||
结论:要保持构象,需要在命令行中执行的时候添加-nc参数,最后选择stout.maegz后缀的文件就可以了。图形界面无法设置-nc参数ligprep -nz -epik -W e,-ph,7.0,-pht,2.0 -s 32 -r 1 -bff 14 -imae ligtest_subjob_1.mae -omae ligtest-out_subjob_1.maegz
ligprep -nc -nz -epik -W e,-ph,7.0,-pht,2.0 -s 32 -r 1 -bff 14 -imae ligtest_subjob_1.mae -omae ligtest-out_subjob_1.maegz
applyhtreat ligtest_subjob_1.mae ligtest-out_subjob_1_htout.maegz All-None all 1 > ligtest-out_subjob_1_ht.log 2>&1
desalter ligtest-out_subjob_1_htout.maegz ligtest-out_subjob_1_dsout.maegz > ligtest-out_subjob_1_ds.log 2>&1
neutralizer ligtest-out_subjob_1_dsout.maegz ligtest-out_subjob_1_nuout.maegz > ligtest-out_subjob_1_nu.log 2>&1
epik -NO_REDIRECT -ph 7.0 -pht 2.0 -tn 8 -ma 200 -imae ligtest-out_subjob_1_nuout.maegz -omae ligtest-out_subjob_1_epikout.maegz > ligtest-out_subjob_1_epik.log 2>&1
stereoizer -n 32 ligtest-out_subjob_1_epikout.maegz ligtest-out_subjob_1_stout.maegz > ligtest-out_subjob_1_st.log 2>&1
ring_conf -l 3 -n 1 ligtest-out_subjob_1_stout.maegz ligtest-out_subjob_1_rcout.maegz > ligtest-out_subjob_1_rc.log 2>&1
premin -lic ligprep -m filter -f 14 -s ligtest-out_subjob_1_prout.maegz -u ligtest-out_subjob_1_prout_bad.maegz ligtest-out_subjob_1_rcout.maegz > ligtest-out_subjob_1_pr.log 2>&1
bmin -LOCAL -INTERVAL 5 -NO_REDIRECT ligtest-out_subjob_1_bmrun > ligtest-out_subjob_1_bm.log 2>&1
bmin
为了保留上面的中间过程,一定要添加-nc 参数
-nc Do not remove intermediate files. Default is to remove intermediate files.
—-图形界面操作下 的log文件
generated by haroopadpara_ligprep. Copyright Schrodinger, LLC. All rights reserved.
Jobid: chenzq-PC-0-54fbb6b0
======================================
Running para_ligprep
Sun, 8 Mar 2015 10:40:52
Version: LIGPREP_VERSION 25111
Command (excluding NJOBS and HOST): para_ligprep -epik -W e,-ph,7.0,-pht,2.0 -s 32 -r 1 -bff 14 -imae ligtest.mae -omae ligtest-out.maegz
NJOBS from command line: 2
Node list: localhost:2
Total Processors: 2……………………………….
All output structures will be stored in one file called ligtest-out.maegz.
Number of structures to process: 1
More jobs requested (2) than number of structures to process (1).
Number of jobs set to 1.Running subjobs.
hostcommandLine: D:schrodinger/ligprep -nz -epik -W e,-ph,7.0,-pht,2.0 -s 32 -r 1 -bff 14 -imae ligtest_subjob_1.mae -omae ligtest-out_subjob_1.maegzSubjob D:schrodinger/ligprep -nz -epik -W e,-ph,7.0,-pht,2.0 -s 32 -r 1 -bff 14 -imae ligtest_subjob_1.mae -omae ligtest-out_subjob_1.maegz ( chenzq-PC-0-54fbb6b6 ) was launched
Waiting for subjobs to finish…
Waiting for subjobs to finish…
Waiting for subjobs to finish…
Done running subjobs.
Subjob ligprep -nz -epik -W e,-ph,7.0,-pht,2.0 -s 32 -r 1 -bff 14 -imae ligtest_subjob_1.mae -omae ligtest-out_subjob_1.maegz (chenzq-PC-0-54fbb6b6) completed.Organizing Output Files.
…………………………………….
Collecting Results from Job: ligtest-out_subjob_1
STARTUP COMMAND:
D:schrodingermacromodel-v9.9binWIN32-x86ligprep.py -W e,-ph,7.0,-pht,2.0 -imae ligtest_subjob_1.mae -omae ligtest-out_subjob_1.maegz -nz -s 32 -r 1 -bff 14 -epik
MMSHARE_EXEC: D:schrodingermmshare-v2.0binWIN32-x86
STARTUP SCRIPT:
D:schrodingermacromodel-v9.9binWIN32-x86ligprep_startup.py
SCHRODINGER: D:schrodingerLIGPREP_VERSION 25111
Ligprep. Copyright Schrodinger, LLC. All rights reserved.JobID: chenzq-PC-0-54fbb6b6
-ph value given in -W option overrides default value for -expand_i
input and output are ligtest_subjob_1.mae ligtest-out_subjob_1.maegz
-pht value given in -W option overrides default value for -expand_iRunning ligprep
of input structures: 1
input file: ligtest_subjob_1.mae
output file: ligtest-out_subjob_1.maegzOptions:
-W e,-ph,7.0,-pht,2.0 -imae ligtest_subjob_1.mae -omae ligtest-out_subjob_1.maegz -nz -s 32 -r 1 -bff 14 -epikligprep running: applyhtreat
applyhtreat # of output structures: 1
applyhtreat ligtest_subjob_1.mae ligtest-out_subjob_1_htout.maegz All-None all 1 > ligtest-out_subjob_1_ht.log 2>&1ligprep running: desalter
desalter # of output structures: 1
desalter ligtest-out_subjob_1_htout.maegz ligtest-out_subjob_1_dsout.maegz > ligtest-out_subjob_1_ds.log 2>&1ligprep running: neutralizer
neutralizer # of output structures: 1
neutralizer ligtest-out_subjob_1_dsout.maegz ligtest-out_subjob_1_nuout.maegz > ligtest-out_subjob_1_nu.log 2>&1ligprep running: epik
epik # of output structures: 1
epik -NO_REDIRECT -ph 7.0 -pht 2.0 -tn 8 -ma 200 -imae ligtest-out_subjob_1_nuout.maegz -omae ligtest-out_subjob_1_epikout.maegz > ligtest-out_subjob_1_epik.log 2>&1ligprep running: stereoizer
stereoizer # of output structures: 1
stereoizer -n 32 ligtest-out_subjob_1_epikout.maegz ligtest-out_subjob_1_stout.maegz > ligtest-out_subjob_1_st.log 2>&1ligprep running: ring_conf
ring_conf # of output structures: 1
ring_conf -l 3 -n 1 ligtest-out_subjob_1_stout.maegz ligtest-out_subjob_1_rcout.maegz > ligtest-out_subjob_1_rc.log 2>&1ligprep running: premin
premin # of output structures: 1
OK structures in: ligtest-out_subjob_1_prout.maegz
problematic structures in: ligtest-out_subjob_1_prout_bad.maegz
premin -lic ligprep -m filter -f 14 -s ligtest-out_subjob_1_prout.maegz -u ligtest-out_subjob_1_prout_bad.maegz ligtest-out_subjob_1_rcout.maegz > ligtest-out_subjob_1_pr.log 2>&1ligprep running: bmin
Copying ligtest-out_subjob_1_bmout.maegz to ligtest-out_subjob_1.maegz
input file: ligtest-out_subjob_1_prout.maegz
output file : ligtest-out_subjob_1_bmout.maegz
bmin -LOCAL -INTERVAL 5 -NO_REDIRECT ligtest-out_subjob_1_bmrun > ligtest-out_subjob_1_bm.log 2>&1
bmin # of output structures: 1ligprep complete.
of structures in output file ( ligtest-out_subjob_1.maegz ): 1Time: 0 hours 0 minutes 29.8 seconds
…………………………………….
End of Log files for subjobs.All structure file output placed in one output structure file: ligtest-out.maegz.
All subjob files being placed in a single gzipped tar file: ligtest-out.tar.gz.
Number of structures placed in ligtest-out.maegz: 1.Sun, 8 Mar 2015 10:41:39
Job Complete
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