On 07/02/2012 07:00 PM, reising...@rostlab.informatik.tu-muenchen.de wrote:
Content of the ipt3p.itp file:
; This file is for backward compatibility only.
; Please directly include the tip3p.itp file from your force field directory.
#ifdef _FF_GROMACS
#include "gmx.ff/tip3p.itp"
#endif
#ifdef _FF_GROMOS96
#include "gromos43a1.ff/tip3p.itp"
#endif
#ifdef _FF_OPLS
#include "oplsaa.ff/tip3p.itp"
#endif
amber03.ff/tip3p.itp has never contained that - you've taken it from the
top-level $GMXLIB directory, from which it can't be moved, and can't
work with AMBER force fields. This completely explains your symptoms.
Since none of those _FF_* are defined, there's no water-related content
in your .top file. However you have constructed your amber03.ff is
wrong. I'd strongly suggest getting a new copy of amber03.ff (possibly
after upgrading to GROMACS 4.5.5) and starting again. The diff tool may
be your friend here.
I additionally included the dum.itp file since grompp seems not to "read"
the changes I made in the several files.
Then you've done something wrong.
http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field
contains the kind of procedure you need to follow.
Mark
I still get the error that the
atomtype "DUM" is not known.
The dummy atoms in the .gro file look like this:
314DUM DUM 4942 4.007 4.409 4.090
my changes are:
atomtypes.atp:
DU 1.00000 ; Dummy atom for the membrane
DUM 1.00000
ffnonbonded.itp:
DU 0 1.0000 0.0000 A 0.00000e+00 0.00000e+00
DUM 0 1.0000 0.0000 A 0.00000e+00 0.00000e+00
aminoacids.rtp:
[ DUM ]
[ atoms ]
DUM DU 0.00 1
residuetypes.dat:
DUM Protein
vdwradii.dat:
??? D 0.15
Is there any problem why it should not "read" my changes?
On 07/02/2012 06:39 PM, reising...@rostlab.informatik.tu-muenchen.de
wrote:
My topology file looks like this:
4924 4940 4939 4941 4
; Include Position restraint file
#ifdef POSRES
#include "posre.itp"
#endif
; Include water topology
#include "amber03.ff/tip3p.itp"
#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
; i funct fcx fcy fcz
1 1 1000 1000 1000
#endif
; Include topology for ions
#include "amber03.ff/ions.itp"
#include "amber03.ff/dum.itp"
[ system ]
; Name
Protein in water
[ molecules ]
; Compound #mols
Protein_chain_A 1
DUM 20088
SOL 13486
So I don't think that the #include of the itp3p is wrong.
OK, and what's inside it?
I also had to #include the dum.itp since I have Dummy atoms in my pdb
file
simulating the membrane around the membrane protein.
Well, this is non-standard, but I can't see how it would matter.
I already included the dummy atoms in the files atomtypes.atp,
ffnonbonded.itp, aminoacids.rtp, residuetypes.dat and vdwradii.dat.
So I was puzzled that it didn't know the atomtype "dum" during the
grompp
run.
So what purpose is being served by that dum.itp?
Mark
On 07/02/2012 06:12 PM, reising...@rostlab.informatik.tu-muenchen.de
wrote:
Okey thank you.
But shell I also
#include "amber03.ff/spc.itp"
Because when I don't include it I get the error:
Fatal error:
No such moleculetype SOL
An when I include it there is no error.
The only thing that makes sense is to use only amber03/tip3p.itp, like
Justin said. It defines the SOL [moleculetype], so your observations do
not seem consistent with #including such a file. Your .top fragment
suggests you're #including them at quite different points, and maybe
the
point at with you #include tip3p is inappropriate (e.g. inside an
#ifdef).
Mark
But in one of the last mails Justin wrote that:
"You're using two different water models, so things are getting
overridden
there.
With AMBER03, you should be using TIP3P, not SPC. The conflicting
water
models suggest you've made manual modifications to the topology.
Perhaps
there is some error as a result."
On 07/02/2012 05:49 PM, reising...@rostlab.informatik.tu-muenchen.de
wrote:
Hi Justin,
I wanted to use the only tip3p but I do not have the tip3p.gro file
but
only the tip3p.tip file.
http://www.gromacs.org/Documentation/How-tos/TIP3P_coordinate_file
I also have the tip4p.gro and tip5p.gro file. Can
I also use them?
No.
Mark
On 6/29/12 5:38 PM, reising...@rostlab.informatik.tu-muenchen.de
wrote:
Hi Justin,
yes I removed all the old resulting files and did everything
again.
So
now
there is the topology and coordinate file with only NA and CL and
not
NA+
or CL-.
I also checked whether the molecules are listed in the same order
as
in
the .gro file and it is the case. So that is also correct.
What do you mean with:
What does your [molecules] directive specify?
My [molecules] part in the topology file looks like this:
[ molecules ]
; Compound #mols
Protein_chain_A 1
DUM 20088
SOL 13428
NA 29
CL 29
I see no reason this would not work. However, I just noticed from
your
previous
message:
; Include water topology
#include "amber03.ff/tip3p.itp"
; Include topology for ions
#include "amber03.ff/ions.itp"
#include "amber03.ff/spc.itp"
#include "amber03.ff/dum.itp"
You're using two different water models, so things are getting
overridden
there.
With AMBER03, you should be using TIP3P, not SPC. The
conflicting
water
models suggest you've made manual modifications to the topology.
Perhaps
there
is some error as a result.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
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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