ligprep的命令组成

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  

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 -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  

• ligprep running: applyhtreat

  applyhtreat ligtest_subjob_1.mae ligtest-out_subjob_1_htout.maegz All-None all 1 > ligtest-out_subjob_1_ht.log 2>&1

• ligprep running: desalter

  desalter ligtest-out_subjob_1_htout.maegz ligtest-out_subjob_1_dsout.maegz > ligtest-out_subjob_1_ds.log 2>&1

• ligprep running: neutralizer

  neutralizer ligtest-out_subjob_1_dsout.maegz ligtest-out_subjob_1_nuout.maegz > ligtest-out_subjob_1_nu.log 2>&1

• ligprep running: epik

  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

• ligprep running: stereoizer

  stereoizer -n 32 ligtest-out_subjob_1_epikout.maegz ligtest-out_subjob_1_stout.maegz > ligtest-out_subjob_1_st.log 2>&1

• ligprep running: ring_conf

  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

• ligprep running: premin

  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

• ligprep running: bmin

  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.

从上面分析可知，我们只需要执行到ligprep running: stereoizer这一步的结果，文件名的后缀是_stout.maegz。后面的环优化，能量优化（premin bmin）不需要执行，否则会改变原来的构象。

—-图形界面操作下 的log文件

para_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

……………………………….
Number of structures to process:                   1
More jobs requested (2) than number of structures to process (1).
Number of jobs set to 1.

All output structures will be stored in one file called ligtest-out.maegz.

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.maegz

 Subjob 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…
  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.

Done running subjobs.

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:schrodinger

LIGPREP_VERSION  25111
Ligprep. Copyright Schrodinger, LLC. All rights reserved.

JobID:  chenzq-PC-0-54fbb6b6
input and output are ligtest_subjob_1.mae ligtest-out_subjob_1.maegz
-pht value given in -W option overrides default value for -expand_i

-ph value given in -W option overrides default value for -expand_i

Running ligprep
input file: ligtest_subjob_1.mae
output file: ligtest-out_subjob_1.maegz

of input structures: 1

Options:

-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

ligprep running: applyhtreat
applyhtreat ligtest_subjob_1.mae ligtest-out_subjob_1_htout.maegz All-None all 1 > ligtest-out_subjob_1_ht.log 2>&1

applyhtreat # of output structures: 1

ligprep running: desalter
desalter ligtest-out_subjob_1_htout.maegz ligtest-out_subjob_1_dsout.maegz > ligtest-out_subjob_1_ds.log 2>&1

desalter # of output structures: 1

ligprep running: neutralizer
neutralizer ligtest-out_subjob_1_dsout.maegz ligtest-out_subjob_1_nuout.maegz > ligtest-out_subjob_1_nu.log 2>&1

neutralizer # of output structures: 1

ligprep running: epik
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

epik # of output structures: 1

ligprep running: stereoizer
stereoizer -n 32 ligtest-out_subjob_1_epikout.maegz ligtest-out_subjob_1_stout.maegz > ligtest-out_subjob_1_st.log 2>&1

stereoizer # of output structures: 1

ligprep running: ring_conf
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

ring_conf # of output structures: 1

ligprep running: premin
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>&1

premin # of output structures: 1

ligprep running: bmin
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: 1

Copying ligtest-out_subjob_1_bmout.maegz to ligtest-out_subjob_1.maegz

ligprep  complete.

of structures in output file ( ligtest-out_subjob_1.maegz ): 1

Time: 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.
Number of structures placed in ligtest-out.maegz: 1.

All subjob files being placed in a single gzipped tar file: ligtest-out.tar.gz.

Sun, 8 Mar 2015 10:41:39
Job Complete

generated by haroopad

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