Dear all<br><br> I am doing simulation of membrane protein ,for this first i did the concatanation of protein in lipid bilayer in proper orientation after that I am using inflategro script of teleman sir <br>
but after doing first step successfully I am getting problem in second step i,e energy minimisation step.<br>problem is related with coordinate file which I putted with grompp and my topology file which I have made like this-<br>
<br>Include forcefield parameters<br>#include "ffG53a6_lipid.itp"<br><br>; Include DMPC chain topology<br>#include "dmpc.itp"<br><br>; Include protein chain topologies<br>#include "tap-mod.itp"<br>
<br>#ifdef POSRES_PROTEIN<br>#include "tap-mod_pr.itp"<br>#endif<br><br>; Include generic topology for ions<br>#include "ions.itp"<br><br>[ system ]<br>; Name<br>Protein in DMPC bilayer<br><br>[ molecules ]<br>
; Name number<br>Protein_X 1<br>DMPC 119<br>NA+ 1<br><br>And the problem I am getting like this--<br>Back Off! I just backed up mdout.mdp to ./#mdout.mdp.12#<br>checking input for internal consistency...<br>
processing topology...<br>Opening library file /usr/local/gromacs/share/gromacs/top/ff_dum.itp<br>Generated 770 of the 2278 non-bonded parameter combinations<br>Opening library file /usr/local/gromacs/share/gromacs/top/ions.itp<br>
Excluding 3 bonded neighbours molecule type 'Protein_X'<br>Excluding 3 bonded neighbours molecule type 'DMPC'<br>Excluding 1 bonded neighbours molecule type 'NA+'<br>processing coordinates...<br><br>
-------------------------------------------------------<br>Program grompp, VERSION 4.0.3<br>Source code file: grompp.c, line: 362<br><br>Fatal error:<br>number of coordinates in coordinate file (inflated_dmpc.gro, 13253)<br>
does not match topology (inflated_dmpc.top, 15392)<br>-------------------------------------------------------<br><br>If anyone have idea about this problem please suggest me something to solve this problem.<br>
<br>Thnks a lot in advance.<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>