On 2/26/13 5:50 PM, Divya Sunil wrote:
Hello
I have a protein consists of 2303 atoms. I simulated it in water using
cubic box. As the protein has a long tail, the no. of water molecules to
fill the box is very high (132235). After simulation I converted the .gro
file to .pdb and in which I have seen that the atom number after 1 lakh is
again started to denote as 1 and also the molecule number after 9999 as 1.
So in this system there are 4 molecules that have number 1. Is this create
any problem during simulation/ before simulation? ( I noted this only after
simulation and the system was not hanged) Also is it possible to remove
some water molecules manually after adding solvation to reduce the number
of atoms?
There is no problem during the simulation, and the fact that atom numbering
starts over is simply a limit of PDB format. Proper representations can
probably be obtained using other file formats. Theoretically, there may be
issues with creating index groups, but likely only if dealing with water, and
these issues can again likely be overcome by choosing a different file format.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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