<br><div class="gmail_quote"><span dir="ltr"></span>Hi Justin,<br><br> sorry for disturbing again. But I really need ur help Becoz u already did all these things, I am stucking in inflatgro procedure after step the problem of topology file comes so the energy minimisation step can't be completed-<br>
<br>I tell u in detail-<br><br>after first step I get the inflated gro file i convert it in Pdb file by using editconf and than i am using command grompp for energy minimisation i.e-<br><br>grompp -f em.mdp -p inflated.top -c inflated_bilayer.pdb -o inflated-em.tpr<br>
<br>and i get error like this- no. of coordinate file in pdb (13253) doesn't match to topology file (15384)<br><br>I my pdb file there is 7779 atoms of protein and 5574 atoms of DMP is present there is no water here so from topology file I deleted all the includes for water now in my topology file -<br>
; Include forcefield parameters<br>#include "ffG53a6_lipid.itp"<br><br>; Include protein chain topologies<br>#include "rr1_A.itp"<br>#include "rr1_B.itp"<br><br>#ifdef POSRES_PROTEIN<br>#include "posre_A.itp"<br>
#include "posre_B.itp"<br>#endif<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>only the .itp file is present for protein and lipid<br><br>is there any possibility to delete anything from .itp file is it correct to delete anything from .itp file???????????<br>
<br><br>Please If U have any idea about these problem please suggest me something .<br>
<br>I am waiting for ur reply.<br><br>thanks<br><font color="#888888"><br>nitu<br><br><br>
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