[gmx-users] About topology protein?

David van der Spoel spoel at xray.bmc.uu.se
Thu Feb 9 20:23:24 CET 2006

Absalom Zamorano wrote:
> Hi gromaxers...
> I want to run MD of assembly of peptides and unfolding
> of proteins, but I have some doubts..
>  1)Which is the best Force field to do that?
For unfolding or for folding?

Just kidding... Read recent literature and choose based on that.

>  2)When I generate the top file by pdb2gmx, Have I to
> print the file and check out it (my problem is that I
> have protein with 240 residues!)?, or Could I feel
> secure about it?, or Are there some key messages in
> the outputs to give traces that some wrong is in the
> top file?
For GROMOS and OPLS you can trust it. I do...
grompp will warn you if something is suspect in most cases (like 
non-integer charge).

> Thanks for advances...
> Dr. Absalom Zamorano Carrillo 
> Profesor Titular A 
> Programa Institucional de Biomedicina Molecular, ENMyH-IPN
> Guillermo Massieu  Helguera  #239 Fracc. "La Escalera"
> Ticomán, D.F. México, C.P  07320
> Tel. (55) 57296000,  ext 55542
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David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel

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