<html>
<head>
<meta content="text/html; charset=ISO-8859-1"
http-equiv="Content-Type">
</head>
<body bgcolor="#FFFFFF" text="#000000">
Hi,<br>
<br>
The easiest solution is probably to write a script that reorders the
structure file (gro for example, just swap the lines in each lipid,
and use "editconf -f file.gro -resnr 1" to renumber) the way it is
written in the topology.<br>
<br>
Cheers<br>
Jon<br>
<br>
On 2012-05-28 08:03, James Starlight wrote:
<blockquote
cite="mid:CAALQopxwhFGF0+8O9Gu=dx3_igF2WXkfrNODQBAKSSNPCsUP=Q@mail.gmail.com"
type="cite">Peter,<br>
<br>
Thanks for advise. <br>
<br>
I've found already pre-equilibrated POPC bilayers with 200 lipids.
I've examined that lipids and found that they are very similar to
the berger's lipids (it consists of equal nymber of atoms ) but
the atom order in each lipid is slightly different than in
Tieleman's popc.itp file so during processing of that lipids I've
got error of non-matching atoms. Is there any trivial way to make
new popc.itp based on existing gro file with correct atom order ?<br>
<br>
<br>
James<br>
<br>
<div class="gmail_quote">2012/5/26 Peter C. Lai <span dir="ltr"><<a
moz-do-not-send="true" href="mailto:pcl@uab.edu"
target="_blank">pcl@uab.edu</a>></span><br>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">
Either use genbox -cs popc128b.gro or genconf -f popc128b.gro
-nbox x y 0<br>
Tieleman's lipids require you to generate a dummy tpr for use
with trjconv<br>
to unwrap the pbc (trjconv -s em.tpr -f popc128b.pdb -o
popc128b-nopbc.gro<br>
-pbc mol -ur compact) first.<br>
<br>
Lots of people have their own bilayer but they may be for
different FFs<br>
which means the atom naming would not be immediately be
compatible with<br>
your FF; for example mine are built for charmm36 and would
require atom<br>
renaming for another FF, even charmm27.<br>
<div>
<div class="h5"><br>
On 2012-05-26 11:24:12AM +0400, James Starlight wrote:<br>
> Dear Gromacs Users!<br>
><br>
><br>
> I want to perform MD simulation of my membrane
protein in POPC or POPE<br>
> bilayer using Tieleman's parameters for lipids by
means of gromos united<br>
> atom force field. The main problem is that the
pre-equilibrated bilayers<br>
> wich I found on the Dr. Tieleman's site consist of no
more that 128 lipids<br>
> but I want to simulate my protein with bigger number
of lipids ( for<br>
> example starting from 200 lipids ).<br>
> What should I do in that case ? Could you provide
me with some tools for<br>
> construction of such united-atoms bilayers with
desired dimensions ?<br>
> Finally is there any others pre-equilibrated bilayers
aviable for<br>
> downloading besides Dr. Tieleman's site ?<br>
><br>
><br>
> thanks for your help,<br>
><br>
> James S.<br>
<br>
</div>
</div>
> --<br>
> gmx-users mailing list <a moz-do-not-send="true"
href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
> <a moz-do-not-send="true"
href="http://lists.gromacs.org/mailman/listinfo/gmx-users"
target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
> Please search the archive at <a moz-do-not-send="true"
href="http://www.gromacs.org/Support/Mailing_Lists/Search"
target="_blank">http://www.gromacs.org/Support/Mailing_Lists/Search</a>
before posting!<br>
> Please don't post (un)subscribe requests to the list. Use
the<br>
> www interface or send it to <a moz-do-not-send="true"
href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>
> Can't post? Read <a moz-do-not-send="true"
href="http://www.gromacs.org/Support/Mailing_Lists"
target="_blank">http://www.gromacs.org/Support/Mailing_Lists</a><br>
<span class="HOEnZb"><font color="#888888"><br>
<br>
--<br>
==================================================================<br>
Peter C. Lai | University of
Alabama-Birmingham<br>
Programmer/Analyst | KAUL 752A<br>
Genetics, Div. of Research | 705 South 20th Street<br>
<a moz-do-not-send="true" href="mailto:pcl@uab.edu">pcl@uab.edu</a>
| Birmingham AL 35294-4461<br>
(205) 690-0808 |<br>
==================================================================<br>
<br>
--<br>
gmx-users mailing list <a moz-do-not-send="true"
href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
<a moz-do-not-send="true"
href="http://lists.gromacs.org/mailman/listinfo/gmx-users"
target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
Please search the archive at <a moz-do-not-send="true"
href="http://www.gromacs.org/Support/Mailing_Lists/Search"
target="_blank">http://www.gromacs.org/Support/Mailing_Lists/Search</a>
before posting!<br>
Please don't post (un)subscribe requests to the list. Use
the<br>
www interface or send it to <a moz-do-not-send="true"
href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>
Can't post? Read <a moz-do-not-send="true"
href="http://www.gromacs.org/Support/Mailing_Lists"
target="_blank">http://www.gromacs.org/Support/Mailing_Lists</a><br>
</font></span></blockquote>
</div>
<br>
<br>
<fieldset class="mimeAttachmentHeader"></fieldset>
<br>
</blockquote>
<br>
<br>
<pre class="moz-signature" cols="72">--
_____________________________________________________
Jon Kapla
Division of Physical Chemistry
Dpt. of Materials and Environmental Chemistry (MMK)
Arrhenius Laboratory
Stockholm University
SE-106 91 Stockholm
Pos: PhD Student
Phone: +46 8 16 11 79 (office)
Phone: +46 70 304 19 89 (cell)
E-mail: <a class="moz-txt-link-abbreviated" href="mailto:jon.kapla@mmk.su.se">jon.kapla@mmk.su.se</a>
_____________________________________________________
</pre>
</body>
</html>