Dear Justin<br><br> I am doing simulation of membrane protein .I follow your tutorial for that I think its perfect for that. But I am getting problem in doing inflategro step, I alredy discuss this problem with you but now I am starting everything fresh I have completed upto concatanation of protein with lipid bilayer after that for packing of lipid around protein I am using inflategro script from teleman website . Problem came in second step of inflategro i.e for energy minimisation for this I need topology file of "protein-lipid system".<br>
I am giving you information in detail i.e -<br>for topology file I have made changes in topol.top file which I got from pdb2gmx command in first step for protein processing ,the topol .top file is like this-<br>File 'topol.top' was generated<br>
; By user: nitu (504)<br>; On host: localhost.localdomain<br>; At date: Thu Apr 16 23:20:48 2009<br>;<br>; This is your topology file<br>; Grunge ROck MAChoS<br>;<br>; Include forcefield parameters<br>
#include "ffG53a6.itp"<br><br>; Include chain topologies<br>#include "topol_A.itp"<br>#include "topol_B.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><br>; Include generic topology for ions<br>#include "ions.itp"<br>
<br>[ system ]<br>; Name<br>Grunge ROck MAChoS<br><br>[ molecules ]<br>; Compound #mols<br>Protein_A 1<br>Protein_B 1<br>**********<br>And the change topology file is like this-<br><br>; Include forcefield parameters<br>
#include "ffG53a6_lipid.itp"<br><br>; Include chain topologies<br>#include "topol_A.itp"<br>#include "topol_B.itp"<br><br>#ifdef POSRES<br>#include "posre_A.itp"<br>#include "posre_B.itp"<br>
#endif<br><br>; Include DMPC chain topology<br>#include "dmpc.itp"<br><br><br>[ system ]<br>; Name<br>Protein in DMPC bilayer<br><br>[ molecules ]<br>; Compound #mols<br>Protein_A 1<br>Protein_B 1<br>
DMPC 128<br><br>but when I gave this topology file to grompp it shws error-<br>no. of coordinates in coordinate file doesn,t mach the topology file .<br><br>Can you suggest me something for making topology file for protein-lipid bilayer system. Is there any other method for making topology file ,I have read in mannual chapter 5 but there is also mentioned same method.<br>
If possible please help me becoz without solving this problem I can't move for furthur processing .<br><br>* My gro file of protein shows 9902 atoms .<br>As you ask in previous mail is .itp file have [ molecules ] section the answer is the .itp file haven't molecules section it have [molecule type ] section can it also create problem for topology file working.<br>
<br> Thanks a lot justin .<br>I am waiting for your reply.<br><br>Nitu sharma<br>School of life sciences<br>Jawaherlal Nehru University<br>New delhi , India<br>