Re: [gmx-users] removing number of sol

2013-03-02 Thread Erik Marklund
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 usi

Re: [gmx-users] removing number of sol

2013-03-02 Thread gromacs query
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

Re: [gmx-users] removing number of sol

2013-03-01 Thread Erik Marklund
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 ab

Re: [gmx-users] removing number of sol

2013-03-01 Thread gromacs query
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

Re: [gmx-users] removing number of sol

2013-03-01 Thread Erik Marklund
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

Re: [gmx-users] removing number of sol

2013-03-01 Thread Erik Marklund
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 '/3

Re: [gmx-users] removing number of sol

2013-03-01 Thread Justin Lemkul
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'

Re: [gmx-users] removing number of sol

2013-03-01 Thread gromacs query
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

Re: [gmx-users] removing number of sol

2013-03-01 Thread Erik Marklund
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 1:4

[gmx-users] removing number of sol

2013-03-01 Thread gromacs query
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 number