[gmx-users] Topology- make bonds with certain cut-off distance

[mohan maruthi sena]

Hi ,
     Thanks for your reply.  I actually want to build an elastic
network model (ENM) for Protein containing 372 residues. According to
literature, ENM model only considers C-alpha atoms of protein and
discards rest of the atoms.The potential only considers bonded term
only. It does not
contain angle,dihedral or non-bonded term.  To build an ENM model the
specified atom makes bond with all other atoms with certain cutoff
distance. I consider the distance between two c-alpha atoms is 0.38nm
and force constant of 69.1 kj/(nm)2.I have written a code which gives
the number of  atoms around a particular atom with in certain cut-off
distance, With this i will know what are the atoms that are needed to
connect a particular atom.I have generated .gro and .top files using
pdb2gmx command .  After generating topology file , I replace bonds
section with the  connectivity information i get from code. The next
steps are equilibration and production. I am not sure whether it takes
connectivity information from topology or not. If it is not then how
can i mention it forms bonds with in certain distance . Finally , if i
run the simulation with all the above mentioned steps  and load the
trajectory in vmd , the protien gets contracted after first step.

Thanks,
Mohan

On Sat, Aug 25, 2012 at 3:43 PM, Erik Marklund <erikm at xray.bmc.uu.se> wrote:
> Hi,
>
> In case you want the "bonds" to be dynamic I think the only way is to use tabulated interactions. A bit tedious to set up, but doable. Note that this will NOT emulate angles or dihedrals, just the stretching term. I can't understand why you would want bonds between all atoms within a certain distance, however, and I hope you know what you're doing.
>
> Erik
>
> 25 aug 2012 kl. 06.54 skrev mohan maruthi sena:
>
>> Hi all,
>>           I want build a toplogy for a protein , for which , each and
>> every atom  has to  make bonds with other atoms with in certain
>> specified cut-off distance. How can i do this ?
>>
>> Please suggest me a way,
>>
>>
>> Thanks in advance,
>> Mohan
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> -----------------------------------------------
> Erik Marklund, PhD
> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596,    75124 Uppsala, Sweden
> phone:    +46 18 471 6688        fax: +46 18 511 755
> erikm at xray.bmc.uu.se
> http://www2.icm.uu.se/molbio/elflab/index.html
>
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