[gmx-users] Re: gmx-users Digest, Vol 74, Issue 189

- –nn 2 –g fws_ion.log Nayef Daher wrote: Hi I am trying to follow the tutorial listed on http://eugen.leitl.org/chem/kerrigje/pdf_files/fwspidr_tutor.pdf with the latest version of Gromacs, 4.0.7 The commands I typed were pdb2gmx –ignh –ff G43a1 –f 1OMB.pdb –o fws.gro –p fws.top editconf –f fw

[gmx-users] FWSpider Tutorial

4996) does not match topology (fws.top 4992) So what additional step do I need to take (or file to re-write) in order to solve this problem? Thanks! Nayef Daher PhD Chemical Engineering University of Alberta, Canada -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs

[gmx-users] Energy minimisation of solvated protein - Tutorial

Hi, I have the same problem as listed below back in February. I am using the latest gromacs version (4.0.7) and tried the solution below by entering genbox -cp 1qlz-PBC.gro -cs spc216.gro -p 1qlz.top -o 1qlz-water.gro instead of making the output as pdb file. Yet the same result occurs w