[gmx-users] Top file modification

[Shima Arasteh]

:)


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?

Thanks for your reply.

Sincerely,
Shima


________________________________
From: Justin Lemkul <jalemkul at vt.edu>
To: Shima Arasteh <shima_arasteh2001 at yahoo.com>; Discussion list for GROMACS users <gmx-users at gromacs.org> 
Sent: Tuesday, March 19, 2013 8:51 PM
Subject: Re: [gmx-users] Top file modification





On Tue, Mar 19, 2013 at 1:07 PM, Shima Arasteh <shima_arasteh2001 at yahoo.com> wrote:


>
> Dear users,
>
>I modified my top file, because I didn't want some bonds. So I deleted them and changed charges on some atoms.
>I want to go on with such a top file, however I am not sure that these changes are implemented properly or not. Would you please let me know if what I did is right or not?
>
>And how would I be sure about the proper modifications?
>
>

Making ad hoc changes to topologies or force fields is generally a bad idea unless you have thoroughly validated what you are doing with a correct parameterization procedure.  What you've described above (especially given the lack of specificity) sounds very dangerous. If you want advice, be specific as to exactly what you are doing. It is your job to convince a skeptical audience (e.g., reviewers) that what you're doing makes sense and thus you must have strong justification for it. "Somebody on the Internet told me it was OK" is generally not an acceptable defense ;)

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