[gmx-users] problem in energy minimisation during inflategro process.

nitu sharma sharmanitu35 at gmail.com
Tue Apr 14 07:28:54 CEST 2009

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
#include "rr1_A_pr.itp"
#include "rr1_B_pr.itp"

; 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

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

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