On 12/02/10 18:17, chiloo777 777 wrote:
If this problem comes from the mismatch forcefield, That mean i should
change forcefield from ffG53a6 to ffgmx, or find popg.itp (which is
matched with ffG53a6), right?
Standard procedure is to choose a forcefield that is known to be able to
model the kind of system you're working on before you do anything else :-)
Mark
On Fri, Feb 12, 2010 at 9:06 AM, Justin A. Lemkul<jalem...@vt.edu> wrote:
chiloo777 777 wrote:
To see topology, please see the attached files
You're using ffG53a6, per my tutorial, but then if you look within popg.itp,
you'll find atom type HO, which is not a recognized type within 53a6 (it is
for ffgmx). The proper type is H. The other warnings are probably due to
some other similar force field type mismatch. Identify which of these is
problematic (grompp should print the line number in the topology), and
assign suitable parameters.
As for this:
; Include water topology
#include "#include "/usr/local/gromacs/share/top/flexspc.itp"
I have no idea how that would even work, you don't even have proper closed
quotes, but in any case you would only ever need:
#include "flexspc.itp"
...although you shouldn't be using a flexible water model for dynamics,
anyway.
-Justin
Jit
On Fri, Feb 12, 2010 at 8:45 AM, Justin A. Lemkul<jalem...@vt.edu> wrote:
chiloo777 777 wrote:
Do you mean i should change the order of #include thing in file.top or
something involving pope.itp?
I try to change order of #include thing, there is the same error.
Do i need to define something like "proper dihedral types" in pope.itp
& popg.itp?
Without seeing your .top it's hard to give any really useful information.
All the bonded parameters for a given lipid should be included within
the
relevant .itp file. If it's coming up as "not found" you're either using
the wrong force field, not #including something at all, or your topology
is
otherwise incorrectly constructed.
-Justin
Thanks
Jit
On Fri, Feb 12, 2010 at 8:24 AM, Mark Abraham<mark.abra...@anu.edu.au>
wrote:
On 12/02/10 12:16, chiloo777 777 wrote:
Dear all,
I face some problem during run grompp (see below), the command is
"grompp -f em.mdp -c ../2add_lipw/b4ion.gro -p ../topol.top -o
b4ion.tpr"
-Before this process, i've changed the ffG53a6nb.itp& ff53Ga6bon.itp
according to the tutorial
(http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/02_topology.html)
my topology, you can see the attached files.
Thanks in advance
Jit
--------------------------------------------------------------------------------------------
Ignoring obsolete mdp entry 'cpp'
Back Off! I just backed up mdout.mdp to ./#mdout.mdp.6#
checking input for internal consistency...
processing topology...
Opening library file /usr/local/gromacs/share/top/ff_dum.itp
Generated 825 of the 2346 non-bonded parameter combinations
ERROR 1 [file /home/jit/Lipid_Bilayers/pope.itp, line 234]:
No default Proper Dih. types
If there's no default proper dihedral types defined, then you've
#included
things in a wrong order.
Mark
-------------------------------------------------------
Program grompp, VERSION 4.0.7
Source code file: toppush.c, line: 947
Fatal error:
Atomtype HO not found
-------------------------------------------------------
"There's Nothing We Can't Fix, 'coz We Can Do It in the Mix" (Indeep)
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========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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