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><br>James<br><br><br><div class="gmail_quote">2011/10/21 Mark Abraham <span dir="ltr"><<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>></span><br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;"><div class="im">On 21/10/2011 5:41 PM, James Starlight wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
I've also tried to make topology for my system parametriesed for charmm36 ff by hands but failed too :(<br>
<br>
This is my topology for the POPC bilayer wich I've made in VMD membrane builder as well as downloaded a pre built membrane 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>
</blockquote>
<br></div>
.rtp files may not be #included<div class="im"><br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<br>
<br>
; Include water topology<br>
#include "/charmm36.ff/tip3p.itp"<br>
</blockquote>
<br></div>
Initial backslash refers to the root of your file system, so is likely wrong.<div class="im"><br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<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>
Source code file: /tmp/gromacs-4.5.4/src/kernel/<u></u>toppush.c, line: 770<br>
<br>
Fatal error:<br>
Unknown bond_atomtype 1<br>
<br>
What does it means? Is here anybody who also tried to parametriesed theis lipids by charmm ff ?<br>
</blockquote>
<br></div>
Don't blame the ff yet :-)<br>
<br>
Mark<br><font color="#888888">
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</font></blockquote></div><br>