[gmx-users] popc

[Justin A. Lemkul]

Quoting Chiara Parravicini <parravicini.chiara at gmail.com>:

> Dear gromacs users,
>
>  I would like to perform  simulations of a protein embedded in popc, using a
> force field of the gromos series and I downloaded popc.pdb, popc.itp,
> lipid.itpa and the force field ffG43a2x extended for lipids.
> Looking throughout the archive I found different suggestions, but none of
> them help me to successfully perform my simulations:
>
> - Using the ffG43a2x* force field, when I run pdb2gmx on the popc.pdb, I get
> this error:
>
>  Fatal error:
>
> Error in hdb file ffG43a2x.hdb:
>
> Wrong number of control atoms (2 iso 3) on line:
>
> 1 1 N -C CA

Right; I think the format of the .hdb file changed somewhere along the way, and
ffG43a2x is formatted in the old style.  What pdb2gmx is complaining about is
that it thinks it is trying to add an atom named 'N', with reference atoms of
-C and CA.  Compare the ffG43a2x.hdb with, say, ffG53a6.hdb, and you will see
the difference.  The first atom specified must be the name of the hydrogen atom
you wish to add, so that line should be something like:

1   1   H   N   -C   CA

For more on .hdb files, read the manual, section 5.5.2.

-Justin

>
>   - If I manually write a topology file for the ffG43a2x force field and
> submit it to grompp to write a .tpr, I get this error:
>
>  Fatal error:
> Atomtype 'CA' not found!
>
>   In the topology file I included both lipid.itp and popc.itp, and I
> commented the following lines in the lipid.itp file as suggested:
>
>  [ defaults ]
>
> 1 1
>
>  - I also tried to add the different sections [ atomtypes ], [ pairtypes ],
> etc... of the lipid.itp files to ffG53a5* files, but I still get the error:
>
>  Atomtype 'CA' not found!
>
>  Does anybody know what I miss? Is there a way to resolve this problem and
> use popc with ffG53a5 or ffG43a2x?
>
>  All comments are very appreciated!
> Thanks in advance!
>
>  Chiara
>



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Justin A. Lemkul
Graduate Research Assistant
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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