On Wed, 16 Jul 2008 15:04:17 +0100
Hans Martin Senn <[EMAIL PROTECTED]> wrote:
Dear all
This is a topic that has come up a couple of times here, see, e.g.,
http://www.gromacs.org/pipermail/gmx-users/2008-January/032114.html .
However, despite the recommendations given in that previous post, I think
the problem is exactly that the information in the manual is not
sufficiently accurate or clear in this case.
Specifically: I have a protein with two bound ligands, ZTRP and FAD.
- For the protein I use ffamber03. pdb2gmx created two itp files for the
two chains.
- For ZTRP, I have built an itp file using AMBER atom types (as defined in
ffamber03.atp or ffamber03nb.itp).
- For FAD, I have an itp file generated using antechamber and amb2gmx. It
contains an [ atomtypes ] section defining the GAFF atom types.
This was my first go at assembling it all in the top file:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
; Include forcefield parameters
#include "ffamber03.itp"
; Include chain topologies
#include "topol_A.itp"
#include "topol_B.itp"
#include "topol_FAD.itp"
#include "topol_ZTRP.itp"
; Include water topology
#include "ffamber_tip3p.itp"
; Include generic topology for ions
#include "ions.itp"
[ system ]
; Name
Full system in water
[ molecules ]
; Compound #mols
Protein_A 1
Protein_B 1
ZTRP 1
FAD 1
SOL 20893
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
However, grompp complained about "Invalid order for directive atomtypes"
when including topol_FAD.itp.
It might be that the same protein name is in two of your different
topology files.
The problem is certainly somewhere in those topologies.
Following a hint from the mailing list, I took the [ atomtypes ] section out
of topol_FAD.itp and put it into a separate itp file "GAFF- types.itp", which
is included before the other molecule itp files. The final top file then
looked like this:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
; Include forcefield parameters
#include "ffamber03.itp"
; Define GAFF atomtypes here (not in molecule itp file) to avoid 'Invalid
order' error
#include "GAFF-types.itp"
; Include chain topologies
#include "topol_A.itp"
#include "topol_B.itp"
#include "topol_FAD.itp"
#include "topol_ZTRP.itp"
; Include water topology
#include "ffamber_tip3p.itp"
; Include generic topology for ions
#include "ions.itp"
[ system ]
; Name
Full system in water
[ molecules ]
; Compound #mols
Protein_A 1
Protein_B 1
ZTRP 1
FAD 1
SOL 20893
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
This solved the problem. However, and this is my main point here, the
manual for GROMACS 3.3, p. 98 says:
"starting with GROMACS version 3.1.3 all directives at the parameter level
can be used multiple times and there are no restrictions on the order..."
In my reading, this means that [ atomtypes ] can be defined anywhere (as
long as it is before they are referred to for the first time), which is
clearly at variance with the observed behaviour. Am I misinterpreting it, or
is the manual not precise enough here?
A final note: Since simulating a protein with bound ligands is an extremely
common case and since this issue about "Invalid order" seems to come up
regularly, it would be very helpful if a corresponding HOWTO was available
in the manual/FAQ/wiki to settle it once and for all.
Best wishes
Hans
.......................................................
Dr. Hans Martin Senn
Lord Kelvin/Adam Smith Research Fellow
E-mail: [EMAIL PROTECTED]
Direct line: +44 (0)141 330 6574
Fax: +44 (0)141 330 4888
Department of Chemistry
Joseph Black Building
University of Glasgow
Glasgow G12 8QQ
Scotland, UK
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-----------------------------------------------------
XAvier Periole - PhD
Molecular Dynamics Group / NMR and Computation
University of Groningen
The Netherlands
-----------------------------------------------------
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