[gmx-users] why no. of atoms doesn't match?
mailmd2011 at gmail.com
Mon Apr 15 20:03:17 CEST 2013
Hello Justin and bv08ay:
thanks a lot for kind reply. I count each component by isolating them
one by one:
1. protein generated by pdb2gmx command: 4739 atoms in all
2. ligand: 79 atoms
3. chelostrol: 74x42= 3108 atoms
4. popc: 116x96= 11368 atoms
5. solvent: 10079x3= 30237 atoms
all the above results I double check the no. of coponent and total line
(which represent the atom no.) with gedit, the total atoms is 49621. The
toplogy give correct no. of each component, and the total no. of such
component should be 49621 instead of what claimed by Gromacs " does not
match topology (topol.top, 51295) "
It is correct with the topology I defined at the end of topol.top file:
[ molecules ]
; Compound #mols
thank you very much
On 04/15/2013 07:45 PM, Justin Lemkul wrote:
> Seriously though, the answer to this question is always the same.
> You're not counting something right. The solution is something only
> you can determine. Applying grep -c is your friend here. You're off
> by 1764 atoms, which may be useful information if any of your
> molecules are evenly divisible into 1764. Water is, but perhaps other
> molecules are, as well, depending on their representation.
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