[gmx-users] COM pulling - speptide

[chris.neale at utoronto.ca]

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