[gmx-users] non protein input

Lambert van Eijck eijck at iri.tudelft.nl
Wed Aug 25 16:12:20 CEST 2004


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.

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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