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

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 --

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

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

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

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 jalem...@vt.edu: ahmet yıldırım wrote:

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

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 tsje...@gmail.com yazdı: Hey, Well, for those things it also doesn't hurt to know a few standard linux tools: grep -v SOL xxx.pdb