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
total: 49531
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
Protein 1
LIG 1
CHL1 42
POPC 98
SOL 10079
thank you very much
best
Albert
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.
-Justin
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