EPB for PB in 0 -> Taken from -1
> Reading ras_raf_II_wt_lig.all.out
> Checking CALC
> WARNING: Missing PBNONPOL for PB in 0 -> Taken from -1
> WARNING: Missing ELRAELE for PB in 0 -> Taken from -1
> WARNING: Missing EPB for PB in 0 -> Taken from -1
> and the last step is
> =>> Calc delta from raw data
>
> When test 04_MMPBSA_Nmode, I get
> /home/pxq/program/amber10/exe/sander -O -i sanmin_lig.in -o sanmin_lig.1.out -c ../01_GenerateSnapshots/ras_raf_II_wt_lig.crd.1 -p ../raf_wt.prmtop -r sanmin_lig.1.restrt not running properly
> and it stopped at
> =>> Calculating energy / entropy contributions
> Calc contrib for ../01_GenerateSnapshots/ras_raf_II_wt_lig.crd.1
> Minimize structure
>
> I am not sure whether provide enough information for you. If other important information is needed please let me know. And if necessary I can send the output files to you.
>
> Thanks for taking time help me out
>
> Xueqin
>
> DICP CAS
>
>
>
>
> --- 10年1月9日，周六, MengJuei Hsieh <mengjueh.uci.edu> 写道：
>
>
> 发件人: MengJuei Hsieh <mengjueh.uci.edu>
> 主题: Re: error when doing mm-pbsa
> 收件人: "Ray Luo" <ray.luo.uci.edu>, "xueqin pang" <pangxueqintea.yahoo.com.cn>
> 日期: 2010年1月9日,周六,上午3:46
>
>
> Hi,
>
> The test cases are not supposed to fail like that even before the last
> mmpbsa bugfix. Can Xueqin tell us more what exactly did you run the test?
> That would be extremely helpful.
>
> Thanks,
>
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Received on Mon Jan 11 2010 - 11:30:02 PST
