Hans Martin Senn wrote:
Hi Xavier
On 16 Jul 2008, at 15:51, Xavier Periole wrote:
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.
By "protein name", do you mean the [ moleculetype ] section? If so, the
answer is no. Each of the molecule itp files specifies exactly one
molecule type (protein chain or ligand); the names are unique.
Of course it is fair to say that the problem is in the topologies, as
demonstrated by my solution to the problem... The point is that it is
apparently not permitted to have [ atomtypes ] (in topol_FAD.itp) after
having read other molecule definitions (in topol_{A,B}.itp), in contrast
to what I think the manual suggests.
Just thinking out loud, and this may or may not do anything, but I know that a
lot of problems encountered involving topologies result from having things in
the wrong order. For example, you've included the FAD.itp before ZTRP.itp, but
then called ZTRP before FAD in the [ molecules ] section. I know things in the
[ molecules ] section need to line up with what's in the .gro/.pdb file, but I
don't know about for certain about order within the topology. I once included a
ligand topology after the water #include statement by mistake, and got a
different error, but fixing the order solved everything.
Try switching the respective molecule definition or .itp call to correspond to
whatever is in your structure file, and see if that does anything.
Again, this may or may not be worth anything, but it's something I'd try if all
else leaves me scratching my head :-)
-Justin
Hans
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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--
========================================
Justin A. Lemkul
Graduate Research Assistant
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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