Justin,<br><br>In that way there was only one point wich was not understood for me<br><br><br>In charmm I already have lipids.rtp with the parametries for my lipids. Also I have a single molecule of my lipid.<br>How via pdb2gmx I could create parametrised itp file except of posre.itp ?<br>
<br>James<br><br><div class="gmail_quote">2011/10/21 Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</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"><br>
<br>
James Starlight wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
I've excluded "charmm36.ff/lipids.rtp" from my topology and obtain new error<br>
Fatal error:<br>
No such moleculetype POPC<br>
<br>
How I could include topology on this lipids ( all of them are present in the lipids.rtp. ) ?<br>
I have itp for the lipids only for the GROMOS ff so it should not be used here<br>
<br>
</blockquote>
<br></div>
I presented the details of this procedure to you already:<br>
<br>
<a href="http://lists.gromacs.org/pipermail/gmx-users/2011-October/065311.html" target="_blank">http://lists.gromacs.org/<u></u>pipermail/gmx-users/2011-<u></u>October/065311.html</a><br>
<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
<br>
James<br>
<br>
<br>
2011/10/21 Mark Abraham <<a href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a> <mailto:<a href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.<u></u>au</a>>><div class="im">
<br>
<br>
On 21/10/2011 5:41 PM, James Starlight wrote:<br>
<br>
I've also tried to make topology for my system parametriesed for<br>
charmm36 ff by hands but failed too :(<br>
<br>
This is my topology for the POPC bilayer wich I've made in VMD<br>
membrane builder as well as downloaded a pre built membrane<br>
system ( I've tested for both cases)<br>
<br>
; Include chain topologies<br>
#include "charmm36.ff/forcefield.itp"<br>
<br>
; Include lipids<br>
#include "charmm36.ff/lipids.rtp"<br>
<br>
<br>
.rtp files may not be #included<br>
<br>
<br>
<br>
<br>
; Include water topology<br>
#include "/charmm36.ff/tip3p.itp"<br>
<br>
<br>
Initial backslash refers to the root of your file system, so is<br>
likely wrong.<br>
<br>
<br>
<br>
; Include ion topologies<br>
#include "charmm36.ff/ions.itp"<br>
<br>
; System specifications<br>
[ system ]<br>
128-Lipid POPC Bilayer in water<br>
<br>
[ molecules ]<br>
POPC 72<br>
<br>
When I've loaded my molecule to grompp I've obtained error<br>
<br>
Program grompp, VERSION 4.5.4<br></div>
Source code file: /tmp/gromacs-4.5.4/src/kernel/<u></u>__toppush.c,<div class="im"><br>
line: 770<br>
<br>
Fatal error:<br>
Unknown bond_atomtype 1<br>
<br>
What does it means? Is here anybody who also tried to<br>
parametriesed theis lipids by charmm ff ?<br>
<br>
<br>
Don't blame the ff yet :-)<br>
<br>
Mark<br>
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</blockquote>
<br>
-- <br>
==============================<u></u>==========<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 href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.<u></u>vt.edu/Pages/Personal/justin</a><br>
<br>
==============================<u></u>==========<div><div></div><div class="h5"><br>
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