[gmx-users] make_ndx: atomname selection

[Javier Cerezo]

Hi all

I'd like to do a selection of atom names such as:

a C1 C3 C2 C4

to get an index file with 4 atoms (no other matches in the file) and 
then use it with g_angle to calculate the dihedral. The problem is that 
make_ndx does not keep the order of atoms in the resulting index file as 
they are added interactively to make_ndx, thus leading to a wrong 
dihedral calculation if the order of the atoms selected in not the same 
as that in the structure.

I don't know if this can be a trouble for someone else or if there is 
any workaround. Actually, make_ndx does not say anything whether it keep 
the order or not, so I would not call it a bug. Anyway, if there is not 
such a workarouund, that might be changed in the code if anything else 
is affected. The required change is in make_ndx.c at select_atomnames 
function (l. 497). Here you have a working modification:


static int select_atomnames(t_atoms *atoms,int n_names,char **names,
                             atom_id *nr,atom_id *index,gmx_bool bType)
{
   char *name;
   int j, counter;
   atom_id i;

   counter=0;
   for(i=0; i<atoms->nr; i++) {
     if (bType)
       name=*(atoms->atomtype[i]);
     else
       name=*(atoms->atomname[i]);
     j=0;
     while (j<n_names && !comp_name(name,names[j]))
       j++;
     if (j<n_names) {
       *nr=j;
       index[*nr]=i;
       counter++;
     }
   }
   *nr=counter;
   printf("Found %u atoms with %s%s",
          *nr,bType ? "type" : "name",(n_names==1)?"":"s");
   for(j=0; (j<n_names); j++)
     printf(" %s",names[j]);
   printf("\n");

   return *nr;
}

-- 
Javier CEREZO BASTIDA
PhD Student
Physical Chemistry
Universidad de Murcia
Murcia (Spain)
Tel: (+34)868887434