Re: [gmx-users] MD simulations of covalent bound protein-ligand complex by gromacs

2012-04-26 Thread Justin A. Lemkul 



On 4/26/12 10:23 AM, mirc...@sjtu.edu.cn wrote:

Dear All:

I am simulating a complex of protein and ligand, however, the ligand is
covalent bound to the protein. I have calculated the charges of the ligand
and the non-standard residue by QM method and trying to use the bond
parameters in the GROMOS force field. However, I don't know how to made the
topology file of the complex, do I need to change the topology file manually
to add the necessary things?



Let pdb2gmx do all the work for you:

http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field

-Justin

--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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 listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.

Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

[gmx-users] MD simulations of covalent bound protein-ligand complex by gromacs

2012-04-26 Thread mircial 
Dear All:

I am simulating a complex of protein and ligand, however, the ligand is 
covalent bound to the protein. I have calculated the charges of the ligand and 
the non-standard residue by QM method and trying to use the bond parameters in 
the GROMOS force field. However, I don't know how to made the topology file of 
the complex, do I need to change the topology file manually to add the 
necessary things?

Thanks in advance!

R.X.G.
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists