[gmx-users] Top file modification

[Shima Arasteh]

Dears,

As I read in some other messages in mailing list, it is supposed to modify bonds, angles and dihedrals in top file to define a peptide bond for the last and first residues as well as other peptide bonds.
I am wondering if it is necessary to define pairs too? 

Thanks in advance.



Sincerely,
Shima


________________________________
From: Justin Lemkul <jalemkul at vt.edu>
To: Shima Arasteh <shima_arasteh2001 at yahoo.com> 
Cc: Discussion list for GROMACS users <gmx-users at gromacs.org> 
Sent: Tuesday, March 19, 2013 9:11 PM
Subject: Re: [gmx-users] Top file modification





On Tue, Mar 19, 2013 at 1:36 PM, Shima Arasteh <shima_arasteh2001 at yahoo.com> wrote:

Would you please let me know if it is acceptable to add dihedrals and angles and bonds? and not to add any pairs to the top? just deleting the pairs which are added by pdb2gmx incorrectly to the terminus?
>
>
>And I don't know that if I don't add all bonds or dihedrals what would happen? How would I be sure that I have added all modifications completely?
>
>

All you're doing is creating a peptide bond like any other. Its description should be identical to any other peptide bond in the protein. An incorrect or incomplete description of the newly created peptide bond would mean an unreliable physical model that would either crash or produce spurious results.

-Justin 

-- 

======================================== Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ========================================