Dear Justin
I am doing inflategro process for scaling and
packing of lipid around my protein . the first step is successfully
completed ,there is 9 lipid removed a/c to that I have updated my topology
file ---
; Include forcefield parameters
#include "ffG53a6_lipid.itp"
; Include chain topologies
#include "rr1_A.itp"
#include "rr1_B.itp"
; Include position restrain protein
#ifdef POSRES_PROTEIN
#include "rr1_A_pr.itp"
#include "rr1_B_pr.itp"
#endif
; Include generic topology for ions
#include "ions.itp"
; Include DMPC chain topology
#include "dmpc.itp"
[ system ]
; Name
Protein in DMPC bilayer
[ molecules ]
; Name number
Protein_A 1
Protein_B 1
DMPC 119
NA+ 1
I have removed also water molecule infomation becoz in inflated system there
is no water molecule
but even after doing this when i I have tried to do second step of
inflategro i.e energy minimisation step I got the error like this--
Fatal error:
number of coordinates in coordinate file (inflated_dmpc.pdb, 13253)
does not match topology (inflated_dmpc.top, 15395)
-------------------------------------------------------
So can you suggest me what possible modification make it successfully
completed.
please If you have any idea let me know.
Thanks a lot justin for solving my problem.
Nitu Sharma
School of life Sciences
Jawaherlal Nehru university
New delhi, India
--More--(94%)
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