[gmx-users] How to use ambconv package...

[Tomas Kubar]

Hi again

> There is also a bug in ambconv.c -- (thanks to Anton Feenstra for
> pointing this out).
> - s_atop* atop; */
>                                                                      
>                                                                      
>    
> +/* DAE Insert Anton Feenstra's suggestion on memory allocation */
>                                                                      
>                                                                      
>    
> +s_atop   satop; /* static */
> +s_atop*  atop;  /* pointer */
>                                                                      
>                                                                      
>   +atop = &satop;  /* set atop to point to satop's adress */

Yes, this is a possibility. Instead, my version includes

s_atop* atop = (s_atop*) xmalloc(sizeof(s_atop));

Futhermore, I have slightly different util.c, line 74 and following 9 
similar lines:

#anything#_filename = (char*) malloc(strlen(argv[i+1])*sizeof(char)+1);

Another problem may arise, if your system contains 1000 atoms or more. 
Should this be your case, I would recommend to modify the file 
write_grotop.c to write 'longer' atom numbers when printing the bonds, 
angles and dihedrals, e.g. line 396

fprintf(grotop, "  %4d%4d%s%12.5f%12.0f%s", ++atom1, ++atom2, "   1", 
bl, bfc,".");

substitute with

fprintf(grotop, "  %6d%6d%s%12.5f%12.0f%s", ++atom1, ++atom2, "   1", 
bl, bfc,".");

Regards
tomas