[gmx-users] problem during inflatgro process
sharmanitu35 at gmail.com
Wed Apr 15 08:25:02 CEST 2009
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 protein chain topologies
; Include DMPC chain topology
[ system ]
Protein in DMPC bilayer
[ molecules ]
; Name number
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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