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

[Mark Abraham]

On 25/08/2012 11:58 PM, mohan maruthi sena wrote:
> 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 .

You can only do this by treating your bonds as what GROMACS calls 
non-bonded interactions, since only those are detected dynamically based 
on distance. So setting up a neighbour-search cut-off and tabulated 
interaction with the same cut-off could implement the above...

>   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.

... but since this model has only an attractive inter-particle 
interaction and  no way to exclude atoms from each other's volume, it is 
garbage. Rather than inventing stuff randomly, find out what has already 
been done in this area and how this (very basic) issue is solved. As a 
general rule, one should build on existing ideas until one has the 
judgement and experience to try something radical and new.

Mark

>
> 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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