[gmx-users] specbond identified by pdb2gmx but not added to topology

Vedat Durmaz durmaz at zib.de
Sat Jun 7 16:32:31 CEST 2014

dear gmx users/team,

i've defined some simple residues (5 monomeric units) in aminoacids.rtp, 
residues.dat and aminoacids.hdb that i want to use for the modelling of 
small polymers. the polymer may be highly bifurcated due to a branching 
T piece among the monomer units.

all possible intermolecular connections (about 20) between the units are 
defined in the specbonds file according to the following pattern:

XYB  CG2 1    XYX        O    1    0.16    XYB        XYX

there is no need for new atom types or changes in ffbonded/ffnonbonded 
since all atoms and the resulting bonds also occur in typical amino 
acids. however, when starting pdb2gmx

pdb2gmx -ff amber99sb -f input.pdb -o polymer.pdb  -p polymer.top -ignh 
-water none

with 12 residues/units (and several bifurcations) requiring 11 
additional intermolecular bonds to be read from the specbond file, i get 
a nice resulting topology containing all desired bonds except for one 
lone 0.143nm bond between atom CG2 (amber type CT) of residue 3 ("XYB") 
and atom O (amber type OS) of residue 7 ("XYX"). curiously, this missing 
bond is listed in the distance matrix output of pdb2gmxt related to 

29 out of 29 lines of specbond.dat converted successfully
Special Atom Distance matrix:

                     XYL1    XYX2    XYX2    XYX2    XYB3 XYB3    XYB3
                     CG25      O6    OG19   CG210     O11 OG114   CG215
     XYX7     O31   0.714   0.635   0.487   0.293   0.483 0.303 
->0.143<- here it is

but when it comes to the linking stage a little further in the output, 
this bond is neglected whereas the other ten bonds are set as desired:

Linking XYL-1 CG2-5 and XYX-2 O-6...
Linking XYX-2 OG1-9 and XYX-4 CG2-20...
Linking XYX-2 CG2-10 and XYB-3 OG1-14...
Linking XYX-4 O-16 and XYL-5 CG2-25...
Linking XYX-4 OG1-19 and XYL-6 CG2-30...
Linking XYX-7 OG1-34 and XYX-8 CG2-40...
Linking XYX-7 CG2-35 and XYR-12 O-56...
Linking XYX-8 O-36 and XYL-9 CG2-45...
Linking XYX-8 OG1-39 and XYB-10 CG2-50...
Linking XYB-10 OG1-49 and XYL-11 CG2-55...

does anyone have some hint or an idea of what might be suppressing the 
linking of that bond? i've tried it with gromacs 4.5 as well as 4.6 
without any difference in the output.

thanks in advance and a good weekend,


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