[gmx-users] COM pulling - speptide

C Johnson helstreak at hotmail.com
Mon Oct 25 00:50:36 CEST 2010

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

I grabbed the md_pull.mdp file from:

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:

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,
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