Hi Fredrik, Basically, you don't (you can't in any case run it on something not in the database). pdb2gmx is designed to build topologies for proteins/dna. There are some more building blocks, and you can add your own, if required. If you mean polyaromatic in terms of a polymer of an aromatic building block, you may want to add these blocks to the appropriate .rtp file to make life easier on you. However, your biggest problem seems to be to obtain good topologies for your building blocks in the first place. I'm not sure whether these (e.g. aniline) are available in GROMOS by default.
Best, Tsjerk On 4/10/07, Fredrik Blomgren <[EMAIL PROTECTED]> wrote:
Dear All I am a new user of Gromacs which means I am in the (somewhat painful) process of learning how to use the program. My goal is to calculate properties for polyaromatics containing nitrogen and sulfur. I want to use a united atom force field and if I have understood it correctly I should be able to use Gromos. My problem is that I find it hard to get started. I am trying to test the program for aniline (benzene with an amino group). I have a pdb-file of the molecule and tried to run pdb2gmx which didn´t work because in my pdb-file I didn´t specify a residue. This leads to my question: How does one run pdb2gmx with a molecule that is not an amino acid residue or something else that is stored in the database of Gromacs? Best regards Fredrik Blomgren _______________________________________________ gmx-users mailing list [email protected] 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
-- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 _______________________________________________ gmx-users mailing list [email protected] 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
