[gmx-users] grompp error and make_hole

[nanyu101]

 Hi,
  I have downloaded make_hole program from Gromacs contribution.But when I run it in Gromacs-3.1.4,there are something wrong.I will show your mistakes below that  I 'v met.Would you please figure it to me which kind of mistakes they are, operation mistakes by me or mistakes by version.
 1.make_hole.pl -f popc128a.pdb -o popc.pdb -r 1.4 -lipat P8 -lipid POPC -cx 2.3 -cy 2.8 
 2.editconf -f popc.pdb -o popc.gro
 3.I have created my popc.top file as below: 
   
#include "ffgmx_lipid.itp"
#include "popc.itp"
;#include "ions.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 

3.editconf -bt cubic -f popc.gro -o popc.gro -c
4.genbox -cp popc.gro -cs spc216.gro -o popc_b4em.gro -p popc.top
5.grompp -f em.mdp -c popc_b4em.gro -p popc.top -o popc.tpr

My puzzle is this step.Every time when I run grompp like that,the system told me like below:

 creating statusfile for 1 node...
' for variable integrator, using 'md'
Next time use one of: 'md' 'steep' 'cg' 'bd' 'sd' 'nm'
' for variable ns-type, using 'Grid'
Next time use one of: 'Grid' 'Simple'
' for variable coulombtype, using 'Cut-off'
Next time use one of: 'Cut-off' 'Reaction-Field' 'Generalized-Reaction-Field' 'PME' 'Ewald' 'PPPM' 'Poisson' 'Switch' 'Shift' 'User'
' for variable optimize_fft, using 'no'
Next time use one of: 'no' 'yes'
' for variable constraints, using 'none'
Next time use one of: 'none' 'h-bonds' 'all-bonds' 'h-angles' 'all-angles'
Back Off! I just backed up mdout.mdp to ./#mdout.mdp.1#
Warning: as of GMX v 2.0 unit of compressibility is truly 1/bar
checking input for internal consistency...
...ling /lib/cpp
: No such file or directory
cpp exit code: 32512
 popc.top > gromppPJar2u'are/top -DFLEX_SPC
' command is defined in the .mdp file
processing topology...
processing coordinates...
Fatal error: number of coordinates in coordinate file (popc_b4em.gro, 204786)
             does not match topology (popc.top, 0)

Would you please figure out this problem?Thanks a lot.I am looking forward to your response.

All your bests,
Xianhui Wu

               
______________________________________

===================================================================
Ãâ·ÑÊÔÓÃÐÂÀË15MÊÕ·ÑÓÊÏä ¸Ï½ôÐж¯£¡ (http://vip.sina.com/sol_mail/promotion/pro_men.html)
ÐÂÀ˶þÊÖÊг¡£ºÒ»ÔªÍ¶È룬ʮ·Ö¾ªÏ²£¬°Ù·ÖÂúÒâ (http://classad.sina.com.cn/2shou/)
ÊýÍòÕÅÊÖ»úͼƬÊýÍòÊ׶ÌÐÅÁåÉùÈÎÄãÌôÑ¡£¬Ã¿Ì춼ÓиüР(http://sms.sina.com.cn/cgi-bin/sms/smspic.cgi)