[gmx-users] lipopeptide problem

[Justin A. Lemkul]

Emine Deniz Tekin wrote:
> Hi Felix,
> Thank you for your help.
> 
> Hi Justin,
> 
> I did not want to write a long e-mail describing what I did and what did 
> not work. All I wanted to learn was whether there was some more detailed 
> information somewhere that I can reach. You do not have to reply to an 
> email if you feel it is not worth it. Lecturing me on "willingness" is 
> crossing the line. How do you know how much I tried? Anyhow, thanks for 
> your earlier help, but you can simply skip my future postings.
> 

I'll respond one last time then, if for no other reason but to defend myself 
against being considered a complete jerk.

I was sincerely trying to help, and in order to do so, I needed to extract a lot 
more information than what you had provided.  I could certainly type out a 
procedure, step by step for you, which would be rather lengthy (because there 
are several ways to do this, each based upon a couple different assumptions 
which need to be considered), and then have it turn out that you've done that 
and come across some error for one reason or another, and all I've done is waste 
both of our time and spammed everyone's inbox with an unnecessary message. 
Instead, I wanted to know what you had done.  Even if it's long, it makes the 
process of helping you exponentially faster in the end.  There are dozens of 
threads in the list archive in recent months alone that go one for dozens of 
messages, all because the original user is not providing adequate or accurate 
detail of their problem and their ideas.  Leaving us to guess serves no one.

But truly, if you don't want me to attempt to help, I certainly won't.  If 
trying to help you both solve your problem and be more efficient is seen as a 
"lecturing" and/or "crossing the line," then I won't attempt to do either.

-Justin

> Best regards,
> 
> Deniz
> 
> 
> 
> On Thu, Mar 17, 2011 at 12:00 AM, Justin A. Lemkul <jalemkul at vt.edu 
> <mailto:jalemkul at vt.edu>> wrote:
> 
> 
> 
>     Emine Deniz Tekin wrote:
> 
>         Hi GROMACS Users,
> 
>         I am using the GROMACS 4.5.3 version with GROMOS53a6 force
>         field. I simulated a peptide before but this is the first time I
>         am trying to combine a lipid with a peptide (to get a
>         lipo-peptide). I would be really happy if you could help me out
>         with the following question
> 
>         I am tring to create a louroic acid connected to and an
>         8-redidue peptide. To create residues, I used ARGUSLAB . For the
>         louric acid I used BERGER lipid parameters. Then, as described
>         in KALP-15 in DPPC tutorial, I combined ffbonded.itp and
>         ffnonbonded.itp with lipid.itp. I also adjusted the topol.top
>         files as described in the manual. But this procedure did not yet
>         give me an attached louric acid and peptide. I
> 
> 
>     Nor should you expect it to.  Building the parent force field does
>     not give you a topology describing some molecular system.
> 
> 
>         still have to play with the aminoacids.hdb, aminoacids.rtp,
>         residuetypes.dat, atomtypes.atp, and specbond.dat files. I would
>         appreciate if you could let me know how to modify these files,
>         especially the aminoacids.hdb file. I tried several things but
>         it not
> 
> 
>     See the manual, section 5.6.4.  The contents and format are
>     discussed at length.
> 
> 
>         work. Note that, I applied the suggestions in
>         http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field,
>         but it was not sufficient.
> 
> 
>     If you want free help, you will have to do substantially better than
>     "it was not sufficient."  What is not clear?  What have you tried
>     and what was the result? If you want free help, you've got to
>     demonstrate a willingness to do some work on your own.
> 
>     -Justin
> 
>         Best regards
> 
>         Deniz
> 
> 
>     -- 
>     ========================================
> 
>     Justin A. Lemkul
>     Ph.D. Candidate
>     ICTAS Doctoral Scholar
>     MILES-IGERT Trainee
>     Department of Biochemistry
>     Virginia Tech
>     Blacksburg, VA
>     jalemkul[at]vt.edu <http://vt.edu/> | (540) 231-9080
>     http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
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> 

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

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

========================================