[gmx-users] Starting a simulation of a peptide

Tsjerk Wassenaar tsjerkw at gmail.com
Thu Apr 26 11:56:32 CEST 2007

Hi Nur,

[defaults] is not all there is. You also have a list of [atomtypes] in
lipid.itp, which contains only the types relevant for the lipid,
probably not including CA (note that I'm guessing my way through a
bit). I'm not completely sure, but either you're not allowed to have
two [atomtypes] sections or the second [atomtypes] section overrides
the first one. You shouldn't have two in any case, and you have to be
sure to have all atomtypes you use listed. Note also that you can't
combine different force fields, you shouldn't use ffgmx, and may be
best off by writing your own lipid.itp, containing only a
[moleculetype] with all the appropriate headings (see Chapter 5..,
again). Try to really, really, really understand the topology format.
Especially since you want to do more than Simple-Protein-Solvent
simulations. YOU have to understand everything your doing, which means
that you have to read up on all these issues. Maybe it's even better
to start from scratch. First understand the topology file for a simple
peptide-water system, following all the includes, having the manual
with chapter 5 open on your desk. Then look what's in that lipid.itp,
and think of how you can use the information in there in your system.


On 4/26/07, nur avneet <nuravneet at yahoo.co.in> wrote:
> Dear
> I am really thankfull to tsjerk and Mark for making me understand the
> defaults.
> I v removed the defaults section from the lipid.itp as it aws also ther in
> ffgmx.itp......
> but now it gives an error "Atomtype CA not found!"
> regards
> nur
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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

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