Dear justin<br><br><br> 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 .<br><br>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 -<br>
; File 'rr1.top' was generated<br>; By user: nitu (504)<br>; On host: localhost.localdomain<br>; At date: Wed Apr 8 23:37:18 2009<br>;<br>; This is your topology file<br><br>; ; Include forcefield parameters<br>
#include "ffG53a6_lipid.itp"<br><br>; Include chain topologies<br>#include "rr1_A.itp"<br>#include "rr1_B.itp"<br>; Include position restrain protein<br>#ifdef POSRES_PROTEIN<br>#include "rr1_A_pr.itp"<br>
#include "rr1_B_pr.itp"<br>#endif<br><br>Include DMPC chain topology<br>#include "dmpc.itp"<br><br>; Include water topology<br>#include "spc.itp"<br><br>#ifdef POSRES_WATER<br>; Position restraint for each water oxygen<br>
[ position_restraints ]<br> i funct fcx fcy fcz<br> 1 1 1000 1000 1000<br>#endif<br>;include generic topology for ion<br>
<br>
; Name num<br>; I#include "ions.itp"<br><br>[ system ]<br>; Name<br>Protein in DMPC bilayer +Water<br><br>[ molecules ]<br>; Name number<br>Protein_A 1<br>Protein_B 1<br>
DMPC 128<br>SOL 3655<br>NA+ 11<br><br>I always get error like this-Program grompp, VERSION 4.0.3<br>Source code file: toppush.c, line: 618<br><br>Fatal error:<br>Unknown atomtype HW<br>
<br>Please let me know what possible error give this problem.<br>I have try everything but this problem is still there.<br><br>Thanks<br><br><br>NITU SHARMA<br>SCHOOL OF LIFE SCIENCES <br>JAWAHERLAL NEHRU UNIVERSITY<br>NEW DELHI,<br>
INDIA<br><br><br><br><br><br>