[gmx-users] Top file modification

[Shima Arasteh]

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?


Sincerely,
Shima


________________________________
From: Justin Lemkul <jalemkul at vt.edu>
To: Shima Arasteh <shima_arasteh2001 at yahoo.com> 
Sent: Tuesday, March 19, 2013 9:00 PM
Subject: Re: [gmx-users] Top file modification





On Tue, Mar 19, 2013 at 1:28 PM, Shima Arasteh <shima_arasteh2001 at yahoo.com> wrote:

:)
>
>
>In fact, I have a NMR pdb file of a cyclic peptide. To get a proper gro and topology files, I ran pdb2gmx without -ter flag. Then tried to modify the top file. Is there any better ideas?
>
>

Manual modification in that case is probably reasonably safe, as long as you are careful to use parameters that are appropriate for all bonded and nonbonded interactions that change as a result of the modification.

-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 ========================================