[gmx-users] FWSpider Tutorial

Nayef Daher elthaher at ualberta.ca
Wed Jun 30 21:23:18 CEST 2010


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?


Nayef Daher
PhD Chemical Engineering
University of Alberta, Canada

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