[gmx-users] non protein input

David van der Spoel spoel at xray.bmc.uu.se
Wed Aug 25 16:53:25 CEST 2004

On Wed, 2004-08-25 at 16:12, Lambert van Eijck wrote:
> Hi, 
> I'd like to do MD on polymers. The pdb2gmx program complains about unknown 
> residues and 'UNK' doesn't seem to  be in the database. I take it, it's 
> not usefull to add this type (?).
> I'm not sure whether I should try Gromacs on non-proteins. Can someone 
> advise me? I've tried the server on the web to convert PDBs to gromacs, 
> but there are to many atoms in my models.

It will run fine, there is an example in the benchmarks. You need to
generate a topology. It depends on your polymer how difficult it is. If
you can describe as simple building blocks you can use pdb2gmx with your
own database files (chapter 5 in the manual).
If your polymer is very simple you might try playing with the x2top

> Babel will convert into Gromos input, but then I'm not sure how to create 
> a .top file, as I just skipped pdb2gmx. 
> I've searched the mailing list but, couldn't find any references to this 
> (basic) questions, except for the web server.
> Can I get Gromacs running an MD on polymers?
> thanks in advance,
> Lambert van Eijck
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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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