[gmx-users] water insertion in hbond analysis

[David van der Spoel]

Lydia wrote:
> Dear all,
> 
>     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:
> ----------------------------------------------------------------------------------------------------------------------
>                        if (ins_d && ins_a && ihb) {
>                           /* add to hbond index if not already there */
>                           add_hbond(hb,ins_d_k,ins_a_k,h,grI,ogrp,
>                                     nframes,TRUE,bMerge,ihb);
>                                                                                                          
> 
>                           /* print insertion info to file */
>                           /*fprintf(fpins,
>                             "%4g: %4u:%3.3s%4d%3.3s -> "
>                             "%4u:%3.3s%4d%3.3s (%4.2f,%2.0f) - "
>                             "%4u:%3.3s%4d%3.3s (%4.2f,%2.0f)\n",t,
>                             a[grIA][ins_d_k]+1,
>                             
> *top.atoms.resname[top.atoms.atom[a[grIA][ins_d_k]].resnr],
>                             top.atoms.atom[a[grIA][ins_d_k]].resnr+1,
>                             *top.atoms.atomname[a[grIA][ins_d_k]],
>                             a[grp+grD][i]+1,
>                             
> *top.atoms.resname[top.atoms.atom[a[grp+grD][i]].resnr],
>                             top.atoms.atom[a[grp+grD][i]].resnr+1,
>                             *top.atoms.atomname[a[grp+grD][i]],
>                             ins_d_dist,ins_d_ang*RAD2DEG,
>                             a[ogrp+grA][j]+1,
>                             
> *top.atoms.resname[top.atoms.atom[a[ogrp+grA][j]].resnr],
>                             top.atoms.atom[a[ogrp+grA][j]].resnr+1,
>                             *top.atoms.atomname[a[ogrp+grA][j]],
>                             ins_a_dist,ins_a_ang*RAD2DEG);*/
>                         }
> ---------------------------------------------------------------------------------------------------------------------
> 
>       Then I notice around line 1506, there are another part of the 
> printout being commented out.
> -------------------------------------------------------------------------------------------------------------------------------
>   if (bInsert) {
>     if (bTwo)
>       fprintf(fp,"[ insert_%s->%s-%s ]",
>               grpnames[2],grpnames[0],grpnames[1]);
>     else
>       fprintf(fp,"[ insert_%s->%s ]",grpnames[2],grpnames[0]);
>     j=0;
>                                                                                                          
> 
>     /*  for(i=0; (i<hb->nrhb); i++) {
>         if (hb->hb[i].bInsert) {
>         fprintf(fp,(j%15)?" ":"\n");
>         fprintf(fp,"%4d",i+1);
>         j++;
>         }
>         }*/
>     fprintf(fp,"\n");
>   }
> -------------------------------------------------------------------------------------------------------------------------------
>       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.

It won't work I'm afraid. This code is rather complex and it has been 
changed quite recently to fix bugs and add features.  There is a 
bugzilla about g_hbond, so it will eventually get fixed.

> Sincerely
> Jianping 
> 
> 
> ------------------------------------------------------------------------
> 
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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