[gmx-users] *.itp files

[Justin A. Lemkul]

Quoting Sagittarius <deckuofm at yahoo.com>:

> Dear Gromacs users,
>
>   I try to use Gromacs at the step:
> pdb2gmx -f C:\Soft\Gromacs\Input\formaldehyde.pdb -o outputName.gro -p
> outputName.top
> pdb2gmx -f C:\Soft\Gromacs\Input\cyanide.pdb -o outputName.gro -p
> outputName.top
>   How can I get formaldehyde.itp and cyanide.itp
> if I have formaldehyde.pdb and cyanide.pdb?

You don't report seeing an error, but I'm guessing you're seeing the following:

http://wiki.gromacs.org/index.php/Errors#Residue_.27XXX.27_not_found_in_residue_topology_database

Read the advice there, as well as having a look through the list archive.  Every
couple of days a similar question is asked, and you may find some information
about how to deal with these molecules, and parameterization in general, as
well as here:

http://wiki.gromacs.org/index.php/Parameterization

-Justin

>
>   Thank you in advance.
>
>   Alexander
>
>
>
> ---------------------------------
> Never miss a thing.   Make Yahoo your homepage.



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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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