[EMAIL PROTECTED] wrote:
Hello all,
I'm very new to Gromacs and am trying to do a simple energy minimization
(potentially doing the full mds later). However, at the first step
(pdb2gmx) I get a fatal error as there is apparently no AMP in the
database. The molecule contains both AMP and Fructose-6-phosphate. I
have gone to the Dundee PRODGR server and generated a Gromacs topology
file for AMP but I'm not entirely sure how to use it. Does it go in the
forcefield .rtp file? The format of what I generated is a bit different
than that. Is there a way to use it as a separate entity? Any help or
direction would be greatly appreciated ;-)
PRODRG will give you a topology (.top) that can be included in your system
topology as an .itp file. A thorough understanding of Chapter 5 of the manual
is required if you don't understand the file types and how they are used. There
are also several good tutorials online for getting used to Gromacs and how it
works, just do a simple Google search.
A caveat about PRODRG - the charges and charge groups it assigns are often
unsatisfactory, requiring manual alteration. Parameterization of new species is
very laborious. See the wiki page for more information, and read the primary
literature pertaining to the force field you want to use.
-Justin
Thank you
Mona Rahman
---------------------------------------------------
Mona N. Rahman, Ph.D.
Dept. of Biochemistry/Pharmacology & Toxicology
Botterell Hall, Rooms 623 and 634 (lab)
Queen's University, Kingston, ON, K7L 3N6
Phone: 613-533-2993, 613-533-6293 (lab)
E-mail: [EMAIL PROTECTED]
------------------------------------------------------------------------
_______________________________________________
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
--
========================================
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
========================================
_______________________________________________
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
