[gmx-users] topology file in DPPC

[Justin A. Lemkul]

On 5/15/12 10:47 AM, scaprari at 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

-- 
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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

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