[gmx-users] KALP in DPPC tutorial reg

[Sathya]

Hi,

I'm doing the KALP-15 IN DPPC through the Justin's tutorial
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/03_solvate.html
 I have few questions. Please help me to solve it.

1) After the topol.top file has generated from pdb2gmx is it necessary to
add DPPC 128 in the molecule section?.

2) I have used DPPC 128 in the molecule section and during adding ions with
the following command shows error.
grompp -f ions.mdp -c system_solv.gro -p topol.top -o ions.tpr
The above command shows this error.

Fatal error:
number of coordinates in coordinate file (system_solv.gro, 27162) does not
match topology (topol.top, 33451)

Please tell me where should i change to solve this problem.

3) If i didnt use DPPC in molecule section of .top file while running
equilibration using make_ndx which ask us to enter the protein+lipids i
could not find the DPPC option there..

please help me to solve this problems.

Thanks in advance.





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