[gmx-users] FWSpider Tutorial

Justin A. Lemkul jalemkul at vt.edu
Wed Jun 30 21:26:45 CEST 2010

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
> editconf –f out.gro –o fws_ctr.gro –center x/2 y/2 z/2
> genbox –cp fws_ctr.gro –cs spc216.gro –o fws_b4em.gro –p fws.top
> 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]
> mdrun –s fws_em.tpr –o fws_em.trr –c fws_b4pr.gro –g em.log –e em.edr &
> open new terminal
> grompp –f pr.mdp –c fws_b4pr.gro –r fws_b4pr.gro –p fws.top –o fws_pr.tpr
> The error I kept getting was
> Fatal error:
> Number of coordinates in coordinate file (fws_b4pr.gro, 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?


Add the -p flag to your genion command, or update the topology manually.


> Thanks!
> Nayef Daher
> PhD Chemical Engineering
> University of Alberta, Canada


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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