Re: [gmx-users] remove all waters from the pdb file

2011-01-27 Thread ahmet yıldırım
Dear Tsjerk, Thank you. Problem is solved. Removing waters from the pdb file: grep -v "HOH" xxx.pdb > nosol.pdb 27 Ocak 2011 21:37 tarihinde Tsjerk Wassenaar yazdı: > Hey, > > Well, for those things it also doesn't hurt to know a few standard linux > tools: > > grep -v "SOL" xxx.pdb > nosol.

Re: [gmx-users] remove all waters from the pdb file

2011-01-27 Thread Tsjerk Wassenaar
Hey, Well, for those things it also doesn't hurt to know a few standard linux tools: grep -v "SOL" xxx.pdb > nosol.pdb And if there are also ions in play: grep -v "\(SOL\|NA\|CL\)" xxx.pdb > nosol.pdb Hope it helps, Tsjerk 2011/1/27 Justin A. Lemkul : > > > ahmet yıldırım wrote: >> >> Dear u

Re: [gmx-users] remove all waters from the pdb file

2011-01-27 Thread Justin A. Lemkul
ahmet yıldırım wrote: Dear users, I want to remove all waters from the xxx.pdb file. Then, I want to save the pdb file (new pdb) without waters because I will use the methanol as a solvent. I looked at mail list but I could not find the answer I wanted. What should I do? Please read trj

[gmx-users] remove all waters from the pdb file

2011-01-27 Thread ahmet yıldırım
Dear users, I want to remove all waters from the xxx.pdb file. Then, I want to save the pdb file (new pdb) without waters because I will use the methanol as a solvent. I looked at mail list but I could not find the answer I wanted. What should I do? Thanks in advance -- Ahmet YILDIRIM -- gmx-