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

[Vedat Durmaz]

hi justin & gmx-users,

meanwhile i had understood that the reference distance in the speconds file is not an upper boundary for possible bonds but the distance itself +/-x. i should have read the manual with more attention before writing to the list.

thanks again,

vedat




> 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
  <http://mackerell.umaryland.edu/%7Ejalemkul>