Dear Joe,
check your fatal error message, it may have a typo in the work
"goups", but it does outline your problem fairly completely. That
said, you did a 99th percentile job in posting your inputs and
outputs, making it easy for us to help.
quoting your post:
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.
so when you "make_ndx -f newbox.gro -o pull.ndx", you'll see that
there is either no group Non-Protein automatically created in the list
or else just add -n pull.ndx to your grompp call.
Chris.
-- original message --
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:
-------------------------------------------------------
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?
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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