Dear Justin<br><br> I am doing inflategro process for scaling and packing of lipid around my protein . the first step is successfully completed ,there is 9 lipid removed a/c to that I have updated my 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><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 generic topology for ions<br>#include "ions.itp"<br><br>; Include DMPC chain topology<br>
#include "dmpc.itp"<br><br>[ system ]<br>; Name<br>Protein in DMPC bilayer<br><br>[ molecules ]<br>; Name number<br>Protein_A 1<br>Protein_B 1<br>DMPC 119<br>NA+ 1<br>
<br>I have removed also water molecule infomation becoz in inflated system there is no water molecule <br><br>but even after doing this when i I have tried to do second step of inflategro i.e energy minimisation step I got the error like this--<br>
<br>Fatal error:<br>number of coordinates in coordinate file (inflated_dmpc.pdb, 13253)<br> does not match topology (inflated_dmpc.top, 15395)<br>-------------------------------------------------------<br>So can you suggest me what possible modification make it successfully completed.<br>
<br>please If you have any idea let me know.<br><br><br>Thanks a lot justin for solving my problem.<br><br><br>Nitu Sharma<br>School of life Sciences<br>Jawaherlal Nehru university<br>New delhi, India<br><br><br><br><br><br>
<br><br><br><br><br><br><br><br><br><br><br><br><br><br><br>--More--(94%)<br><br><br><br><br><br>