Dear all,<br>
<br>
I'm doing hbond analysis with the option -ins in gromacs 3.3 to
find the water mediated hydrogen bonds. In the output file, I
found no list of bridging water in the files (insert.dat and
hbond.ndx). Then I look at the source code src/tools/gmx_hbond.c
, I notice that the output command lines about bridging water are
commented out. For example, around line 1986 in gmx_hbond.c:<br>
----------------------------------------------------------------------------------------------------------------------<br>
if (ins_d && ins_a && ihb) {<br>
/* add to hbond index if not already there */<br>
add_hbond(hb,ins_d_k,ins_a_k,h,grI,ogrp,<br>
nframes,TRUE,bMerge,ihb);<br>
<br>
/* print insertion info to file */<br>
/*fprintf(fpins,<br>
"%4g: %4u:%3.3s%4d%3.3s -> "<br>
"%4u:%3.3s%4d%3.3s (%4.2f,%2.0f) - "<br>
"%4u:%3.3s%4d%3.3s (%4.2f,%2.0f)\n",t,<br>
a[grIA][ins_d_k]+1,<br>
*top.atoms.resname[top.atoms.atom[a[grIA][ins_d_k]].resnr],<br>
top.atoms.atom[a[grIA][ins_d_k]].resnr+1,<br>
*top.atoms.atomname[a[grIA][ins_d_k]],<br>
a[grp+grD][i]+1,<br>
*top.atoms.resname[top.atoms.atom[a[grp+grD][i]].resnr],<br>
top.atoms.atom[a[grp+grD][i]].resnr+1,<br>
*top.atoms.atomname[a[grp+grD][i]],<br>
ins_d_dist,ins_d_ang*RAD2DEG,<br>
a[ogrp+grA][j]+1,<br>
*top.atoms.resname[top.atoms.atom[a[ogrp+grA][j]].resnr],<br>
top.atoms.atom[a[ogrp+grA][j]].resnr+1,<br>
*top.atoms.atomname[a[ogrp+grA][j]],<br>
ins_a_dist,ins_a_ang*RAD2DEG);*/<br>
}<br>
---------------------------------------------------------------------------------------------------------------------<br>
<br>
Then I notice around line 1506, there are another part of the printout being commented out. <br>
-------------------------------------------------------------------------------------------------------------------------------<br>
if (bInsert) {<br>
if (bTwo)<br>
fprintf(fp,"[ insert_%s->%s-%s ]",<br>
grpnames[2],grpnames[0],grpnames[1]);<br>
else<br>
fprintf(fp,"[ insert_%s->%s ]",grpnames[2],grpnames[0]);<br>
j=0;<br>
<br>
/* for(i=0; (i<hb->nrhb); i++) {<br>
if (hb->hb[i].bInsert) {<br>
fprintf(fp,(j%15)?" ":"\n");<br>
fprintf(fp,"%4d",i+1);<br>
j++;<br>
}<br>
}*/<br>
fprintf(fp,"\n");<br>
}<br>
-------------------------------------------------------------------------------------------------------------------------------<br>
Is there a reason for commenting out the
printout function? Can I uncomment it and recompile to see
the list of inserted water correctly? Any help and suggestions are
greatly appreciated. <br>
Sincerely<br>
Jianping <br>