[gmx-users] problem during inflatgro process

nitu sharma sharmanitu35 at gmail.com
Wed Apr 15 08:25:02 CEST 2009

Hi  Justin,

                 sorry for disturbing again. But I really need ur help Becoz
u already did all these things, I am stucking in inflatgro procedure after
step the problem of topology file comes so the energy minimisation step
can't be completed-

I tell u in detail-

after first step  I get the inflated gro file i convert it in Pdb file by
using editconf  and than i am using command grompp for energy minimisation

grompp -f  em.mdp  -p inflated.top -c inflated_bilayer.pdb  -o

and i get error like this- no. of coordinate file in pdb  (13253) doesn't
match to topology file (15384)

I my pdb file there is 7779 atoms of protein and 5574 atoms of DMP is
present  there is no water here so from topology file I deleted all the
includes for water now in my topology file -
; Include forcefield parameters
#include "ffG53a6_lipid.itp"

; Include protein chain topologies
#include "rr1_A.itp"
#include "rr1_B.itp"

#include "posre_A.itp"
#include "posre_B.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
only the .itp file is present for protein and lipid

is there any possibility to delete anything from .itp file is it correct to
delete anything from .itp file???????????

Please If U have any idea about these problem please suggest me something .

I am waiting for ur reply.


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