[gmx-users] Restraining bilayer/water system

[Yang Ye]

You may move

#ifdef POSRES_L
#include "/home/tripos/lipid/dopc/minidopc/POSRE_L.itp" in water
#endif

just under
#include "/home/tripos/lipid/ffgmx2_lipid.itp"

It still depends on the content of ffgmx2_lipid.itp and POSRE_L.itp.

Please read chapter 5 of the manual. With a bit knowledge of C macro, 
you will understand the structure of topology file.

Yang Ye

Farid Sa'adedin wrote:
> Dear Yang Ye,
>
> Apologies for the late reply.
>
> Here is my top file:
>
> TOP FILE:
>
> #include "/home/tripos/lipid/ffgmx2_lipid.itp"
> #include "/home/tripos/lipid/DOPCHT.itp"
> #include "/usr/local/share/gromacs/top/spc.itp"
>
>
> [ system ]
> ; name
> DOPC in water
>
> #ifdef POSRES_L
> #include "/home/tripos/lipid/dopc/minidopc/POSRE_L.itp" in water
> #endif
>
> [ molecules ]
> ; name number
>
> DOPC    18
>
>
>
> SOL              1463
>
> In my mdp files I specified under preprocessing:
>
> define  = -DPOSRES_L
>
> but I still obtain this message when I run grompp:
>
>  cpp exit code: 256
>   cpp: too many input files
>   [tripos]dopc/minidopc$ Tried to execute: '/lib/cpp -I
>   -I/usr/local/share/gromacs/top
>  -DPOSRES_L dopc.top > grompptByAm1'
>
>
> Thank you for allowing me to send you the top.
>
> Yours sincerely,
>
> Farid
>