[gmx-users] COM pulling - speptide

[Justin A. Lemkul]

C Johnson wrote:
> Hi all,
> 
> I'm trying to do some pulling on the speptide.pdb file given in the tutor.
> 
> I first ran pdb2gmx:
> 
>  >>> pdb2gmx -f speptide.pdb -p speptide.top -o speptide.gro
> 
> Then did editconf to put speptide at the bottom (y-axis) center of a 
> longer box:
> 
>  >>>  editconf -f speptide.gro -o newbox.gro -center 3.280 2.181 2.4775 
> -box 6.560 12 4.362
> 
> After that I made the index file:
> 
>  >>> make_ndx -f newbox.gro -o pull.ndx
>          r 1
>          r 19
>          q
> 
> I grabbed the md_pull.mdp file from:
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/Files/md_pull.mdp
> 
> and removed the section
> "define = -DPOSRES_B"
> 
> and edited the sections:
> "pull_dim = N N Y" to "pull_dim = N Y N"
> "pull_group0 = Chain_B" to "pull_group0 = r_19"
> "pull_group1 = Chain_A" to "pull_group1 = r_1"
> 
> After all that I finally ran grompp
>  >>> grompp -f md_pull.mdp -c newbox.gro -p speptide.top -n pull.ndx -o 
> pull.tpr
> 
> I  knew I was probably doing this all wrong since I haven't really got a 
> clue what I'm doing so out of no surprise received an error:
> 

If you're proceeding blindly, then you're likely going to frustrate yourself to 
no end.  There is literature relevant to what you're doing - pulling on 
peptides/proteins to unfold them is something that's been done.  So you should 
have some methodological precedent.

> -------------------------------------------------------
> Program grompp, VERSION 4.0.7
> Source code file: ../../../../src/kernel/readir.c, line: 1007
> 
> Fatal error:
> Group Non-Protein not found in indexfile.
> Maybe you have non-default goups in your mdp file, while not using the 
> '-n' option of grompp.
> In that case use the '-n' option.
> 
> -------------------------------------------------------
> 
> Where did I got wrong?
> 

"Non-Protein" is a default group that should have been written to the .ndx file 
by make_ndx.  The only reason I can see for this error to come up is if you've 
removed it from the pull.ndx file.  If you're using my .mdp file, then 
Non-Protein is a temperature coupling group.

-Justin

> Basically what I would like to do is highlighted in my previous posts:
> http://lists.gromacs.org/pipermail/gmx-users/2010-October/055198.html
> http://lists.gromacs.org/pipermail/gmx-users/2010-October/055201.html
> 
> But in a nutshell I would eventually, once I know what I'm doing, like 
> to be able to pull (constant velocity) on a single folded peptide with 
> one end anchored so that I can generate a force vs displacement plot.
> 
> Thanks for your help,
> Joe
> 

-- 
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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

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