<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
<html>
<head>
<meta content="text/html;charset=ISO-8859-1" http-equiv="Content-Type">
</head>
<body bgcolor="#ffffff" text="#000000">
<br>
Bob Johnson wrote:
<blockquote cite="mid1123804311.42fbe49710969@webmail.sas.upenn.edu"
type="cite">
<pre wrap="">Hello everyone,
I'm currently studying the interaction between single stranded DNA and a carbon
nanotube. Because the DNA seems to distort the nanotube, I'm trying to restrain
the positions of the carbon atoms in a nanotube. However, I'm having problems
with this step as I'm not sure how to implement the posre.itp file.
Here is a list of what I have.
1. Coordinate file containing positions of DNA, nanotube, and water that numbers
all the atoms in the system sequentially from 1-2809.
2. Topology file of nanotube that numbers carbons from 1-2080
3. Force field file for nanotube C-C interactions
4. Topology file of dna that numbers atoms from 1-357
5. Force field file for DNA interactions
6. Topology file of water that numbers atoms from 1-3
7. Force field file for water
8. Index file that defines three groups: nanotube ssdna water
9. Topology file for system that includes 1 nanotube molecule, 1 ssdna molecule
and 124 water molecules
10. posre_nanotube.itp file that is in this form
[ position_restraints]
;atom type fx fy fz
1 1 1e9 1e9 1e9
2 1 1e9 1e9 1e9
3 1 1e9 1e9 1e9
4 1 1e9 1e9 1e9
5 1 1e9 1e9 1e9
..
This posre_nanotube.itp file lists atoms 1-2080 as the atoms that are to be
restrained (note that these are the nanotube atoms as listed in the .g96 file).
I add the keyword -DPOSRES_NANOTUBE to the input file and placed the necessary
include statements in the nanotube topology file. However, I get the
following error upon execution of grompp.
WARNING 1 [file "posre_nanotube.itp", line 5]:
No default Position Rest. types for perturbed atoms, using normal values
WARNING 2 [file "posre_nanotube.itp", line 6]:
No default Position Rest. types for perturbed atoms, using normal values
WARNING 3 [file "posre_nanotube.itp", line 7]:
No default Position Rest. types for perturbed atoms, using normal values
WARNING 4 [file "posre_nanotube.itp", line 8]:
No default Position Rest. types for perturbed atoms, using normal values
Is this because the include statement is in the wrong place? I've tried placing
the include statement elsewhere but got other error messages. Does anyone know
how to use the position restraint feature?
</pre>
</blockquote>
Please let us have your .top to show where you place the #include
statement.<br>
<blockquote cite="mid1123804311.42fbe49710969@webmail.sas.upenn.edu"
type="cite">
<pre wrap="">Thanks,
Bob Johnson
_______________________________________________
gmx-users mailing list
<a class="moz-txt-link-abbreviated" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>
<a class="moz-txt-link-freetext" href="http://www.gromacs.org/mailman/listinfo/gmx-users">http://www.gromacs.org/mailman/listinfo/gmx-users</a>
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to <a class="moz-txt-link-abbreviated" href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.
</pre>
</blockquote>
<div class="moz-signature"><i>Regards,</i><br>
Yang Ye<br>
<small><i>Computational Biology Lab<br>
School of Biological Sciences<br>
Nanyang Technological University<br>
Singapore<br>
Tel: 6316-2884<br>
</i></small>
</div>
</body>
</html>