Dear all, I'm meticulously following the tutorial KALP-15 in DPPC in order to carry on the simulation of a protein of mine in a extended patch of DPPC. I have already modified the ffnonbonded.itp and ffbonded.itp. At this point I'm reading that I should change my topology file but I'm not able to find within my topology file (obtained by using pdb2gmx on my protein) #include"gromos53a6.ff/forcefield.itp"statement so as to replace this line with #include "gromos53a6_lipid.ff/forcefield.itp", as reported in the tutorial. Indeed, at the top of my topology file I have got;
; Include forcefield parameters #include "ffG53a6.itp" and, after the list of all atoms, at the bottom of the file; ; Include Position restraint file #ifdef POSRES #include "posre.itp" #endif ; Include water topology #include "spc.itp" #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcx fcy fcz 1 1 1000 1000 1000 #endif ; Include generic topology for ions #include "ions.itp" [ system ] ; Name PHOSPHOLIPASE A2, AMMODYTOXIN A [ molecules ] ; Compound #mols Protein_A 1 I'm wondering if it may depend on the fact I have got the version gromacs-4.0.7 and not the version 4.5.3 or newer or if I have to change some options when I launch the command pdb2gmx in order to build my topology file. I used the following command: pdb2gmx -f 3G8G.pdb -o 3G8G_membr.gro -p 3G8G_membr.top -i 3G8G_membr.itp -ignh -water spc and I chose GROMOS96 53A6 Please, let me know. Silvia -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
