[gmx-users] FWSpider Tutorial

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 fws.gro –d 0.7 editconf –f out.gro –o

Re: [gmx-users] FWSpider Tutorial

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 fws.gro –d 0.7

Re: [gmx-users] FWSpider Tutorial

Hi Nayef, grompp –f em.mdp –c fws_b4em.gro –p fws.top –o fws_em.tpr genion –s fws_em.tpr –o fws_ion.gro –nname CL- –nn 2 –g fws_ion.log [select Group 12: SOL] pico fws.top [reduce number of SOL by two and add 2 CL- at the end of the file] This is all fine. You take the structure before em,

Re: [gmx-users] FWSpider Tutorial

...@gmail.com To: jalem...@vt.edu; Discussion list for GROMACS users gmx-users@gromacs.org Sent: Wednesday, June 30, 2010 10:51 PM Subject: Re: [gmx-users] FWSpider Tutorial Hi Nayef, grompp –f em.mdp –c fws_b4em.gro –p fws.top –o fws_em.tpr genion –s fws_em.tpr –o fws_ion.gro –nname CL- –nn 2 –g