Dear Erik, I am new to Gromacs and used AMBER before, and I am exploring various options in GROMACS too. Surely I will look in to g_select. Also as I was using sed, one should include an extra space (using vi) in gro file just before residue number and then can use sed to remove like this: sed -e '/ 35SOL/d' -e '/ 36SOL/d' -e '/ 38SOL/d' -e '/ 39SOL/d' old.gro > new2.gro
But please note I included an extra space / 35SOL/d (instead of /35SOL/d) by this sed will remove 35SOL not 135SOL. regards, On Fri, Mar 1, 2013 at 5:27 PM, Erik Marklund <er...@xray.bmc.uu.se> wrote: > Hi, > > Then the problem lies in automating what molecules are to be removed, > right? Try g_select or look into trjorder. > > Erik > > > On Mar 1, 2013, at 2:45 PM, gromacs query wrote: > > 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. 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