Re: [gmx-users] removing number of sol
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. But I want del.gro file without the residues mentioned in index file. regards, -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users htt**p://lists.gromacs.org/mailman/listinfo/gmx-usershttp://lists.gromacs.org/**mailman/listinfo/gmx-users htt**p://lists.gromacs.org/**mailman/**listinfo/gmx-usershttp://lists.gromacs.org/mailman/**listinfo/gmx-users h**ttp://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://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/**http://www.gromacs.org/Support/** Mailing_Lists/Searchhttp://**www.gromacs.org/Support/** Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www
Re: [gmx-users] removing number of sol
If you have a pdb file instead of a gro file then e.g. pymol might be useful. Erik On Mar 2, 2013, at 2:01 PM, gromacs query wrote: 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. But I want del.gro file without the residues mentioned in index file. regards, -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users htt**p://lists.gromacs.org/mailman/listinfo/gmx-usershttp://lists.gromacs.org/**mailman/listinfo/gmx-users htt**p://lists.gromacs.org/**mailman/**listinfo/gmx-usershttp://lists.gromacs.org/mailman/**listinfo/gmx-users h**ttp://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://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/** http://www.gromacs.org/Support/** Mailing_Lists/Searchhttp://**www.gromacs.org/Support/**
[gmx-users] removing number of sol
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 listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at 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
Re: [gmx-users] removing number of sol
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 listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at 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 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at 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
Re: [gmx-users] removing number of sol
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: 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 listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at 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
Re: [gmx-users] removing number of sol
On 3/1/13 7:58 AM, 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: 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 . I don't know about editconf, but trjconv can do this. -Justin 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 listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at 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
Re: [gmx-users] removing number of sol
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? 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 listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://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_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://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? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at 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 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at 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
Re: [gmx-users] removing number of sol
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 listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://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_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://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? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at 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 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at 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? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to
Re: [gmx-users] removing number of sol
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 listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-usershttp://lists.gromacs.org/**mailman/listinfo/gmx-users htt**p://lists.gromacs.org/mailman/**listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchh**ttp://www.gromacs.org/Support/** Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://www.gromacs.org/**Support/Mailing_Lists http://**www.gromacs.org/Support/**Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-usershttp://lists.gromacs.org/**mailman/listinfo/gmx-users htt**p://lists.gromacs.org/mailman/**listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchh**ttp://www.gromacs.org/Support/** Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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? Read http://www.gromacs.org/Support/Mailing_Listshttp://www.gromacs.org/**Support/Mailing_Lists http://**www.gromacs.org/Support/**Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing
Re: [gmx-users] removing number of sol
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. But I want del.gro file without the residues mentioned in index file. regards, -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-usershttp://lists.gromacs.org/**mailman/listinfo/gmx-users htt**p://lists.gromacs.org/mailman/**listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchh**ttp://www.gromacs.org/Support/** Mailing_Lists/Searchhttp://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_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-usershttp://lists.gromacs.org/**mailman/listinfo/gmx-users htt**p://lists.gromacs.org/mailman/**listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchh**ttp://www.gromacs.org/Support/** Mailing_Lists/Searchhttp://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? Read
