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How to use Dendrimer Builder Toolkit: (DBT)

There are two options in DBT; auto (dbtv2.pl) and manual (dbtv1_2.pl). It is worth mentioning the difference between two options here itself, though separate tutorials have been provided for both.

dbtv2.pl helps in building dendrimer (polymers; linear or branched) just with single click on "sander minimization" button. With this user can build one dendrimer generation as well as number  of generations in just single run.

dbtv1_2.pl helps in building manually. Here one can build dendrimer layer by layer. This option one should not use unless the dendrimer system is too complex to be handled. There can be such systems one would like to handle or may encounter. One has to do more manual clicks (e.g. "sander minimization" clicks one by one as layers are added) which can be useful for 'heavy systems'.


Important:

NOTE: DBT (dbtv2.pl and dbtv1_2.pl) uses top2mol2 command which will write mol2 file having charges with four decimal places. But residues that we have provided in library files have charges upto six decimal places. So in order to obtain neutral or integral over all charge one need to use mol2 with charges upto six decimal places. If you try without applying following modifications its quite possible one may get over all charge being 0.002 or something like that.

Please make sure and apply following modifications (for AmberTools1.2):

1) Edit line 366 in top2mol2.c (in the /src/antechamber directory)
 

fprintf(fpout, "%7ld %-8s%10.4lf%10.4lf%10.4lf %-6s%5ld %-8s%10.4lf\n", tmpint, atomname[i].str,

TO

fprintf(fpout, "%7ld %-8s%10.4lf%10.4lf%10.4lf %-6s%5ld %-8s%10.6lf\n", tmpint, atomname[i].str,

2) go to  /src/antechamber and type this in your terminal:

make install
(if getting error see FAQ number 2)
it will recompile the things in antechamber directory alone (which has required top2mol2.c)



Tutorial with example


1) PAMAM (neutral pH)


   a) auto (dbtv2.pl)

   b) manual (dbtv1_2.pl)

2) PPI (high pH)
   
   auto
 (dbtv2.pl)

3) PPI (neutral pH; 2/3rd protonated)

(contributed by Vaibhav Jain, NIPER)
   
   Download PDF
 and library  (using dbtv1_2.pl and ppi_neutral_DAB.lib)