Hi Liang,
Do you have to define ffoplsaa.itp in your top file? isn't it enough to
generate your protein topology with the OPLS forcefield using pdb2gmx and
include the protein's generated itp files?
I don't use OPLS, but my own definition of the .top file goes like this:
; generic + lipid topology
#include "ffgmx.itp"
#include "lipid.itp"
#include "dmpc.itp"
#include "ions.itp"
; protein
#include "chain_A.itp"
#include "chain_B.itp"
#include "chain_C.itp"
#include "chain_D.itp"
; water
#include "spc.itp"
Rest of my molecule definitions are similar (protein first, then lipid, then
water, and finally ions to neutralize the system).
Hope it helps,
Hadas.
----- Original Message -----
From: "liang" <[EMAIL PROTECTED]>
To: "Justin A. Lemkul" <[EMAIL PROTECTED]>
Cc: <gmx-users@gromacs.org>
Sent: Sunday, November 25, 2007 7:41 AM
Subject: Re: [gmx-users] how to write the correct top file for
membraneprotein system?
Dear Justin,
Thanks for you quickly reply.
I have tried before to comment out the section of [ defaults ] in the next
itp file, but still too many warnings and final crashed.
And i think it would not be the best method to solve this problem, because
i have to use ffgmx.itp to deal with DPPC.
Is there any other method i can try?
Thanks
Liang
----- Original Message -----
From: "Justin A. Lemkul" <[EMAIL PROTECTED]>
To: "liang" <[EMAIL PROTECTED]>; "Discussion list for GROMACS
users" <gmx-users@gromacs.org>
Sent: Sunday, November 25, 2007 12:23 PM
Subject: Re: [gmx-users] how to write the correct top file for membrane
protein system?
Quoting liang <[EMAIL PROTECTED]>:
Dear User,
i try to perform simulation on membrane protein ( proterin + DPPC ).
And i use OPLS for protein, Berger force field for DPPC.
But after i construct this system, i cannot obtain tpr file by using
grompp.
Here is my topol.top :
; protein
#include "ffoplsaa.itp"
#include "protein-opls.itp"
; membrane
#include "ffgmx.itp"
#include "lipid.itp"
#include "dppc.itp"
; Include water topology
#include "spc.itp"
[ system ]
; name
Membrane in water
[ molecules ]
; name number
Protein 1
DPPC 123
SOL 14189
here is the result:
--------------------------------------------------------------------------------------------------------------------
Fatal error:
Invalid order for directive defaults, file
""/home/gmx331/share/gromacs/top/ffgmx.itp"", line 4
--------------------------------------------------------------------------------------------------------------------
I suspect it is a result of using two different force fields. The [
defaults ]
will be defined in the first force field (in your case, ffoplsaa.itp),
but then
grompp is finding a second [ defaults ] in ffgmx.itp. See here:
http://wiki.gromacs.org/index.php/Errors#Found_a_second_defaults_directive_file
-Justin
Could you please give me some suggestion? i appreciate your help.
Thanks so much!
========================================
Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
[EMAIL PROTECTED] | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/
========================================
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