Quoting Sagittarius <[EMAIL PROTECTED]>: > 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. ======================================== Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA [EMAIL PROTECTED] | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ ======================================== _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
