[gmx-users] protein membrane simulation

[Tsjerk Wassenaar]

Hi Maite,

In addition, you should be careful with G53a*. Beware that atom
bond/angle/dihedral type definitions have changed. If these are
referenced by a number (gb_/ga_/gd_) then you have to check each one
of them. Also, it appears that the G53a* force fields have problems
with the backbone dihedral terms, resulting in a destabilization of
helices and more. No references on that yet, but the differences
between the new and the previous GROMOS force fields (53a5/53a6/43a2)
will be discussed in a soon-to-appear paper in JPCB (I think it was
B...). You might want to stick to 43a2...

Best,

Tsjerk

On 4/4/07, Chris Neale <chris.neale at utoronto.ca> wrote:
> As mentioned by another user, you need POPC in the [ molecules ]
> section. In addition, I see a lack of reference to popc.itp in yout .top
> file. If it is truely absent, this next bit is important.
>
> You have referenced this link:
> 1) http://www.gromacs.org/pipermail/gmx-users/2006-September/023639.html
> and that page includes a link to:
> 2) http://www.gromacs.org/pipermail/gmx-users/2006-May/021416.html
> and that link includes the following information:
>
> ######################
>
> 4. make a topology file like this:
>
> #include "ffoplsaa.itp"
> #include "myprotein.itp"
> #include "spc.itp"
> #include "pope.itp"
>
> [ system ]
> system_name
>
> [ molecules ]
> ; Compound        #mols
> Protein             1
> POPE              299
> SOL              8991
>
> ######################
>
> But your email doesn't mention popc.itp. Download that file and include it.
>
> If you did miss that bit then I would recommend going back through the
> instructions to see if you missed something else as well.
>
> Also, I would at least think about doing something like this:
> http://www.gromacs.org/pipermail/gmx-users/2006-September/023761.html
>
>
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-- 
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623