[gmx-users] about make_hole

[nanyu101]

Hi,
  I am a novice in Gromacs.To me,my project is the most difficult work.Maybe you will agree that Gromacs is not very friendly.
  There are some questions about make_hole in lipid bilayer.The coordinates of POPC was downloaded from Tieleman's web.And I think you have had make_hole program from Groamcs contribution.
  This morning I tried to run make_hole.pl to make home in POPC.I have encountered grompp -f run.mdp -s insert.tpr -c outbilayer.pdb -r outbilayer.pdb -p ...,the system told me that -s is an unknown argument.The double "outbilayer" confused me,too.So,I tried to change it as below.
grompp -f run.mdp -c insert.tpr -r outbilayer.pdb -p popc.top -p popc.tpr
But the system told me the coordinates of tpr file didn't match the coordinate of top file.And it told me topology file is zero.My information of topology is below:

¡¡¡¡
#include "ffgmx_lipid.itp"
#include "popc.itp"
;#includeions.itp"
#ifdef POSRES
 "#include "lipid_posre.itp"
#endif
#ifdef FLEX_SPC
#include "flexspc.itp"
#else
#include "spc.itp"
#endif

[ system ]
; name
popc + h2o
[ molecules ]
; name number
POPC   106 
SOL             66371
Could you give me some advices.Thanks for your kind assistant.I am looking forward to your response.

Best wishes,
Wu
¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡
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