[gmx-users] topology file in DPPC

[scaprari at uniroma3.it]

Do you know where  I should look to find the solution to my problem?

Silvia



>
> 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
>
> --
> ========================================
>
> 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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