Dear justin
I am stuck with one problem , as in your given tutorial I
made the modified ffG53a6_lipid.itp file I have removed all the HW from that
file which comes from lipid.itp .
I have done all the modification which written their is no any atom type in
ffG53a6nb_lipid.itp .But when I run the grompp command with my prepared
topology file -
; File 'rr1.top' was generated
; By user: nitu (504)
; On host: localhost.localdomain
; At date: Wed Apr 8 23:37:18 2009
;
; This is your 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 DMPC chain topology
#include "dmpc.itp"
; Include water topology
#include "spc.itp"
#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
i funct fcx fcy fcz
1 1 1000 1000 1000
#endif
;include generic topology for ion
; Name num
; I#include "ions.itp"
[ system ]
; Name
Protein in DMPC bilayer +Water
[ molecules ]
; Name number
Protein_A 1
Protein_B 1
DMPC 128
SOL 3655
NA+ 11
I always get error like this-Program grompp, VERSION 4.0.3
Source code file: toppush.c, line: 618
Fatal error:
Unknown atomtype HW
Please let me know what possible error give this problem.
I have try everything but this problem is still there.
Thanks
NITU SHARMA
SCHOOL OF LIFE SCIENCES
JAWAHERLAL NEHRU UNIVERSITY
NEW DELHI,
INDIA
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