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.
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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