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