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 <er...@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
er...@xray.bmc.uu.se
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