[gmx-users] Topology- make bonds with certain cut-off distance
mohan maruthi sena
maruthi.sena at gmail.com
Sat Aug 25 15:58:09 CEST 2012
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.
On Sat, Aug 25, 2012 at 3:43 PM, Erik Marklund <erikm at xray.bmc.uu.se> wrote:
> 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.
> 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,
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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
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