No, in my case it recognize ? like a ? in script I have
for sim in ${HOME}/${tit}* ; do if [[ -d $sim ]]; then simulation=$(basename "$sim") cd ${sim} rm dd_dump_err*.pdb trjconv -s md_${tit}?.tpr -f md_${tit}?.trr -o ${HOME}/output/${simulation}.xtc -n -pbc mol -ur compact -fit trans < ${HOME}/enter.txt and gromacs sent trjconv -s md_resp_complex?.tpr -f md_resp_complex?.trr -o /nfs_homes/clouddyn/MD_bench/Resp_cyt_cluster/output/resp_complex_conf7.xtc -n -pbc mol -ur compact -fit trans Is it possible specify more flexible e.g 1 of any character or 2 of any characters within the file name etc like REGEX syntax Thanks! J. 2016-04-26 12:45 GMT+02:00 Kutzner, Carsten <ckut...@gwdg.de>: > >> On 26 Apr 2016, at 11:22, James Starlight <jmsstarli...@gmail.com> wrote: >> >> Exactly the problem was there! >> >> BTW how to define selection more carefully (avoiding using *) tpr and >> trr to be sure that always only 1 file is selected assuming that all >> relevant trajectories and topologies are differs only on the digit e.g >> >> resp_complex_conf7/md_resp_complex_conf7.tpr >> resp_complex_conf7/md_resp_complex_conf6.tpr >> .. >> resp_complex_conf7/md_resp_complex_conf1.tpr > For a single-character wildcard you can use a '?', > e.g. > >> resp_complex_conf7/md_resp_complex_conf?.tpr > > > Carsten > > >> >> the same for trr >> >> J. >> >> 2016-04-26 11:11 GMT+02:00 Kutzner, Carsten <ckut...@gwdg.de>: >>> >>>> On 26 Apr 2016, at 11:00, James Starlight <jmsstarli...@gmail.com> wrote: >>>> >>>> Hello, >>>> >>>> I faced with the folliwing problem: >>>> >>>> I try to make small script which will loop several folders >>>> corresponded to the invididual simulations and procecc each trajectory >>>> searching them by the keyword >>>> trr_file="md_resp_complex_conf" >>>> >>>> >>>> #!/bin/bash >>>> >>>> HOME="/nfs_homes/clouddyn/MD_bench/Resp_cyt_cluster" >>>> trr_file="md_resp_complex_conf" >>>> tit="resp_complex" >>>> >>>> rm -r ${HOME}/output >>>> mkdir ${HOME}/output >>>> source /prog/gm502/bin/GMXRC >>>> >>>> for sim in ${HOME}/${tit}* ; do >>>> if [[ -d $sim ]]; then >>>> simulation=$(basename "$sim") >>>> pushd ${sim} >>>> rm dd_dump_err*.pdb >>>> trjconv -s ${HOME}/ref.gro -f ${trr_file}*.trr -o >>> if there are several files that match your ${trr_file}* pattern, then >>> bash will give you all of those. Try leaving away the * >>> or delete the other .trr files in that dir to make get only >>> one file there. >>> >>> Carsten >>> >>>> ${HOME}/output/${simulation}.xtc -n >>>> popd >>>> fi >>>> done >>>> >>>> >>>> >>>> finally I ontained >>>> >>>> trjconv -s /nfs_homes/clouddyn/MD_bench/Resp_cyt_cluster/ref.gro -f >>>> md_resp_complex_conf7_go.trr md_resp_complex_conf7.trr -o >>>> /nfs_homes/clouddyn/MD_bench/Resp_cyt_cluster/output/resp_complex_conf7.xtc >>>> -n -pbc nojump -ur compact -fit trans >>>> >>>> >>>> here you see that the problem that the trajectory is repeated twisely >>>> after -f which is the source of the error: >>>> >>>> -f md_resp_complex_conf7_go.trr md_resp_complex_conf7.trr >>>> >>>> Why this issue occures? As you see in my scriopt I defined all proprly >>>> >>>> trjconv -s ${HOME}/ref.gro -f ${trr_file}*.trr -o >>>> ${HOME}/output/${simulation}.xtc -n >>>> >>>> >>>> Thanks! >>>> >>>> J, >>>> -- >>>> Gromacs Users mailing list >>>> >>>> * Please search the archive at >>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! >>>> >>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>>> >>>> * For (un)subscribe requests visit >>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send >>>> a mail to gmx-users-requ...@gromacs.org. >>> >>> -- >>> Gromacs Users mailing list >>> >>> * Please search the archive at >>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! >>> >>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>> >>> * For (un)subscribe requests visit >>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send >>> a mail to gmx-users-requ...@gromacs.org. >> -- >> Gromacs Users mailing list >> >> * Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! >> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> * For (un)subscribe requests visit >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a >> mail to gmx-users-requ...@gromacs.org. > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a > mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.