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On 3/11/2011 9:32 PM, James Starlight wrote:
<blockquote
cite="mid:CAALQopx1uNdbCW+dp7E6utr0b9nbfhFDM0ytZPikgGuFW1BREg@mail.gmail.com"
type="cite">Mark,<br>
<br>
Firstly I've downloaded Berger's dppc.itp and dppc.gro ( I've
already have had gromos lipid ff)<br>
<br>
than I made pdb file for just 1 molecule of the dppc lipid
consisted of 50 atoms and generate for that new molecule
lipid_posres.itp via pdb2gmx<br>
<br>
than I've included lipid_posre.itp to the dppc.itp at the end of
file where the reference for the posres_lipid was already existed
as POSRES_LIPID.<br>
</blockquote>
<br>
Your free use of "lipid_posres.itp", "lipid_posre.itp" and
"posres_lipid" in your sentences above make it seem like you might
not have been using a file name that matches your #include.<br>
<br>
<blockquote
cite="mid:CAALQopx1uNdbCW+dp7E6utr0b9nbfhFDM0ytZPikgGuFW1BREg@mail.gmail.com"
type="cite"><br>
I've included in the minim.mdp<br>
define= - DPOSRES_LIPID<br>
</blockquote>
<br>
There's an extra space in that line. There's a reason people want to
see actual input and output and contents of files. Stuff filtered
through your head is stuff that you might have made an extra mistake
with.<br>
<br>
<blockquote
cite="mid:CAALQopx1uNdbCW+dp7E6utr0b9nbfhFDM0ytZPikgGuFW1BREg@mail.gmail.com"
type="cite">
<br>
than I've minimized my bilayer dppc.gro and checked by VMD if the
bilayer was perturbed after simulation<br>
<br>
So althought posres were included in the minim.pdb the bilayer was
perturbed ( tails of lipids were less ordered in comprison to the
initial bilayer )<br>
</blockquote>
<br>
Sounds like Andreas has the right idea.<br>
<br>
<blockquote
cite="mid:CAALQopx1uNdbCW+dp7E6utr0b9nbfhFDM0ytZPikgGuFW1BREg@mail.gmail.com"
type="cite">
<br>
Why posres didnt work?<br>
</blockquote>
<br>
Position restraints aren't magic - they're only applied to specific
atoms. You need to choose which. The genrestr GROMACS tool may be
your friend here.<br>
<br>
Mark<br>
<br>
<br>
<blockquote
cite="mid:CAALQopx1uNdbCW+dp7E6utr0b9nbfhFDM0ytZPikgGuFW1BREg@mail.gmail.com"
type="cite"><br>
<br>
<div class="gmail_quote">2011/11/2 Mark Abraham <span dir="ltr"><<a
moz-do-not-send="true" href="mailto:mark.abraham@anu.edu.au">mark.abraham@anu.edu.au</a>></span><br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt
0.8ex; border-left: 1px solid rgb(204, 204, 204);
padding-left: 1ex;">
<div class="im">
<div> </div>
<div> </div>
<span>On 02/11/11, <b>James Starlight </b><<a
moz-do-not-send="true"
href="mailto:jmsstarlight@gmail.com" target="_blank">jmsstarlight@gmail.com</a>>
wrote:</span>
<blockquote style="border-left: 1px solid rgb(0, 0, 255);
padding-left: 13px; margin-left: 0px;" type="cite">Justin,
Mark,<br>
<br>
Ok<br>
not I've included posre only to the lipid.itp wich consist
of parameters for just 1 lipid<br>
<br>
#ifdef POSRES_LIPID<br>
#include "posre_lipid.itp"<br>
#endif<br>
<br>
to the minim.mdp I've included<br>
define = -DPOSRES_LIPID ; position restrain the
lipids<br>
<br>
As the result I have not obtained any error in grompp but
after minimization my lipid bilayer was perturbed. I've
used very strong posres. Why it have not worked ?</blockquote>
<div> </div>
</div>
<div>We can't know, because we don't know what's in any files,
nor why you think the bilayer was perturbed. If you would
like useful help, you need to be exhaustive in your
description of what you have done, what you have observed
and what you think about those. It is easier for people who
might volunteer free help to do something else with their
time than to ask follow-up questions when few details were
given originally.</div>
<div> </div>
<font color="#888888">
<div>Mark </div>
</font>
<div>
<div class="h5">
<div> </div>
<blockquote style="border-left: 1px solid rgb(0, 0, 255);
padding-left: 13px; margin-left: 0px;" type="cite">
<div><br>
<br>
<div class="gmail_quote">2011/10/31 Justin A. Lemkul <span
dir="ltr"><<a moz-do-not-send="true"
href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>></span><br>
<blockquote style="border-left: 1px solid rgb(204,
204, 204); margin: 0px 0px 0px 0.8ex;
padding-left: 1ex;" class="gmail_quote">
<div>
<div><br>
<br>
James Starlight wrote:<br>
<blockquote style="border-left: 1px solid
rgb(204, 204, 204); margin: 0px 0px 0px
0.8ex; padding-left: 1ex;"
class="gmail_quote">I've done all of that<br>
i have "posre_lipid.itp" - for 1 lipid (
posres for each of 50 atoms )<br>
<br>
<br>
I've included this in the topology of the
bilayer<br>
<br>
; Include chain topologies<br>
#include "gromos53a6_lipid.ff/forcefield.itp"<br>
#include "dppc.itp"<br>
<br>
; Include water topology<br>
#include "gromos53a6_lipid.ff/spc.itp"<br>
<br>
; Include ion topologies<br>
#include "gromos53a6_lipid.ff/ions.itp"<br>
<br>
#ifdef POSRES_LIPID<br>
#include "posre_lipid.itp"<br>
#endif<br>
<br>
; System specifications<br>
[ system ]<br>
128-Lipid DMPC Bilayer in water<br>
<br>
[ molecules ]<br>
; molecule name nr.<br>
DPPC 64<br>
SOL 1193<br>
SOL 690<br>
<br>
<br>
Also I've tried to make posre for whole
system ( large posres ) but it also was
finished with same error<br>
<br>
Fatal error:<br>
[ file posre_lipid.itp, line 6 ]:<br>
Atom index (2) in position_restraints out of
bounds (1-1).<br>
This probably means that you have inserted
topology section "position_restraints"<br>
in a part belonging to a different molecule
than you intended to.<br>
In that case move the "position_restraints"
section to the right molecule.<br>
For more information and tips for
troubleshooting, please check the GROMACS<br>
website at <a moz-do-not-send="true"
href="http://www.gromacs.org/Documentation/Errors"
target="_blank">http://www.gromacs.org/Documentation/Errors</a><br>
<br>
What's most true for such multy system.
Generate posre only for 1 part or for whole
system?<br>
<br>
</blockquote>
<br>
</div>
</div>
Position restraints can only be applied on a
[moleculetype] basis. Thus, order matters a lot,
and the whole system cannot be restrained in one
file. See the example here:<br>
<br>
<a moz-do-not-send="true"
href="http://www.gromacs.org/Documentation/Errors#Atom_index_n_in_position_restraints_out_of_bounds"
target="_blank">http://www.gromacs.org/Documentation/Errors#Atom_index_n_in_position_restraints_out_of_bounds</a><br>
<br>
As it stands now, the topology you've shown tries
to apply lipid position restraints after the ions
have been #included, which makes no sense at all.
<div>
<div><br>
<br>
-Justin<br>
<br>
-- <br>
========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a moz-do-not-send="true"
href="http://vt.edu/" target="_blank">vt.edu</a>
| (540) 231-9080<br>
<a moz-do-not-send="true"
href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin"
target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<br>
========================================<br>
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