On Wed, 16 Jul 2008 17:24:22 +0100
Hans Martin Senn <[EMAIL PROTECTED]> 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.
Then you got a solution!? Great!
I actually do not know if atomtypes can be after moleculetypes. But you
could try to include the topol_TAD.itp first, or put the atomtypes with
the other ones. If you actually need a solution.
XAvier
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
_______________________________________________
gmx-users mailing list gmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the www interface
or send it to [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
-----------------------------------------------------
XAvier Periole - PhD
Molecular Dynamics Group / NMR and Computation
University of Groningen
The Netherlands
-----------------------------------------------------
_______________________________________________
gmx-users mailing list gmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
