Do you know where I should look to find the solution to my problem? Silvia
> > On 5/15/12 10:47 AM, scapr...@uniroma3.it wrote: >> 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. >> > > The problem is you're using an old version. The tutorial states that you > are > expected to be using a version in the 4.5.x series. If you don't, then > the > procedure will be somewhat different. > > -Justin > > -- > ======================================== > > Justin A. Lemkul, Ph.D. > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > -- > gmx-users mailing list gmx-users@gromacs.org > 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 gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- gmx-users mailing list gmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists