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On 1/11/2011 3:00 AM, James Starlight wrote:
<blockquote
cite="mid:CAALQopw0-kSe-N6HOpeHX7-Q2iLx9M6FUrSzV-HkWmB11fOAng@mail.gmail.com"
type="cite">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">http://www.gromacs.org/Documentation/Errors</a><br>
</blockquote>
<br>
The text of the error is exactly right about what is wrong. Please
read and take time to understand before firing off email. You will
learn more and faster if you read and understand documentation
relevant to a situation before asking questions, and you will use
less of everyone else's volunteer time. Also, if you follow that
link, you will find a worked example of fixing your problem.<br>
<br>
<blockquote
cite="mid:CAALQopw0-kSe-N6HOpeHX7-Q2iLx9M6FUrSzV-HkWmB11fOAng@mail.gmail.com"
type="cite"><br>
What's most true for such multy system. Generate posre only for 1
part or for whole system?<br>
</blockquote>
<br>
It is often more profitable to understand why the error occurs,
rather than guess at the form of the solution.<br>
<br>
Mark<br>
<br>
<blockquote
cite="mid:CAALQopw0-kSe-N6HOpeHX7-Q2iLx9M6FUrSzV-HkWmB11fOAng@mail.gmail.com"
type="cite">
<br>
James<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">jalemkul@vt.edu</a>></span><br>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex;">
<div class="im"><br>
<br>
James Starlight wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">
Thanks, Justin<br>
I'll test your program soon.<br>
<br>
Today also I have some problems with generation of the
posre for lipids<br>
<br>
I have lipid bilayer in pdb. Then I selected one lipid
molecule and move it to separate pdb and convert it to
gro via editconf.<br>
Than I've used genres and generate posre file for 1 lipid.
Than I include tis posre to topology of my bilayer<br>
using gropt I obtain eror that I'm using wrong posre
topology<br>
<br>
Also I've tried to include posre.itp to my lipid.itp (
this file contain link to posre on default) This run didnt
produce any errors but as the result posres have not been
worked ( I obtained perturbed bilayer after minimization)<br>
<br>
How I can generate work posre for my bilayer to prevent
perturbation after equilibration or minimization ?<br>
<br>
</blockquote>
<br>
</div>
Since posre.itp is the default name given to the protein
position restraint file by pdb2gmx, the first step is to use a
different name. Then, you have to add the new #include
statement in the correct location in the topology. Presuming
you do that, the lipids should be restrained in whatever
manner you've specified.
<div>
<div class="h5"><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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