Hi Justin
On 16 Jul 2008, at 17:50, Justin A. Lemkul wrote:
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.
It does not (I should have said that I tried that). As you point out,
the order in which the components are listed in the [ molecules ]
section DOES matter. However, it seems that the corresponding itp
files can be included in a different (arbitrary?) order.
Cheers
Hans
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
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 [email protected]
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
