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