[gmx-users] protein structure prediction

Per Larsson per.larsson at sbc.su.se
Mon Feb 23 13:01:54 CET 2009

23 feb 2009 kl. 12.55 skrev Mark Abraham:

> José Carlos Calvo Tudela wrote:
>> can I use the GROMACS software to get the energy of a protein  
>> conformation?
> Yes, but your question is not well-formed. Only energy differences  
> can have meaning.
>> Up to now I am using TINKER library (analyze program). Is there any  
>> similar software in GROMACS?
> I don't know.

If I'm not mistaken, the energy you get from analyse.x  program in  
Tinker is the potential energy for a protein in is current  
conformation, given a particular force-field.

In that case, you might be able to get the same from Gromacs if you do  
a simulation with 0 steps, ie without any integration, and then look  
at the potential energy terms in the log file (or do many steps, and  
look at the energy before the first step)


> Mark
> _______________________________________________
> gmx-users mailing list    gmx-users at 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 gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php

More information about the gromacs.org_gmx-users mailing list