Aha! thanks Erik (and Justin), I really feel sorry 35 and 135 will be removed by sed. I must have given a thought about that. So this was reason sed was over doing the things. Also as you asked: They are random residue number water molecules so not continuous and they were selected on the criteria based on X Y Z coordinates (some space fixed and outlier waters are to be removed)
regards, On Fri, Mar 1, 2013 at 3:09 PM, Erik Marklund <er...@xray.bmc.uu.se> wrote: > > On Mar 1, 2013, at 2:08 PM, Erik Marklund wrote: > > >> On Mar 1, 2013, at 1:58 PM, gromacs query wrote: >> >> Dear Erik, >>> >>> so you can filter out the unwanted residues there instead of using an >>>>> >>>> index file. >>> >>> There are thousands of water to be removed so simple commands like sed >>> exhausts when I run it in loops. e.g. Just to say : >>> >>> sed -e '/35SOL/d' -e '/36SOL/d' -e '/38SOL/d' -e '/39SOL/d' -e '/40SOL/d' >>> -e '/41SOL/d' -e '/42SOL/d' -e '/43SOL/d' -e '/44SOL/d' -e '/45SOL/d' >>> old.gro > new2.gro >>> >>> this will remove such 10 residues but if you run this again and again (in >>> text exe format) say 1000 times it exhausts some how and remove waters >>> which are not even mentioned in sed command! I have checked it many >>> times. >>> So I thought if index file could help me. But please reply for point 3: >>> >> >> First of all, that's not a safe way of removing waters. Note that both >> SOL 35, SOL 135, ... will be removed by that command. Secondly, I'm sure >> you can think of a better way of scripting it, using e.g. sed or awk. By >> which criteria do you select the waters to be removed? >> > > If its a contiguous chunk then it's dead simple. > > > >> >>> 3) Also once I get index file can editconf help to write a new gro >>>>>> >>>>> without the residues mentioned in index file?. I used this editconf -f >>> my.gro -n index.ndx -o del.gro . >>> >>> >>> thanks, >>> >>> This gave me del.gro having residues mentioned in index file. But I want >>> del.gro file without the residues mentioned in index file. >>> >>> On Fri, Mar 1, 2013 at 2:48 PM, Erik Marklund <er...@xray.bmc.uu.se> >>> wrote: >>> >>> The ndx format is really simple. You can easily script your way to a new >>>> index group as long as the selection of atoms can be automated. >>>> Furthermore, the gro format is also simple, so you can filter out the >>>> unwanted residues there instead of using an index file. >>>> >>>> Erik >>>> >>>> >>>> On Mar 1, 2013, at 1:42 PM, gromacs query wrote: >>>> >>>> Dear All, >>>> >>>>> >>>>> I know the residue numbers of SOL molecules (which are more than >>>>> thousands) >>>>> which I want to remove them from a gro file. I searched that make_ndx >>>>> can >>>>> be used make a index file to define residues. But It is a prompt based >>>>> tool >>>>> and its difficult to type manually thousands of residue numbers. >>>>> >>>>> 1) Is there some way to feed the residue numbers to make_ndx? Or I >>>>> need to >>>>> make index file format my self by some scritpting Or is there is rather >>>>> easier way of doing in gromacs. >>>>> >>>>> 2) Also is there any direct command which helps to remove a residue >>>>> number >>>>> directly from a gro file without using index file input; means residue >>>>> defined in command itself? >>>>> >>>>> 3) Also once I get index file can editconf help to write a new gro >>>>> without >>>>> the residues mentioned in index file?. I used this editconf -f my.gro >>>>> -n >>>>> index.ndx -o del.gro . >>>>> >>>>> This gave me del.gro having residues mentioned in index file. But I >>>>> want >>>>> del.gro file without the residues mentioned in index file. >>>>> >>>>> >>>>> regards, >>>>> -- >>>>> gmx-users mailing list gmx-users@gromacs.org >>>>> http://lists.gromacs.org/****mailman/listinfo/gmx-users<http://lists.gromacs.org/**mailman/listinfo/gmx-users> >>>>> <htt**p://lists.gromacs.org/mailman/**listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> >>>>> > >>>>> * Please search the archive at http://www.gromacs.org/** >>>>> Support/Mailing_Lists/Search<h**ttp://www.gromacs.org/Support/** >>>>> Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>>before >>>>> posting! >>>>> * Please don't post (un)subscribe requests to the list. Use the >>>>> www interface or send it to gmx-users-requ...@gromacs.org. >>>>> * Can't post? Read >>>>> http://www.gromacs.org/****Support/Mailing_Lists<http://www.gromacs.org/**Support/Mailing_Lists> >>>>> <http://**www.gromacs.org/Support/**Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> >>>>> > >>>>> >>>>> >>>> -- >>>> gmx-users mailing list gmx-users@gromacs.org >>>> http://lists.gromacs.org/****mailman/listinfo/gmx-users<http://lists.gromacs.org/**mailman/listinfo/gmx-users> >>>> <htt**p://lists.gromacs.org/mailman/**listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> >>>> > >>>> * Please search the archive at http://www.gromacs.org/** >>>> Support/Mailing_Lists/Search<h**ttp://www.gromacs.org/Support/** >>>> Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>>before >>>> posting! >>>> * Please don't post (un)subscribe requests to the list. Use thewww >>>> interface or send it to gmx-users-requ...@gromacs.org. >>>> * Can't post? 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Read >>> http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> >>> >> >> -- >> gmx-users mailing list gmx-users@gromacs.org >> http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> >> * Please search the archive at http://www.gromacs.org/** >> Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before >> posting! >> * Please don't post (un)subscribe requests to the list. Use thewww >> interface or send it to gmx-users-requ...@gromacs.org. >> * Can't post? 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