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

[Justin Lemkul]

On 6/7/14, 10:32 AM, Vedat Durmaz wrote:
> 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 specbond:
>
> ------------------------------------------------
> ...
> 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.
>

Bonds are added if the distance between the atoms is ± 10% of the reference 
distance specified in specbonds.dat.  That's not true in the case of a 0.16-nm 
reference distance, since 0.144 nm is the lower boundary.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==================================================